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1.
Newkirk, Edward S.
Billiards with Bombs.
Degree: PhD, Mathematics, 2016, Brown University
URL: https://repository.library.brown.edu/studio/item/bdr:674241/ 
► In this article, we define a variant of billiards in which the ball bounces around a square grid erasing walls as it goes. We prove…
(more)
▼ In this article, we define a variant of billiards in
which the ball bounces around a square grid erasing walls as it
goes. We prove that there exist periodic tunnels with arbitrarily
large period from any possible starting point, that there exist
nonperiodic tunnels from any possible starting point, and that
there are versions of the problem for which the same starting point
and initial direction result in periodic tunnels of arbitrarily
large period. We conjecture that there exist starting conditions
which do not lead to tunnels, justify the conjecture with
simulation evidence, and discuss the difficulty of proving
it.
Advisors/Committee Members: Schwartz, Richard (Director), Kenyon, Richard (Reader), Brock, Jeffrey (Reader).
Subjects/Keywords: cutting sequence
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APA (6th Edition):
Newkirk, E. S. (2016). Billiards with Bombs. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:674241/
Chicago Manual of Style (16th Edition):
Newkirk, Edward S. “Billiards with Bombs.” 2016. Doctoral Dissertation, Brown University. Accessed March 03, 2021.
https://repository.library.brown.edu/studio/item/bdr:674241/.
MLA Handbook (7th Edition):
Newkirk, Edward S. “Billiards with Bombs.” 2016. Web. 03 Mar 2021.
Vancouver:
Newkirk ES. Billiards with Bombs. [Internet] [Doctoral dissertation]. Brown University; 2016. [cited 2021 Mar 03].
Available from: https://repository.library.brown.edu/studio/item/bdr:674241/.
Council of Science Editors:
Newkirk ES. Billiards with Bombs. [Doctoral Dissertation]. Brown University; 2016. Available from: https://repository.library.brown.edu/studio/item/bdr:674241/
California State Polytechnic University – Pomona
2.
Webster, Richard.
One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order.
Degree: MS, Mathematics, 2015, California State Polytechnic University – Pomona
URL: http://hdl.handle.net/10211.3/145515
► We will examine the ruler sequence and its relation to the discrete logarithm, prim??itive roots modulo powers of a prime, p-adic ordinals, odd perfect numbers,…
(more)
▼ We will examine the ruler
sequence and its relation to the discrete logarithm, prim??itive roots modulo powers of a prime, p-adic ordinals, odd perfect numbers, and the 3n + 1 problem. Emphasis is placed on the multiplicative order of an integer modulo powers of a prime and odd perfect numbers. Additionally alternate proofs using the ruler
sequence are given for Euler???s criterion and Touchard???s theorem for odd perfect numbers.
Advisors/Committee Members: Mitsuo, Kobayashi (advisor), John, Rock (committee member).
Subjects/Keywords: ruler sequence
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APA (6th Edition):
Webster, R. (2015). One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order. (Masters Thesis). California State Polytechnic University – Pomona. Retrieved from http://hdl.handle.net/10211.3/145515
Chicago Manual of Style (16th Edition):
Webster, Richard. “One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order.” 2015. Masters Thesis, California State Polytechnic University – Pomona. Accessed March 03, 2021.
http://hdl.handle.net/10211.3/145515.
MLA Handbook (7th Edition):
Webster, Richard. “One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order.” 2015. Web. 03 Mar 2021.
Vancouver:
Webster R. One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order. [Internet] [Masters thesis]. California State Polytechnic University – Pomona; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10211.3/145515.
Council of Science Editors:
Webster R. One sequence to rule them all: the ruler sequence and its relation to odd perfect numbers and multiplicative order. [Masters Thesis]. California State Polytechnic University – Pomona; 2015. Available from: http://hdl.handle.net/10211.3/145515
University College Cork
3.
Pai, Anjali.
Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA.
Degree: 2018, University College Cork
URL: http://hdl.handle.net/10468/7466
► Translation initiation is a complex process. The efficiency of translation initiation is determined not just by activity and availability of the translation initiation apparatus, but…
(more)
▼ Translation initiation is a complex process. The efficiency of translation initiation is determined not just by activity and availability of the translation initiation apparatus, but also the properties of mRNA 5’transcript leaders (5’TL). In most cases of cap-dependent translation, translation initiation begins with the formation of the preinitiation complex (PIC) loading and accommodation onto the m7G capped 5’end of mRNA, facilitated by m7G cap – eIF4F interactions. The PIC accommodation onto the 5’end of mRNA is a point of control in translation initiation where the role of 5’ cap proximal mRNA
sequence determinants are poorly understood. To explore the effect of the nucleotides in the extreme 5’ end of mRNA on translation initiation, a library of mRNA molecules was synthesized containing all possible permutations of the first 10 nucleotides, referred to as E5S (Early 5'
Sequence). The library was transfected into HEK293T cells. The lysates obtained from transfected cells were separated on a sucrose density gradient to isolate mRNAs bound to polysomes. Based on the assumption that efficiently translated mRNAs are associated with polysomes, the effect of E5S on translation initiation was measured by comparing frequencies of nucleotides (and their combinations) at specific positions in E5S from mRNAs in polysome fractions to their frequencies in E5S of the original library using massively parallel sequencing. The second position of E5S was found to have a markedly higher influence on translation initiation than positions further downstream (for technical reasons it was not possible to estimate the influence of the first position of E5S). In this position G was the most enriched nucleotide, and U was the most depleted nucleotide. Analysis of available ribosome profiling datasets did not reveal a significant association between E5S and ribosome footprint densities at the coding regions. While this work clearly suggests the influence of nucleotide context on translation initiation, it is possible that such as uORFs and RNA secondary structures, have a higher influence on translation initiation than E5S. The E5S is a previously unappreciated determinant of translation initiation, and this work suggests that differences in mRNA 5' end accessibility defined by the cap proximal
sequence may be an important determinant in modulating the rate of translation initiation.
Advisors/Committee Members: Baranov, Pavel V., HRB, SFI.
Subjects/Keywords: Leader sequence
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APA (6th Edition):
Pai, A. (2018). Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA. (Thesis). University College Cork. Retrieved from http://hdl.handle.net/10468/7466
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Pai, Anjali. “Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA.” 2018. Thesis, University College Cork. Accessed March 03, 2021.
http://hdl.handle.net/10468/7466.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pai, Anjali. “Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA.” 2018. Web. 03 Mar 2021.
Vancouver:
Pai A. Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA. [Internet] [Thesis]. University College Cork; 2018. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10468/7466.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pai A. Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA. [Thesis]. University College Cork; 2018. Available from: http://hdl.handle.net/10468/7466
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Georgia Tech
4.
Xu, Chen.
Topics in percolation and sequence analysis.
Degree: PhD, Mathematics, 2018, Georgia Tech
URL: http://hdl.handle.net/1853/60260
► This thesis studies three topics, two in percolation system and one in sequence analysis. In the first part, we prove that, for directed Bernoulli last…
(more)
▼ This thesis studies three topics, two in percolation system and one in
sequence analysis. In the first part, we prove that, for directed Bernoulli last passage percolation with i.i.d.~weights on vertices over a n × n grid and for n large enough, the geodesics are shown to be concentrated in a cylinder, centered on the main diagonal and of width of order n
(2κ+2)/(2κ+3)√{\ln n}, where 1 ≤ κ<∞ is the curvature power-index of the shape function at (1,1). The methodology of proof is robust enough to also apply to directed Bernoulli first passage site percolation, and further to longest common subsequences in random words. In the second part, we prove that, in directed last passage site percolation over a n × \lfloor n
α\rfloor-grid and for i.i.d.~random weights having finite support, the order of the r-th central moment, 1 ≤ r<+∞, of the last passage time is, for n large enough,
lower bounded by n
r(1-α)/2, 0<α<1/3. In the last part, we address a question and a conjecture on the expected length of the longest common subsequences of two i.i.d. random permutations of [n]:={1,2,...,n}. The question is resolved by showing that the minimal expectation is not attained in the uniform case. The conjecture asserts that √{n} is a lower bound on
this expectation, but we only obtain √[3]{n} for it.
Advisors/Committee Members: Damron, Michael (committee member), Hanson, Jack (committee member), Brito, Gerandy (committee member).
Subjects/Keywords: Percolation; Sequence
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APA (6th Edition):
Xu, C. (2018). Topics in percolation and sequence analysis. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/60260
Chicago Manual of Style (16th Edition):
Xu, Chen. “Topics in percolation and sequence analysis.” 2018. Doctoral Dissertation, Georgia Tech. Accessed March 03, 2021.
http://hdl.handle.net/1853/60260.
MLA Handbook (7th Edition):
Xu, Chen. “Topics in percolation and sequence analysis.” 2018. Web. 03 Mar 2021.
Vancouver:
Xu C. Topics in percolation and sequence analysis. [Internet] [Doctoral dissertation]. Georgia Tech; 2018. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/1853/60260.
Council of Science Editors:
Xu C. Topics in percolation and sequence analysis. [Doctoral Dissertation]. Georgia Tech; 2018. Available from: http://hdl.handle.net/1853/60260
University of Alberta
5.
Deng, Kang.
Contrasting sequence groups by emerging sequences.
Degree: MS, Department of Computing Science, 2009, University of Alberta
URL: https://era.library.ualberta.ca/files/4m90dw68d
► Group comparison per se is a fundamental task in many scientific endeavours but is also the basis of any classifier. Comparing groups of sequence data…
(more)
▼ Group comparison per se is a fundamental task in many
scientific endeavours but is also the basis of any classifier.
Comparing groups of sequence data is a relevant task. To contrast
sequence groups, we define Emerging Sequences (ESs) as subsequences
that are frequent in sequences of one group and less frequent in
another, and thus distinguishing sequences of different classes.
There are two challenges to distinguish sequence classes by ESs:
the extraction of ESs is not trivially efficient and only exact
matches of sequences are considered. In our work we address those
problems by a suffix tree-based framework and a sliding window
matching mechanism. A classification model based on ESs is also
proposed. Evaluating against several other learning algorithms, the
experiments on two datasets show that our similar ESs-based
classification model outperforms the baseline approaches. With the
ESs' high discriminative power, our proposed model achieves
satisfactory F-measures on classifying sequences.
Subjects/Keywords: Sequence Classification; Sequence Similarity; Emerging Sequences
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APA (6th Edition):
Deng, K. (2009). Contrasting sequence groups by emerging sequences. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/4m90dw68d
Chicago Manual of Style (16th Edition):
Deng, Kang. “Contrasting sequence groups by emerging sequences.” 2009. Masters Thesis, University of Alberta. Accessed March 03, 2021.
https://era.library.ualberta.ca/files/4m90dw68d.
MLA Handbook (7th Edition):
Deng, Kang. “Contrasting sequence groups by emerging sequences.” 2009. Web. 03 Mar 2021.
Vancouver:
Deng K. Contrasting sequence groups by emerging sequences. [Internet] [Masters thesis]. University of Alberta; 2009. [cited 2021 Mar 03].
Available from: https://era.library.ualberta.ca/files/4m90dw68d.
Council of Science Editors:
Deng K. Contrasting sequence groups by emerging sequences. [Masters Thesis]. University of Alberta; 2009. Available from: https://era.library.ualberta.ca/files/4m90dw68d
University of Saskatchewan
6.
Islam, T M Rezwanul.
CSA-X: Modularized Constrained Multiple Sequence Alignment.
Degree: 2015, University of Saskatchewan
URL: http://hdl.handle.net/10388/ETD-2015-10-2276
► Imposing additional constraints on multiple sequence alignment (MSA) algorithms can often produce more biologically meaningful alignments. Hence, various constrained multiple sequence alignment (CMSA) algorithms have…
(more)
▼ Imposing additional constraints on multiple
sequence alignment (MSA) algorithms can often produce more biologically meaningful alignments. Hence, various constrained multiple
sequence alignment (CMSA) algorithms have been developed in the literature, where researchers used anchor points, regular expressions, or context-free-grammars to specify the constraints, wherein alignments produced are forced to align around segments that match the constraints.
In this thesis, we propose CSA-X, a modularized program of constrained multiple
sequence alignment that accepts constraints in the form of regular expressions. It uses an arbitrary underlying multiple
sequence alignment program to generate alignments, and is therefore modular. The name CSA-X refers to our proposed program generally, where the letter X is substituted with the name of a (non-constrained) multiple
sequence alignment algorithm which is used as underlying MSA engine in the proposed program. We compare the accuracy of our program with another constrained multiple
sequence alignment program called RE-MuSiC that similarly uses regular expressions for constraints. In addition, comparisons are also made to the underlying MSA programs (without constraints).
The BAliBASE 3.0 benchmark database is used to assess the performance of the proposed program CSA-X, other MSA programs, and CMSA programs considered in this study. Based on the results presented herein, CSA-X outperforms RE-MuSiC, and scores well against the underlying alignment programs. It also shows that the use of regular expression constraints, if chosen well, created from the least conserved region of the correct alignments, improves the alignment accuracy. In this study, ProbCons and T-Coffee are used as the underlying MSA programs in CSA-X, and the accuracy of the alignments are measured in terms of Q score and TC score. On average, CSA-X used with constraints identified from the least conserved regions of the correct alignments achieves results that are 17.65% more for Q score, and 23.7% more for TC score compared to RE-MuSiC. In fact, CSA-X with ProbCons (CSA-PC) achieves a higher score in over 97.9% of the cases for Q score, and over 96.4% of the cases for TC score. In addition, CSA-X with T-Coffee (CSA-TCOF) achieves a higher score in over 97.7% of the cases for Q score, and over 94.8% of the cases for TC score. Furthermore, CSA-X with regular expressions created from the least conserved regions of the correct alignments achieves higher accuracy scores compared to standalone ProbCons and T-Coffee. To measure the statistical significance of CSA-X results, the Wilcoxon rank-sum test and Wilcoxon signed-rank test are performed, and these tests show that CSA-X results for the least conserved regular expression constraint sets from the correct BAliBASE 3.0 alignments are significantly different than those from RE-MuSiC, ProbCons, and T-Coffee.
Advisors/Committee Members: McQuillan, Ian, Kusalik, Anthony, Keil, Mark, Wu, FangXiang.
Subjects/Keywords: Multiple Sequence Alignment; Constrained Multiple Sequence Alignment.
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APA (6th Edition):
Islam, T. M. R. (2015). CSA-X: Modularized Constrained Multiple Sequence Alignment. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/ETD-2015-10-2276
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Islam, T M Rezwanul. “CSA-X: Modularized Constrained Multiple Sequence Alignment.” 2015. Thesis, University of Saskatchewan. Accessed March 03, 2021.
http://hdl.handle.net/10388/ETD-2015-10-2276.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Islam, T M Rezwanul. “CSA-X: Modularized Constrained Multiple Sequence Alignment.” 2015. Web. 03 Mar 2021.
Vancouver:
Islam TMR. CSA-X: Modularized Constrained Multiple Sequence Alignment. [Internet] [Thesis]. University of Saskatchewan; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10388/ETD-2015-10-2276.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Islam TMR. CSA-X: Modularized Constrained Multiple Sequence Alignment. [Thesis]. University of Saskatchewan; 2015. Available from: http://hdl.handle.net/10388/ETD-2015-10-2276
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Utah
7.
Page, Sam Ray.
DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection.
Degree: MS;, Pathology;, 2007, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1016/rec/358
► Hepatitis B Virus (HBV) is a small, partially double-stranded, DNA virus that is hepatotropic. In the United states, there are 1.25 million chronically infected people…
(more)
▼ Hepatitis B Virus (HBV) is a small, partially double-stranded, DNA virus that is hepatotropic. In the United states, there are 1.25 million chronically infected people with 140.000 to 320, 000 new infections added each year. Diseases caused by HBV include liver cirrhosis and hepatocellular carcinoma. It is estimated that as many as 1 million deaths can be attributed to HBV around the world each year. Currently, chronic HBV infection is treated with pegylated interferon alpha or nucleoside analogues (NA), both of which have been shown to be effective at promoting seroconversion. However, both treatments can cause serious side effects and the NA drugs can select for resistant viral populations. Eight HBV geontypes (A-H) have been identified. Although type A virus accounts for most chronic infections in North America, an increasing numbers of non-A-HBV infections have been documented. Recent studies suggest that HBV genotype may influence a patient’s response to both interferon and NA treatments. Current NA drugs used for HBV treatment include: lamivudine, adefovir, entecavir telbivuding and tenofovir. Mutations that arise in the reverse transcriptase domain of the HBV polymerase gene may confer resistance to these drugs and have been described. Mutations in the overlapping surface gene have been associated with vaccine-induced and Antibody therapy immune escape. Also, it has been reported that current HBsAg immunoassays (monoclonal) may be unable to detect mutant viral population (especially if the mutations occure in the “a” domain) causing false negative results. This thesis describes an assay that sequences 941 bp if the HBV polymerase gene. The assay covers the six conserved subdomains (A-F) of the RT region that contains antiviral resistance mutation and other domains that contain polymorphisms related to viral genotype. Also, surface antigen mutations for vaccine variants and diagnostic escape are assayed by changing the analysis reading frame. Using this assay, 1000 HBV DNA positive serum/plasma samples from diverse US populations have been processed. These data described the genotype distribution and frequencies of mutation associated with NA resistance and immune escape of HBV infections found in the US.
Subjects/Keywords: Genotyping; Sequence Basecalling
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APA (6th Edition):
Page, S. R. (2007). DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection. (Masters Thesis). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1016/rec/358
Chicago Manual of Style (16th Edition):
Page, Sam Ray. “DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection.” 2007. Masters Thesis, University of Utah. Accessed March 03, 2021.
http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1016/rec/358.
MLA Handbook (7th Edition):
Page, Sam Ray. “DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection.” 2007. Web. 03 Mar 2021.
Vancouver:
Page SR. DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection. [Internet] [Masters thesis]. University of Utah; 2007. [cited 2021 Mar 03].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1016/rec/358.
Council of Science Editors:
Page SR. DNA sequencing of the hepatits B virus for genotyping, antiviral resistance and HBSAG mutant detection. [Masters Thesis]. University of Utah; 2007. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1016/rec/358
8.
Skitt, Troy JD.
Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota.
Degree: MS, Geology, 2013, University of North Dakota
URL: https://commons.und.edu/theses/279
► The Frobisher-Alida interval consists of eight log-defined subintervals or “beds” within the Mississippian upper Mission Canyon and lower Charles Formations of the Madison Group…
(more)
▼ The Frobisher-Alida interval consists of eight log-defined subintervals or “beds” within the Mississippian upper Mission Canyon and lower Charles Formations of the Madison Group in the Williston Basin. The subintervals are composed of predominantly evaporite and carbonate lithologies, and include in descending order: 1) Midale, 2) Rival, 3) Bluell, 4) Sherwood, 5) Mohall, 6) Glenburn, 7) Wayne, and 8) Landa. The top of the lower six subintervals are separated by thin but areal extensive log-defined markers of contrasting lithologies and include in descending order: 1) State A, 2) Sherwood Argillaceous Marker (S.A.M.), 3) K-1, 4) K-2, 5) K-3, and 6) Landa Marker. An additional localized marker, State A2, is identified defining the lower boundary of an Upper Bluell subinterval. This study focuses on the lithologic and
sequence stratigraphic significance of markers with the exception of the Landa Marker. The area studied covers Burke, Mountrail, Renville, Ward, western Bottineau and northwestern McHenry Counties in North Dakota. Geologically, the region is situated on the eastern flank of the Williston Basin; characterized by a shallow dipping (between 0.25 and 0.5 degrees) carbonate platform of an epicontinental sea on the western flank of the North American craton. Seventy-three marker descriptions were completed on the six markers from fifty-eight different cores throughout the study area. Six lithotypes reflecting unique depositional conditions were identified within the markers and include: 1) anhydrite, 2) dolomudstone, 3) dolomitic sandstone, 4) calc-mud/wackestone, 5) grain-supported, and 6) skeletal wackestone. Of these, the dolomudstone and dolomitic sandstone lithotypes are considered characteristic marker bed lithotypes, while the remaining are present as interbeds. The lithotypes reflect deposition in a variety of environments from a supralittoral, salina-like embayment to the east, through shallow sublittoral settings and into an open marine environment to the west. The section studied lies within the first-order Kaskaskian megasequence and second-order Madison
sequence which includes part of the upper Bakken shale and extends to the basinwide Madison unconformity. The Frobisher-Alida interval represents a single third-order
sequence spanning 2-3 million years and the compositional subintervals are considered fourth-order sequences. The subintervals are progradational and become increasingly restrictive up section and therefore represent individual fourth-order regressive systems tracts. Markers dominated by the dolomudstone lithotype (State A, State A2, S.A.M.) reflect deposition during a highstand systems tract where the basal contact represents a fourth-order maximum flooding surface. Dolomitic sandstone markers reflect initial deposition during a lowstand systems tract with unconsolidated sediments reworked and further cemented with the subsequent transgressive tract. Contrasting sediment input and consolidating mechanisms obscure definitive
sequence surfaces; therefore,…
Advisors/Committee Members: R.D. LeFever.
Subjects/Keywords: Sequence stratigraphy; Geology
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APA (6th Edition):
Skitt, T. J. (2013). Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota. (Masters Thesis). University of North Dakota. Retrieved from https://commons.und.edu/theses/279
Chicago Manual of Style (16th Edition):
Skitt, Troy JD. “Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota.” 2013. Masters Thesis, University of North Dakota. Accessed March 03, 2021.
https://commons.und.edu/theses/279.
MLA Handbook (7th Edition):
Skitt, Troy JD. “Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota.” 2013. Web. 03 Mar 2021.
Vancouver:
Skitt TJ. Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota. [Internet] [Masters thesis]. University of North Dakota; 2013. [cited 2021 Mar 03].
Available from: https://commons.und.edu/theses/279.
Council of Science Editors:
Skitt TJ. Lithological and sequence stratigraphic examination of the Madison Group marker beds, eastern Williston Basin margin, North Dakota. [Masters Thesis]. University of North Dakota; 2013. Available from: https://commons.und.edu/theses/279
9.
Yousef Mohamad, Khalil.
Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers.
Degree: Docteur es, Sciences de la Vie et de la Santé, 2009, Université François-Rabelais de Tours
URL: http://www.theses.fr/2009TOUR4012
► Chlamydophila pecorum est une espèce bactérienne intracellulaire obligatoire de la famille Chlamydiaceae. Le criblage d’une banque génomique de C. pecorum en utilisant un sérum ovin…
(more)
▼ Chlamydophila pecorum est une espèce bactérienne intracellulaire obligatoire de la famille Chlamydiaceae. Le criblage d’une banque génomique de C. pecorum en utilisant un sérum ovin spécifique a permis d’identifier la protéine de la membrane d’inclusion (IncA) comme un candidat potentiel pour le sérodiagnostic de C. pecorum et de mettre en évidence une séquence répétée codante (CTR) riche en alanine et proline dans le gène incA de C. pecorum. Cette CTR présente des motifs d’acides aminés différents suivant la pathogénicité des souches de C. pecorum. La variabilité génétique de 19 souches de C. pecorum isolées de ruminant a été étudiée par MVLST (multi-virulence sequence typing). Les gènes ompA qui code pour la protéine majeure de la membrane externe, incA et l’ORF663 (cadre ouvert de lecture) permettent de différencier les souches pathogènes de C. pecorum des souches non-pathogènes. Cette hypothèse a été confirmée sur 32 autres souches comprenant 11 souches isolées de porcs. Les souches de C. pecorum isolées de lésions sont génétiquement différentes des souches isolées d’animaux asymptomatiques. Les 3 gènes ompA, incA et l’ORF663 sont des marqueurs moléculaire épidémiologiques potentiels qui pourraient être liés à la virulence de C. pecorum.
Chlamydophila pecorum, an obligate intracellular bacterium belonged to Chlamydiaceae family. Screening of a genomic DNA library of C. pecorum by using a specific ovine serum, allowed to identify inclusion membrane protein (IncA) as a potential candidate for C. pecorum serodiagnosis and to highlight a coding tandem repeat (CTR) rich in alanine and proline in the C. pecorum incA gene. The CTR presents several amino acids motifs according to the pathogenesis of C. pecorum strains. The genetic variability of 19 C. pecorum strains isolated from ruminants was studied using MVLST (multi-virulence sequence typing) system. The genes ompA that code for the major outer membrane protein, incA and ORF663 (open reading frame) allowed to distinguish the pathogenic C. pecorum strains from non-pathogenic strains. This hypothesis was confirmed on additional 32 strains including 11 strains isolated from swine. The C. pecorum strains isolated from clinical cases are genetically different from strains isolated from healthy animals. ompA, incA and ORF663 genes are epidemiological molecular markers which could be related to the virulence of C. pecorum.
Advisors/Committee Members: Rodolakis, Annie (thesis director).
Subjects/Keywords: Sequence repetee codante
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APA (6th Edition):
Yousef Mohamad, K. (2009). Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers. (Doctoral Dissertation). Université François-Rabelais de Tours. Retrieved from http://www.theses.fr/2009TOUR4012
Chicago Manual of Style (16th Edition):
Yousef Mohamad, Khalil. “Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers.” 2009. Doctoral Dissertation, Université François-Rabelais de Tours. Accessed March 03, 2021.
http://www.theses.fr/2009TOUR4012.
MLA Handbook (7th Edition):
Yousef Mohamad, Khalil. “Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers.” 2009. Web. 03 Mar 2021.
Vancouver:
Yousef Mohamad K. Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers. [Internet] [Doctoral dissertation]. Université François-Rabelais de Tours; 2009. [cited 2021 Mar 03].
Available from: http://www.theses.fr/2009TOUR4012.
Council of Science Editors:
Yousef Mohamad K. Diversité génétique des souches de chlamydophila pecorum : recherche et identification des marqueurs épidémiologiques. : Genetic diversity of chlamydophila pecorum strains : research and identification of epidemiological markers. [Doctoral Dissertation]. Université François-Rabelais de Tours; 2009. Available from: http://www.theses.fr/2009TOUR4012
University of Florida
10.
Rodriguez, Miguel.
Reasoning over Multi-Source and Dynamic Knowledge Graphs.
Degree: PhD, Computer Engineering - Computer and Information Science and Engineering, 2019, University of Florida
URL: https://ufdc.ufl.edu/UFE0056138
► Innovative approaches to Information Extraction (IE) have enabled the creation of large Knowledge Graphs (KGs) (e.g., YAGO, NELL, DBPedia, Wikidata) and Dynamic Knowledge Graphs (e.g.,…
(more)
▼ Innovative approaches to Information Extraction (IE) have enabled the creation of large Knowledge Graphs (KGs) (e.g., YAGO, NELL, DBPedia, Wikidata) and Dynamic Knowledge Graphs (e.g., ICEWS, GDELT). These knowledge graphs have become an increasingly popular domain knowledge representation used in semantic search, recommendation systems, question-answering, natural language processing, etc.
Advisors/Committee Members: Wang,Zhe (committee chair), Dobra,Alin Viorel (committee member), Raup-Krieger,Janice (committee member).
Subjects/Keywords: fusion – graphs – sequence
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APA (6th Edition):
Rodriguez, M. (2019). Reasoning over Multi-Source and Dynamic Knowledge Graphs. (Doctoral Dissertation). University of Florida. Retrieved from https://ufdc.ufl.edu/UFE0056138
Chicago Manual of Style (16th Edition):
Rodriguez, Miguel. “Reasoning over Multi-Source and Dynamic Knowledge Graphs.” 2019. Doctoral Dissertation, University of Florida. Accessed March 03, 2021.
https://ufdc.ufl.edu/UFE0056138.
MLA Handbook (7th Edition):
Rodriguez, Miguel. “Reasoning over Multi-Source and Dynamic Knowledge Graphs.” 2019. Web. 03 Mar 2021.
Vancouver:
Rodriguez M. Reasoning over Multi-Source and Dynamic Knowledge Graphs. [Internet] [Doctoral dissertation]. University of Florida; 2019. [cited 2021 Mar 03].
Available from: https://ufdc.ufl.edu/UFE0056138.
Council of Science Editors:
Rodriguez M. Reasoning over Multi-Source and Dynamic Knowledge Graphs. [Doctoral Dissertation]. University of Florida; 2019. Available from: https://ufdc.ufl.edu/UFE0056138
Louisiana State University
11.
Hendershott, Zachary Paul.
Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas.
Degree: MS, Earth Sciences, 2012, Louisiana State University
URL: etd-11052012-134539
;
https://digitalcommons.lsu.edu/gradschool_theses/863
► The Upper Cretaceous Eagle Ford Formation of South Texas records a mixed siliciclastic/carbonate depositional environment across the Late Cretaceous Platform of the Gulf of Mexico.…
(more)
▼ The Upper Cretaceous Eagle Ford Formation of South Texas records a mixed siliciclastic/carbonate depositional environment across the Late Cretaceous Platform of the Gulf of Mexico. During the Late Cretaceous, LaSalle and McMullen Counties was part of the Hawkville Trough, a wedged shaped region between the Edwards and Sligo carbonate reefs. Well logs from 21 wells and seismic data were used to construct structure and isopach maps of the Eagle Ford Formation throughout the Hawkville Trough. Only the unconformable bottom (Buda-Eagle Ford) and top (Eagle Ford-Austin Chalk) boundaries plus the conformable boundary between the upper and lower Eagle Ford can be consistently correlated in the area. The Eagle Ford-Austin Chalk boundary is variable/gradational due to variable erosion of the Eagle Ford prior to deposition of the Austin Chalk. This variability is also observed in core data. The Lower and Upper Eagle Ford are trough shaped deposits that strike northeast roughly parallel with the Edwards reef. Maximum thickness of the Lower Eagle Ford is more than 180 ft in LaSalle County and 140 ft in McMullen County. The Upper Eagle Ford has a maximum thickness of 160 ft along the LaSalle-McMullen County Border. Both the Lower and Upper Eagle Ford thin to half their maximum thickness within 5-6 miles of the axis. Depth to the top of the Eagle Ford varies from 9600 ft to 15000 ft and strikes parallel to the Edwards and Sligo reefs. Numerous faults are visible. Most faults are post-depositional with modest offsets. Few faults are syn-depositional growth faults and the Eagle Ford is thicker on the down thrown side. Well and seismic data document dramatic decreases in thickness of the Upper Eagle Ford over a few miles. In the most extreme case in southwest LaSalle County, the Upper Eagle Ford is entirely missing in 2 wells and has been replaced by a sand unit not previously reported. A seismic cross section, or time slice, just above the top of the Eagle Ford shows a channel structure running west to east along southern LaSalle County. This channel is likely the cause of observed erosion and sand deposition.
Subjects/Keywords: correlations; sequence stratigraphy
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APA (6th Edition):
Hendershott, Z. P. (2012). Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas. (Masters Thesis). Louisiana State University. Retrieved from etd-11052012-134539 ; https://digitalcommons.lsu.edu/gradschool_theses/863
Chicago Manual of Style (16th Edition):
Hendershott, Zachary Paul. “Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas.” 2012. Masters Thesis, Louisiana State University. Accessed March 03, 2021.
etd-11052012-134539 ; https://digitalcommons.lsu.edu/gradschool_theses/863.
MLA Handbook (7th Edition):
Hendershott, Zachary Paul. “Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas.” 2012. Web. 03 Mar 2021.
Vancouver:
Hendershott ZP. Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas. [Internet] [Masters thesis]. Louisiana State University; 2012. [cited 2021 Mar 03].
Available from: etd-11052012-134539 ; https://digitalcommons.lsu.edu/gradschool_theses/863.
Council of Science Editors:
Hendershott ZP. Evaluation of the depositional environment of the Eagle Ford Formation using well log, seismic, and core data in the Hawkville Trough, LaSalle and McMullen counties, south Texas. [Masters Thesis]. Louisiana State University; 2012. Available from: etd-11052012-134539 ; https://digitalcommons.lsu.edu/gradschool_theses/863
12.
-8259-8688.
A functional cortical network for sensorimotor sequence generation.
Degree: PhD, Neuroscience, 2020, Johns Hopkins University
URL: http://jhir.library.jhu.edu/handle/1774.2/63454
► The brain generates complex sequences of movements that can be flexibly reconfigured in real-time based on sensory feedback, but how this occurs is not fully…
(more)
▼ The brain generates complex sequences of movements that can be flexibly reconfigured in real-time based on sensory feedback, but how this occurs is not fully understood. We developed a novel ‘
sequence licking’ task in which mice directed their tongue to a target that moved through a series of locations. Mice could rapidly reconfigure the
sequence online based on tactile feedback. Closed-loop optogenetics and electrophysiology revealed that tongue/jaw regions of somatosensory (S1TJ) and motor (M1TJ) cortex encoded and controlled tongue kinematics at the level of individual licks. Tongue premotor (anterolateral motor, ALM) cortex encoded intended tongue angle in a smooth manner that spanned individual licks and even whole sequences, and progress toward the reward that marked successful
sequence execution. ALM activity regulated
sequence initiation, but multiple cortical areas collectively controlled termination of licking. Our results define a functional cortical network for hierarchical control of sensory- and reward-guided orofacial
sequence generation.
Advisors/Committee Members: Worley, Paul F (advisor), Nielsen, Kristina J (committee member), O'Connor, Daniel H (committee member), Brown, Solange P (committee member), Mysore, Shreesh P (committee member).
Subjects/Keywords: Sensorimotor; Sequence; Tongue
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APA (6th Edition):
-8259-8688. (2020). A functional cortical network for sensorimotor sequence generation. (Doctoral Dissertation). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/63454
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Chicago Manual of Style (16th Edition):
-8259-8688. “A functional cortical network for sensorimotor sequence generation.” 2020. Doctoral Dissertation, Johns Hopkins University. Accessed March 03, 2021.
http://jhir.library.jhu.edu/handle/1774.2/63454.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
MLA Handbook (7th Edition):
-8259-8688. “A functional cortical network for sensorimotor sequence generation.” 2020. Web. 03 Mar 2021.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
-8259-8688. A functional cortical network for sensorimotor sequence generation. [Internet] [Doctoral dissertation]. Johns Hopkins University; 2020. [cited 2021 Mar 03].
Available from: http://jhir.library.jhu.edu/handle/1774.2/63454.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Council of Science Editors:
-8259-8688. A functional cortical network for sensorimotor sequence generation. [Doctoral Dissertation]. Johns Hopkins University; 2020. Available from: http://jhir.library.jhu.edu/handle/1774.2/63454
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Rutgers University
13.
Lin, Timothy, 1986-.
Developing a nanopore sequencing data processing pipeline for structure variation identification.
Degree: MS, Microbiology and Molecular Genetics, 2019, Rutgers University
URL: https://rucore.libraries.rutgers.edu/rutgers-lib/61799/
► Many genomic sequencing technologies have been developed since the Human Genome Project. These next-generation sequencing (NGS) technologies from various companies reshaped the genomics field and…
(more)
▼ Many genomic sequencing technologies have been developed since the Human Genome Project. These next-generation sequencing (NGS) technologies from various companies reshaped the genomics field and have improved rapidly. However, NGS has limitations for certain applications due to its short read length. The third generation of sequencing technology uses single molecule real-time sequencer that can generate long reads. Recently Oxford Nanopore entered the market with the release of its MinION sequencer. Oxford Nanopore's unique third generation sequencing technology allows for much longer read length than NGS technologies, potentially addressing some of the limitations of NGS. Due to the novelty of nanopore sequencing technology, the available tools for aligning long read data and detecting structural variants have not been thoroughly evaluated. Here we evaluate the performance of several alignment and structural variation detection tools on long read MinION data.
Advisors/Committee Members: Xing, Jinchuan (chair), Shah, Premal (internal member), Ellison, Christopher (internal member), School of Graduate Studies.
Subjects/Keywords: Nanopores; Nucleotide sequence
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APA (6th Edition):
Lin, Timothy, 1. (2019). Developing a nanopore sequencing data processing pipeline for structure variation identification. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/61799/
Chicago Manual of Style (16th Edition):
Lin, Timothy, 1986-. “Developing a nanopore sequencing data processing pipeline for structure variation identification.” 2019. Masters Thesis, Rutgers University. Accessed March 03, 2021.
https://rucore.libraries.rutgers.edu/rutgers-lib/61799/.
MLA Handbook (7th Edition):
Lin, Timothy, 1986-. “Developing a nanopore sequencing data processing pipeline for structure variation identification.” 2019. Web. 03 Mar 2021.
Vancouver:
Lin, Timothy 1. Developing a nanopore sequencing data processing pipeline for structure variation identification. [Internet] [Masters thesis]. Rutgers University; 2019. [cited 2021 Mar 03].
Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61799/.
Council of Science Editors:
Lin, Timothy 1. Developing a nanopore sequencing data processing pipeline for structure variation identification. [Masters Thesis]. Rutgers University; 2019. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61799/
Penn State University
14.
Sun, Yazhou.
DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.
Degree: 2012, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/13771
► Understanding the sequential information coded in DNA, RNA and proteins is important for both basic and applied researches in life sciences. Extensive efforts have been…
(more)
▼ Understanding the sequential information coded in DNA, RNA and proteins is important for both basic and applied researches in life sciences. Extensive efforts have been devoted to the research and development of DNA
sequence analysis methods. The studies described in this dissertation explored new applications of existing methods in the context of the recent development of ultra-high throughput sequencing technologies. This dissertation also included new methods developed for studying gene families and human haplogroups. The theories, algorithms and tools for analyzing DNA
sequence information concerning these studies are reviewed in Chapter 1 of this dissertation.
With the recent development in DNA sequencing technologies, came many new research opportunities. Great challenges also came along, mainly because of the large data size of the latest high throughput sequencing technologies. The potential of these new technologies was exploited to complete a 100,000 years old ancient polar bear mitochondrial genome. With this and some additional modern bear data, the matrilineal polar bear’s divergence time was estimated to be around 130,000 years ago, which is significantly older than some recent estimates. This estimate indicated that modern polar bear matrilineal ancestors adapted to the niche polar environment within 30,000 years after the speciation event and propagated along the entire Arctic Circle for the next 100,000 years. This recent speciation and rapid expansion process is analogous to the evolution and migration of modern humans. The lineage characteristics of the latter were also briefly studied using the same technologies. (Chapter 2)
Because of the increased efficiency from the latest sequencing technologies, more and more complete human mitochondrial genomes have been generated at an increasingly faster speed. Although mitochondrial haplogroups, and their classification and identification were widely used in human evolution and population studies, the current tools could not fully take advantage of the rapidly growing number of new mitochondrial genomes. An updated mitochondrial haplogroup classification system was thus developed with evolutionary models that incorporate the mitochondrial genomic variations within the human population. These variations have not been considered by previous methods, which could lead to incorrectly classified haplogroups. The variation parameters, including the whole-genome substitution rate (0.013 - 0.1 substitutions per generation), the rate heterogeneity among sites (Gamma distribution shape parameter α = 0.7078) and the percentage of invariant sites (64%), were estimated based on 7985 full-length human mitochondrial genome sequences. Haplogroups were then classified based on the corrected genetic distance estimation and modeled with position specific matrices. A new haplogroup identification system was developed based on the resulting matrices and the maximum-likelihood estimation (MLE) method, permitting fast and accurate haplogroup assignment for both known and new…
Advisors/Committee Members: Hong Ma, Dissertation Advisor/Co-Advisor, Stephen Wade Schaeffer, Committee Chair/Co-Chair, Gong Chen, Committee Member, Naomi S Altman, Special Member, Anton Nekrutenko, Committee Member.
Subjects/Keywords: DNA sequence analysis; DNA sequence analysis methods; DNA sequence analysis applications
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APA (6th Edition):
Sun, Y. (2012). DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13771
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Sun, Yazhou. “DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.” 2012. Thesis, Penn State University. Accessed March 03, 2021.
https://submit-etda.libraries.psu.edu/catalog/13771.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sun, Yazhou. “DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.” 2012. Web. 03 Mar 2021.
Vancouver:
Sun Y. DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Mar 03].
Available from: https://submit-etda.libraries.psu.edu/catalog/13771.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sun Y. DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/13771
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Oregon State University
15.
Holloway, James Lee.
Algorithms for string matching with applications in molecular biology.
Degree: PhD, Computer Science, 2009, Oregon State University
URL: http://hdl.handle.net/1957/11518
► As the volume of genetic sequence data increases due to improved sequencing techniques and increased interest, the computational tools available to analyze the data are…
(more)
▼ As the volume of genetic
sequence data increases due to improved sequencing
techniques and increased interest, the computational tools available to analyze
the data are becoming inadequate. This thesis seeks to improve a few of the computational
methods available to access and analyze data in the genetic
sequence
databases. The first two results are parallel algorithms based on previously known
sequential algorithms. The third result is a new approach, based on assumptions
that we believe make sense in the biological context of the problem, to approximating
an NP complete problem. The final result is a fundamentally new approach
to approximate string matching using the divide and conquer paradigm instead
of the dynamic programming approach that has been used almost exclusively in
the past.
Dynamic programming algorithms to measure the distance between sequences
have been known since at least 1972. Recently there has been interest
in developing parallel algorithms to measure the distance between two sequences.
We have developed an optimal parallel algorithm to find the edit distance, a metric
frequently used to measure distance, between two sequences.
It is often interesting to find the substrings of length k that appear most
frequently in a given string. We give a simple sequential algorithm to solve this problem and an efficient parallel version of the algorithm. The parallel algorithm
uses an efficient novel parallel bucket sort.
When sequencing a large segment of DNA, the original DNA
sequence is
reconstructed using the results of sequencing fragments, that may or may not
contain errors, of many copies of the original DNA. New algorithms are given to
solve the problem of reconstructing the original DNA
sequence with and without
errors introduced into the fragments. A program based on this algorithm is used
to reconstruct the human beta globin region (HUMHBB) when given a set of 300
to 500 mers drawn randomly from the HUMHBB region.
Approximate string matching is used in a biological context to model the
steps of evolution. While such evolution may proceed base by base using the
change, insert, or delete operators, there is also evidence that whole genes may
be moved or inverted. We introduce a new problem, the string to string rearrangement
problem, that allows movement and inversion of substrings. We give
a divide and conquer algorithm for finding a rearrangement of one string within
another.
Advisors/Committee Members: Cull, Paul (advisor), D'Ambrosio, Bruce (committee member).
Subjects/Keywords: Nucleotide sequence – Data processing
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APA (6th Edition):
Holloway, J. L. (2009). Algorithms for string matching with applications in molecular biology. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/11518
Chicago Manual of Style (16th Edition):
Holloway, James Lee. “Algorithms for string matching with applications in molecular biology.” 2009. Doctoral Dissertation, Oregon State University. Accessed March 03, 2021.
http://hdl.handle.net/1957/11518.
MLA Handbook (7th Edition):
Holloway, James Lee. “Algorithms for string matching with applications in molecular biology.” 2009. Web. 03 Mar 2021.
Vancouver:
Holloway JL. Algorithms for string matching with applications in molecular biology. [Internet] [Doctoral dissertation]. Oregon State University; 2009. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/1957/11518.
Council of Science Editors:
Holloway JL. Algorithms for string matching with applications in molecular biology. [Doctoral Dissertation]. Oregon State University; 2009. Available from: http://hdl.handle.net/1957/11518
UCLA
16.
Schroeder, Julia.
The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans.
Degree: Psychology, 2016, UCLA
URL: http://www.escholarship.org/uc/item/29s9d1f2
► Animals and humans may learn much information when presented with a series of images at various locations. The order in which the objects appear, the…
(more)
▼ Animals and humans may learn much information when presented with a series of images at various locations. The order in which the objects appear, the order of locations in which they appear, and whether those locations vary or are stable for any given object will impact how and what the subject may learn. Encoding these patterns can allow for optimal responses in identifying objects and locations in the future. Many studies have examined object-location learning, and sequence learning in mammals. However, there is less research in other phyla. Birds offer a prime taxonomic group in which to investigate these abilities. Though separated from mammals for 300 million years they are able to learn to perform many spatial and memory feats necessary to survive. As many of these abilities are shared with mammals, birds offer us two opportunities first, to look into our own evolutionary and possibly developmental past, and second, to investigate alternative ways of completing the same cognitive functions. This research will focus primarily on learning through the incidental encoding of object and location sequences. Incidental encoding is the learning of relationships and functions with the explicit knowledge of what is learned. Incidental encoding is of particular interest in this research as it plays a key role in survival under changing and unpredictable conditions. Incidental learning relies on a separate encoding mechanism from explicit encoding and goes through separate aging processes (Krinsky-McHale, Kittler, Brown, Jenkins, & Devenny, 2005; Naveh-Benjamin et al., 2009; Neill, Beck, Bottalico, & Molloy, 1990; Qin et al., 2014; Smith, Urgolites, Hopkins, & Squire, 2014). As every day in the world exposes an animal to a wide variety of stimuli, it is important to understand what and how information is selected for encoding. Such selection is necessary as it would be cumbersome for the animal to remember everything it experienced., However, it is never known exactly what information will be necessary in the future. Memory processes may have been shaped to be sensitive to many aspects within a task and use such information to direct such incidental encoding.
Subjects/Keywords: Psychology; Pattern Learning; Pigeon; Sequence
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APA (6th Edition):
Schroeder, J. (2016). The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/29s9d1f2
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Schroeder, Julia. “The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans.” 2016. Thesis, UCLA. Accessed March 03, 2021.
http://www.escholarship.org/uc/item/29s9d1f2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Schroeder, Julia. “The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans.” 2016. Web. 03 Mar 2021.
Vancouver:
Schroeder J. The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans. [Internet] [Thesis]. UCLA; 2016. [cited 2021 Mar 03].
Available from: http://www.escholarship.org/uc/item/29s9d1f2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Schroeder J. The Role of Object Location and Identity in Sequence Encoding in Pigeons and Humans. [Thesis]. UCLA; 2016. Available from: http://www.escholarship.org/uc/item/29s9d1f2
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Utah
17.
Harris, Nancy J.
Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah.
Degree: MS;, Geology & Geophysics;, 2008, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/101/rec/523
► Gamma ray spectroscopy and magnetic susceptibility can be used to help recognize stratigraphic sequences in a formation. Relative water depth is usually determined by examining…
(more)
▼ Gamma ray spectroscopy and magnetic susceptibility can be used to help recognize stratigraphic sequences in a formation. Relative water depth is usually determined by examining the lithologic characteristics and sedimentary structures. Trends of shallowing upward and deepening upward are determined and, from these, the system tracts are determined. This study examines the utility of two geophysical field techniques, spectral gamma ray and magnetic susceptibility, in determining relative abundance of carbonate vs. terrigenous components in sedimentary rocks. These data can be used in conjunction with sedimentary facies to identify variations in relative water depth for the Wheeler Formation, in western central Utah. The Wheeler Formation is a Middle Cambrian formation consisting of alternating shale and limestone. Exposures of the Wheeler Formation were examined at the Marjum Pass (House Range) and the Drum Mountains. During the Middle Cambrian, the area was a mixed carbonate-siliciclastic ramp, and strata in the Drum Mountains were deposited in a more proximal environment, whereas strata at Marjum Pass were deposited in a more distal environment. Thus, the Wheeler Formation in the Drum Mountains has a higher level of carbonate than at Marjum Pass. The first Transgressive Systems Tract (TST) was determined to be between 0-80 m above the Swasey/Wheeler Formation boundary in the Drum Mountains, and 0-30 m above the Swasey/Wheeler Formation boundary in Marjum Pass. The first Highstand Systems Tract (HST) was determined to be 80- 170 m in the Drum Mountains and 30-100 m in Marjum Pass. Between 170-200 m in the Drum Mountains, and between 100-115 m in Marjum Pass, may be a Lowstand Systems Tract (LST) or the beginning of the second TST, an unconformity for the LST. The second TST was determined to be between 200- 240 m in the Drum Mountains and 115-130 m in Marjum Pass. The second HST was determined to be between 240-278 m in the Drum Mountains and 130-160 m in Marjum Pass.
Subjects/Keywords: Sequence stratigraphy; Gamma ray spectrometry
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APA (6th Edition):
Harris, N. J. (2008). Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah. (Masters Thesis). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/101/rec/523
Chicago Manual of Style (16th Edition):
Harris, Nancy J. “Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah.” 2008. Masters Thesis, University of Utah. Accessed March 03, 2021.
http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/101/rec/523.
MLA Handbook (7th Edition):
Harris, Nancy J. “Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah.” 2008. Web. 03 Mar 2021.
Vancouver:
Harris NJ. Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah. [Internet] [Masters thesis]. University of Utah; 2008. [cited 2021 Mar 03].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/101/rec/523.
Council of Science Editors:
Harris NJ. Gamma ray spectroscopy and magnetic susceptibility of stratigraphic sequences in the Wheeler Formation, West Central Utah. [Masters Thesis]. University of Utah; 2008. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/101/rec/523
Cornell University
18.
Chen, Shuo.
Representation Learning For Sequence And Comparison Data.
Degree: PhD, Computer Science, 2016, Cornell University
URL: http://hdl.handle.net/1813/43697
► The core idea of representation learning is to learn semantically more meaningful features (usually represented by a vector or vectors for each data point) from…
(more)
▼ The core idea of representation learning is to learn semantically more meaningful features (usually represented by a vector or vectors for each data point) from the dataset, so that they contain more discriminative information and make the given prediction task easier. It often provides better generalization performance and data visualization. In this thesis work, we improve the foundation and practice of representation learning methods for two types of data, namely sequences and comparisons: 1. Using music playlist data as an example, we propose Logistic Markov Embedding method that learns from
sequence of songs and yields vectorized representations of songs. We demonstrate its better generalization performance in predicting the next song to play in a coherent playlist, as well as its capability in producing meaningful visualization for songs. We also propose an accompanying scalable training method that can be easily parallelized for learning representations on sequences. 2. Motivated by modeling intransitivity (rock-paper-scissors relation) in competitive matchup (two-player games or sports) data, we propose the blade-chest model for learning vectorized representations of players. It is then extended to a general framework that predicts the outcome of pairwise comparisons, making use of both object and context features. We see its successful application in matchup and preference prediction. The two lines of works have the same underlying theme: the object we study is first represented by a parameter vector or vectors, which are used to explain the interac- tions in the proposed models. These parameter vectors are learned by training on the datasets that contain interactions. The learned vectors can be used to predict any future interaction by simply plugging them back into the proposed models. Also, when the dimensionality of the vector is small (e.g. 2), plotting them gives interesting insight into the data.
Advisors/Committee Members: Joachims,Thorsten (chair), Van Loan,Charles Francis (committee member), Bindel,David S. (committee member).
Subjects/Keywords: Representation learning; Sequence; Pairwise comparison
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APA (6th Edition):
Chen, S. (2016). Representation Learning For Sequence And Comparison Data. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/43697
Chicago Manual of Style (16th Edition):
Chen, Shuo. “Representation Learning For Sequence And Comparison Data.” 2016. Doctoral Dissertation, Cornell University. Accessed March 03, 2021.
http://hdl.handle.net/1813/43697.
MLA Handbook (7th Edition):
Chen, Shuo. “Representation Learning For Sequence And Comparison Data.” 2016. Web. 03 Mar 2021.
Vancouver:
Chen S. Representation Learning For Sequence And Comparison Data. [Internet] [Doctoral dissertation]. Cornell University; 2016. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/1813/43697.
Council of Science Editors:
Chen S. Representation Learning For Sequence And Comparison Data. [Doctoral Dissertation]. Cornell University; 2016. Available from: http://hdl.handle.net/1813/43697
Stellenbosch University
19.
Van der Merwe, Pieter de Wet.
Systematic and genomic studies in the plant genus
Zygophyllum.
Degree: MSc, Biochemistry, 2015, Stellenbosch University
URL: http://hdl.handle.net/10019.1/96877
► ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz from Namibia were described in the late 1800’s. Recent comparisons of these…
(more)
▼ ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz
from Namibia were described in the late 1800’s. Recent comparisons of these two species
revealed that they were morphologically very similar except that Zygophyllum orbiculatum has
unifoliolate leaves and Zygophyllum stapffii has bifoliolate leaves. The similarity of these two
species was investigated using nuclear ITS (Internal Transcribed Spacer, i.e. ITS1, 5.8SrDNA,
ITS2) region sequence data as phylogenetic markers. Due to almost identical sequences and
phylogenetic grouping, it was concluded that they were conspecific. However, the phylogenetic
relationships of the major groups within the subfamily Zygophylloideae based on ITS sequences,
were unresolved and unsupported, as was found in previous studies using chloroplast gene
marker sequences.
To resolve the phylogenetic relationships of the major groups within the subfamily
Zygophylloideae, a next generation sequencing (NGS) approach was taken. Chloroplasts of taxa
representing the major groups within the subfamily were isolated and chloroplast genome
sequence data were generated using the Ion Torrent™ sequencer. Additional nuclear ITS
cassette data (18SrDNA, ITS1, 5.8SrDNA, ITS2, 26SrDNA) were generated as a by-product and
used to produce a large combined aligned sequence matrix for phylogenetic analysis.
Model-based phylogenetic programs were able to retrieve strongly supported and resolved
phylogenetic relationships of the major groups within Zygophylloideae. Two basal groupings
were retrieved in the subfamily. The first grouping consisted of the genera Tetraena, Fagonia
and Melocarpum. The second grouping consisted of the monotypic genus Augea and
Zygophyllum orbiculatum/stapffii which were embedded within the genus Roepera. Using a gene
duplication approach, the chloroplast marker data of genus Zygophyllum sensu stricto placed this
genus basal to the Augea, Zygophyllum orbiculatum/stapffii, Roepera clade whilst the nuclear
marker data of Zygophyllum sensu stricto, was found in a basal position to the entire subfamily. From this it is concluded that Zygophyllum sensu stricto shows evidence of incomplete lineage
sorting. A revised taxonomy for the entire subfamily Zygophylloideae is proposed.
AFRIKAANSE OPSOMMING: Zygophyllum orbiculatum Welwitsch ex Oliv. uit Angola en Zygophyllum stapffii Schinz van
Namibië is in die laat 1800's beskryf. Onlangse vergelykings van hierdie twee spesies het getoon
dat hulle morfologies baie eners is, behalwe dat Zygophyllum orbiculatum unifoliolate blare
besit en dat Zygophyllum stapffii bifoliolate blare besit. Hierdie ooreenkoms is ondersoek, met
behulp van die nukleêre “ITS” (Internal Transcribed Spacer d.w.s. ITS1, 5.8SrDNA, ITS2)
DNS-strook volgordedata as filogenetiese merkers. As gevolg van feitlik identiese
geenopeenvolgings is bevind dat die twee spesies konspesifiek is. Die filogenetiese
verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae, gebaseer op ITS
…
Advisors/Committee Members: Bellstedt, Dirk Uwe, Pirie, Michael David, Stellenbosch University. Faculty of Science. Dept. of Biochemistry..
Subjects/Keywords: Zygophyllaceae; Genomics; Nucleotide sequence; UCTD
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Van der Merwe, P. d. W. (2015). Systematic and genomic studies in the plant genus
Zygophyllum. (Masters Thesis). Stellenbosch University. Retrieved from http://hdl.handle.net/10019.1/96877
Chicago Manual of Style (16th Edition):
Van der Merwe, Pieter de Wet. “Systematic and genomic studies in the plant genus
Zygophyllum.” 2015. Masters Thesis, Stellenbosch University. Accessed March 03, 2021.
http://hdl.handle.net/10019.1/96877.
MLA Handbook (7th Edition):
Van der Merwe, Pieter de Wet. “Systematic and genomic studies in the plant genus
Zygophyllum.” 2015. Web. 03 Mar 2021.
Vancouver:
Van der Merwe PdW. Systematic and genomic studies in the plant genus
Zygophyllum. [Internet] [Masters thesis]. Stellenbosch University; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10019.1/96877.
Council of Science Editors:
Van der Merwe PdW. Systematic and genomic studies in the plant genus
Zygophyllum. [Masters Thesis]. Stellenbosch University; 2015. Available from: http://hdl.handle.net/10019.1/96877
Penn State University
20.
Jiang, Xueyuan.
Sequence and Expression Evolution of Animal and Plant Genes.
Degree: 2019, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/17132xjj5003
► Understanding the origins of phenotypic innovation is a key goal in biology. Phenotypic innovation via modification of gene function can occur either through mutations in…
(more)
▼ Understanding the origins of phenotypic innovation is a key goal in biology. Phenotypic innovation via modification of gene function can occur either through mutations in protein-coding sequences, which may result in changes of gene products, or mutations in regulatory sequences, which can affect gene expression. Although phenotypic evolution is thought to often occur through modifications in gene expression, evolution of coding
sequence has been studied almost exclusively for decades. The recent availability of high-throughput RNA sequencing (RNA-seq) data provides an opportunity to examine expression evolution. Therefore, combining analyses of protein-coding
sequence evolution and gene expression evolution may be crucial to answering fundamental questions in evolutionary biology. Using both types of data, a major topic of this dissertation is gene duplication, as it is a key player in genetic and phenotypic novelty. First, I use population-genetic inference to interrogate the role of natural selection in the functional evolution of young duplicate genes in Drosophila. I find that different types of selection act on genes with different levels of functional divergence, suggesting that natural selection may determine whether and how duplicate genes are retained. Second, I use multi-tissue gene expression profiles to assess functional divergence after gene duplication in grasses. I find that expression divergence is prevalent and is positively correlated with both
sequence evolutionary rate and tissue specificity. Finally, I develop a new summary statistic and apply it to investigate population-specific
sequence and expression divergence in three European populations. I identify candidate genes that potentially drive population-specific adaptation. Taken together, this work shows that using a combination of genetic and expression data, we are able to address critical questions in evolutionary biology.
Advisors/Committee Members: Raquel Assis, Dissertation Advisor/Co-Advisor, Stephen Wade Schaeffer, Committee Chair/Co-Chair, Shaun Mahony, Committee Member, Yifei Huang, Committee Member, Qunhua Li, Outside Member, Melissa Rolls, Program Head/Chair, Raquel Assis, Committee Chair/Co-Chair, Stephen Wade Schaeffer, Dissertation Advisor/Co-Advisor.
Subjects/Keywords: Sequence evolution; Expression evolution
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APA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jiang, X. (2019). Sequence and Expression Evolution of Animal and Plant Genes. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/17132xjj5003
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Jiang, Xueyuan. “Sequence and Expression Evolution of Animal and Plant Genes.” 2019. Thesis, Penn State University. Accessed March 03, 2021.
https://submit-etda.libraries.psu.edu/catalog/17132xjj5003.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Jiang, Xueyuan. “Sequence and Expression Evolution of Animal and Plant Genes.” 2019. Web. 03 Mar 2021.
Vancouver:
Jiang X. Sequence and Expression Evolution of Animal and Plant Genes. [Internet] [Thesis]. Penn State University; 2019. [cited 2021 Mar 03].
Available from: https://submit-etda.libraries.psu.edu/catalog/17132xjj5003.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Jiang X. Sequence and Expression Evolution of Animal and Plant Genes. [Thesis]. Penn State University; 2019. Available from: https://submit-etda.libraries.psu.edu/catalog/17132xjj5003
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Waterloo
21.
Mandal, Kalikinkar.
Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID.
Degree: 2013, University of Waterloo
URL: http://hdl.handle.net/10012/7730
► This thesis is concerned with the design and analysis of strong de Bruijn sequences and span n sequences, and nonlinear feedback shift register (NLFSR) based…
(more)
▼ This thesis is concerned with the design and analysis of strong de Bruijn sequences and span n sequences, and nonlinear feedback shift register (NLFSR) based pseudorandom number generators for radio frequency identification (RFID) tags. We study the generation of span n sequences using structured searching in which an NLFSR with a class of feedback functions is employed to find span n sequences. Some properties of the recurrence relation for the structured search are discovered. We use five classes of functions in this structured search, and present the number of span n sequences for 6 <= n <= 20. The linear span of a new span n sequence lies between near-optimal and optimal. According to our empirical studies, a span n sequence can be found in the structured search with a better probability of success. Newly found span n sequences can be used in the composited construction and in designing lightweight pseudorandom number generators.
We first refine the composited construction based on a span n sequence for generating long de Bruijn sequences. A de Bruijn sequence produced by the composited construction is referred to as a composited de Bruijn sequence. The linear complexity of a composited de Bruijn sequence is determined. We analyze the feedback function of the composited construction from an approximation point of view for producing strong de Bruijn sequences. The cycle structure of an approximated feedback function and the linear complexity of a sequence produced by an approximated feedback function are determined. A few examples of strong de Bruijn sequences with the implementation issues of the feedback functions of an (n+16)-stage NLFSR are presented.
We propose a new lightweight pseudorandom number generator family, named Warbler family based on NLFSRs for smart devices. Warbler family is comprised of a combination of modified de Bruijn blocks (CMDB) and a nonlinear feedback Welch-Gong (WG) generator. We derive the randomness properties such as period and linear complexity of an output sequence produced by the Warbler family. Two instances, Warbler-I and Warbler-II, of the Warbler family are proposed for passive RFID tags. The CMDBs of both Warbler-I and Warbler-II contain span n sequences that are produced by the structured search. We analyze the security properties of Warbler-I and Warbler-II by considering the statistical tests and several cryptanalytic attacks. Hardware implementations of both instances in VHDL show that Warbler-I and Warbler-II require 46 slices and 58 slices, respectively. Warbler-I can be used to generate 16-bit random numbers in the tag identification protocol of the EPC Class 1 Generation 2 standard, and Warbler-II can be employed as a random number generator in the tag identification as well as an authentication protocol for RFID systems.
Subjects/Keywords: Cryptography; Sequence; RFID; Security; De Bruijn Sequence; nonlinear feedback shift register; Pseudorandom sequence; Span n sequence
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APA ·
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Manager
APA (6th Edition):
Mandal, K. (2013). Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/7730
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Mandal, Kalikinkar. “Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID.” 2013. Thesis, University of Waterloo. Accessed March 03, 2021.
http://hdl.handle.net/10012/7730.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Mandal, Kalikinkar. “Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID.” 2013. Web. 03 Mar 2021.
Vancouver:
Mandal K. Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID. [Internet] [Thesis]. University of Waterloo; 2013. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10012/7730.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Mandal K. Design and Analysis of Cryptographic Pseudorandom Number/Sequence Generators with Applications in RFID. [Thesis]. University of Waterloo; 2013. Available from: http://hdl.handle.net/10012/7730
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
McMaster University
22.
Gibson, Laura C.
The Mental Sequence Line: Its Development and Stability.
Degree: PhD, 2015, McMaster University
URL: http://hdl.handle.net/11375/16706
► The mental sequence line is a cognitive construct by which sequences are perceived as beginning on the left and extending rightwards. Its developmental origins are…
(more)
▼ The mental sequence line is a cognitive construct by which sequences are perceived as beginning on the left and extending rightwards. Its developmental origins are unknown. In the first experiment, 4- and 5-year-old children placed items in order from four ordinal sequences, two of which they may have seen in print (i.e., letters and numbers) and two they would not have (i.e., times of day and meals). Four-year-olds systematically ordered letters from left to right; by age 5, numbers and times of day, but not meals, were ordered this way as well. These data suggest experience that cultural text direction, rather than inherent cortical organization, is responsible for development of the mental sequence line. The second experiment measured the mental sequence line in 6-, 7-, and 8-year-old children, and assessed its relation to visuospatial skills and mathematics ability. Mental sequence lines were measured by Spatial-Numerical Association of Response Codes (SNARC) and distance effects. Children’s mental rotation ability was moderately correlated (r=.303) with the distance effect but neither it nor the SNARC effect correlated with mathematic ability. These data suggest the mental sequence line is not at the core of children’s number sense, as previously hypothesized. The final experiment assessed consistency across time of SNARC and distance effects in adults for numbers, weekdays, and months. Despite often being described as trait variables, SNARC and distance effects were only moderately consistent for numbers, with even more variable results for months and weekdays, results suggesting mental sequence lines are not byproducts of stable, inflexible neural architectures. Combined, my data show sequence-space associations first emerge for letters, and subsequent development supports an enculturation hypothesis. By middle childhood, individual differences are evident in these effects that, as in adults, correlate with measures of spatial cognition. By adulthood, those individual differences have become modestly stable.
Dissertation
Doctor of Philosophy (PhD)
Advisors/Committee Members: Maurer, Daphne, Psychology.
Subjects/Keywords: Mental sequence line; Development; Cognition
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APA ·
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MLA ·
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Export
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APA (6th Edition):
Gibson, L. C. (2015). The Mental Sequence Line: Its Development and Stability. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/16706
Chicago Manual of Style (16th Edition):
Gibson, Laura C. “The Mental Sequence Line: Its Development and Stability.” 2015. Doctoral Dissertation, McMaster University. Accessed March 03, 2021.
http://hdl.handle.net/11375/16706.
MLA Handbook (7th Edition):
Gibson, Laura C. “The Mental Sequence Line: Its Development and Stability.” 2015. Web. 03 Mar 2021.
Vancouver:
Gibson LC. The Mental Sequence Line: Its Development and Stability. [Internet] [Doctoral dissertation]. McMaster University; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/11375/16706.
Council of Science Editors:
Gibson LC. The Mental Sequence Line: Its Development and Stability. [Doctoral Dissertation]. McMaster University; 2015. Available from: http://hdl.handle.net/11375/16706
Addis Ababa University
23.
Medhanit, Tamerat.
" Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
.
Degree: 2015, Addis Ababa University
URL: http://etd.aau.edu.et/dspace/handle/123456789/8012
► Mochena Borago rock shelter is a very rich archaeological site with one of the most complete late Pleistocene cultural sequence in the Horn of Africa.…
(more)
▼ Mochena Borago rock shelter is a very rich archaeological site with one of the most
complete late Pleistocene cultural
sequence in the Horn of Africa. Despite the rich
cultural
sequence, the pre-history and historic period of human and plant interaction and
ecological history of this site are poorly documented and reconstructed. The objective of
this study was to reconstruct food systems of the ancient inhabitants of Mochena Borago
rock shelter in the Late Holocene period. Archaeobotanical investigation was conducted
on a 27 soil sample bags of 2000 and 2001 French Field seasons at the Laboratory of the
ARCCH (Authority for Research and Conservation of Cultural Heritage).For the better
interpretation of the archaeaobotanical materials and data, ethnoarcheological studies
were undertaken in the five Kebeles of Sodo Zurea Woreda. Based on this, a total of 64
plant spices were documented and 112 seeds and fruit stones were identified by the
Archaeobotanical investigation which included Sapindaceae cf. Deinbollia type (n=55),
Myrtaceae cf. Syzigium guineense type (n=33), Plectranthus edulis (n=9),
Euphorbiaceae Croton sp. (n=7), Cordia cf. africana (n=2), Ebenaceae cf. Diospyros
(n=1), Olea europaea sub sp. cuspidate (n=1) and the rest four were unidentified. The
ethnobotanical documentation reveled that five plant types that were used as food,
medicine and raw materials to be similar with the plants recovered by Archaeobotanical
investigation. Among the identified botanical remains, Plectranthus edulis which is an
indigenous crop for the study area, Cordia cf.africana and Olea europaea sub sp.
cusipdata are reported for the first time in archaeobotanical context in the whole region
of Ethiopia.
Advisors/Committee Members: Alemseged Beldados (PhD) (advisor).
Subjects/Keywords: Cultural sequence; Ecological history
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APA ·
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CSE |
Export
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Manager
APA (6th Edition):
Medhanit, T. (2015). " Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
. (Thesis). Addis Ababa University. Retrieved from http://etd.aau.edu.et/dspace/handle/123456789/8012
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Medhanit, Tamerat. “" Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
.” 2015. Thesis, Addis Ababa University. Accessed March 03, 2021.
http://etd.aau.edu.et/dspace/handle/123456789/8012.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Medhanit, Tamerat. “" Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
.” 2015. Web. 03 Mar 2021.
Vancouver:
Medhanit T. " Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
. [Internet] [Thesis]. Addis Ababa University; 2015. [cited 2021 Mar 03].
Available from: http://etd.aau.edu.et/dspace/handle/123456789/8012.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Medhanit T. " Reconstructing Food Systems from the Late Holocene Context of Mochena Borrego Rock shelter, Wolayta, Southern Ethiopia "
. [Thesis]. Addis Ababa University; 2015. Available from: http://etd.aau.edu.et/dspace/handle/123456789/8012
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Harvard University
24.
Peterman, Neil.
Sequence-Function Models of Regulatory RNA in E. Coli.
Degree: PhD, 2017, Harvard University
URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061506
► The tremendous progress in genome sequencing has highlighted a challenging and important problem in connecting known sequences to biological function, known or unknown. In bacteria,…
(more)
▼ The tremendous progress in genome sequencing has highlighted a challenging and important problem in connecting known sequences to biological function, known or unknown. In bacteria, small regulatory RNAs (sRNAs) 50-200 nucleotides in length control the expression of genes across the gene regulatory network. They achieve this post-transcriptionally by modulating stability and translation initiation of their target mRNAs. In many cases these RNA-RNA regulatory interactions have been connected to base-pairing, and depend on specific interactions with protein co-factors. However, the sequence determinants of function for sRNAs remain poorly defined on two levels. First, parts of the nucleotide sequence have not been classified or characterized, even for well-studied sRNAs. Second, known or suspected sequence elements such as target pairing regions, which vary widely in length, and are often supported by limited evidence such as experiments from one or a few point mutants.
We have sought to explore the relations between an sRNA sequence and its regulatory functions systematically. We have employed sort-seq, a parallelized approach based on sequencing of pools of cells sorted by florescence, to measure the regulatory activity of large libraries of sRNA variants generated by random mutagenesis. In addition to demonstrating and validating the method for analysis of bacterial sRNAs, we have optimized several consequential aspects of sort-seq experiments. Simulations elucidate key sources of measurement bias and error driven by cell-to-cell variability and the configuration of sorting. With informed experimental design choices, we have demonstrated extremely precise measurements where variants have sufficient coverage – RMS replicate error less than 5% at 150X coverage. Our work has established sort-seq as a measurement platform for trans-acting RNA regulators.
We have used sort-seq to explore the sequence-function relations of two sRNAs of E. coli, RyhB and DsrA. Our results define functional sequence elements for the maintenance and activity of the sRNA as well as specific interactions with different mRNA targets. The data show a relationship between thermodynamic stability of the RNA-RNA duplex between the regulator and target as well as stability of individual stem-loop structures. A survey of sort-seq measurements across a range of environmental temperatures reveals sequence elements with temperature-dependent function. We have used sequence-function models, constrained by sort-seq measurements, to uncover sequence and environmental determinants of regulatory specificity of RyhB.
Physics
Advisors/Committee Members: Levine, Erel (advisor), Eddy, Sean (committee member), Shakhnovich, Eugene (committee member).
Subjects/Keywords: Biophysics; Sequence-function relations
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APA (6th Edition):
Peterman, N. (2017). Sequence-Function Models of Regulatory RNA in E. Coli. (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061506
Chicago Manual of Style (16th Edition):
Peterman, Neil. “Sequence-Function Models of Regulatory RNA in E. Coli.” 2017. Doctoral Dissertation, Harvard University. Accessed March 03, 2021.
http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061506.
MLA Handbook (7th Edition):
Peterman, Neil. “Sequence-Function Models of Regulatory RNA in E. Coli.” 2017. Web. 03 Mar 2021.
Vancouver:
Peterman N. Sequence-Function Models of Regulatory RNA in E. Coli. [Internet] [Doctoral dissertation]. Harvard University; 2017. [cited 2021 Mar 03].
Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061506.
Council of Science Editors:
Peterman N. Sequence-Function Models of Regulatory RNA in E. Coli. [Doctoral Dissertation]. Harvard University; 2017. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:42061506
University of Waikato
25.
Prentice, Erica Jean.
Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
.
Degree: 2013, University of Waikato
URL: http://hdl.handle.net/10289/8717
► Through ancestral sequence reconstruction (ASR) techniques, ancient enzymes can be recreated and biochemically tested, giving insight into the enzymes’ evolutionary history. A previous study by…
(more)
▼ Through ancestral
sequence reconstruction (ASR) techniques, ancient enzymes can be recreated and biochemically tested, giving insight into the enzymes’ evolutionary history. A previous study by Hobbs et al. (2012) has shown that some ancestral 3-isopropylmalate dehydrogenase (IPMDH) enzymes of the Bacillus lineage are more catalytically efficient and kinetically stable than extant counterparts. Given these characteristics, this trend raises questions as to why ancestral Bacillus IPMDH enzymes have been superseded by catalytically slower and less kinetically stable counterparts. The homology between IPMDH and the dehydrogenases of tartrate, malate and isocitrate makes IPMDH an interesting model enzyme in terms of the evolution of substrate specificity.
Here, the reconstruction of a 2.7 billion year old enzyme has been attempted to extend the reconstruction of IPMDH back to the last common ancestor of the Firmicutes. This reconstruction tested the limits of ASR techniques in terms of time and levels of
sequence divergence, especially for such a structurally complex enzyme. However, upon expression and purification, the enzyme was found to form an inactive, soluble aggregate. This suggests that current ASR techniques are too simplistic to reconstruct the complexity and divergence of IPMDH back as far as the last common ancestor of the Firmicutes. Enzyme evolution was investigated with ancestors from the Bacillus genus. Substrate promiscuity of ancestral enzymes was compared to a contemporary counterpart. It was concluded that the ancestral IPMDH enzymes tested do not show additional substrate promiscuity when compared to contemporary counterparts. The fitness of organisms carrying the IPMDH ancestors was assessed to establish what effects the high turnover rates and kinetic stability possessed by some ancestral IPMDH enzymes had on cells when functioning within the normal catalytic pathway for leucine. In vivo, the fastest and most kinetically stable ancestral IPMDH resulted in slower growth rates. This detrimental effect in vivo clarifies why this enzyme has been lost over evolutionary time. The X-ray crystal structure of the most recent IPMDH ancestor was also determined at 2.6 Å resolution. The structure of this ancestral IPMDH was found to be similar to other IPMDH structures, including the previously solved IPMDH from the last common ancestor of the Bacillus.
Advisors/Committee Members: Arcus, Vickery L (advisor).
Subjects/Keywords: ancestral sequence reconstructio;
isopropylmalate dehydrogenase
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Manager
APA (6th Edition):
Prentice, E. J. (2013). Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
. (Masters Thesis). University of Waikato. Retrieved from http://hdl.handle.net/10289/8717
Chicago Manual of Style (16th Edition):
Prentice, Erica Jean. “Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
.” 2013. Masters Thesis, University of Waikato. Accessed March 03, 2021.
http://hdl.handle.net/10289/8717.
MLA Handbook (7th Edition):
Prentice, Erica Jean. “Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
.” 2013. Web. 03 Mar 2021.
Vancouver:
Prentice EJ. Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
. [Internet] [Masters thesis]. University of Waikato; 2013. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10289/8717.
Council of Science Editors:
Prentice EJ. Characterisation of Enzyme Evolution through Ancestral Enzyme Reconstruction
. [Masters Thesis]. University of Waikato; 2013. Available from: http://hdl.handle.net/10289/8717
Brno University of Technology
26.
Richtarik, Lukáš.
Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks.
Degree: 2019, Brno University of Technology
URL: http://hdl.handle.net/11012/85037
► This work deals with the issue of chatbots, which are based on artificial neural networks and generative models. It also describes options and process of…
(more)
▼ This work deals with the issue of chatbots, which are based on artificial neural networks and generative models. It also describes options and process of designing the chatbot as well as an implementation and testing using BLEU metrics. The work contains multiple experiments with different models of chatbots, their performance evaluation and comparison, user experience and several suggestions for future enhancements.
Advisors/Committee Members: Szőke, Igor (advisor), Beneš, Karel (referee).
Subjects/Keywords: chatbot; neurónová sieť; BLEU; generatívny model; sequence to sequence; chatbot; neural network; BLEU; generative model; sequence to sequence
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APA ·
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APA (6th Edition):
Richtarik, L. (2019). Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/85037
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Richtarik, Lukáš. “Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks.” 2019. Thesis, Brno University of Technology. Accessed March 03, 2021.
http://hdl.handle.net/11012/85037.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Richtarik, Lukáš. “Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks.” 2019. Web. 03 Mar 2021.
Vancouver:
Richtarik L. Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/11012/85037.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Richtarik L. Chatbot postavený na umělých neuronových sítích: Chatbot Based on Artificial Neural Networks. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/85037
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Chicago
27.
Tracey, Sara.
The Bullet In Her Pocket.
Degree: 2016, University of Illinois – Chicago
URL: http://hdl.handle.net/10027/20233
► The Bullet In Her Pocket is a narrative, book-length poetic sequence that explores the ontology and ethics of secrets while interrogating the way history is…
(more)
▼ The Bullet In Her Pocket is a narrative, book-length poetic
sequence that explores the ontology and ethics of secrets while interrogating the way history is archived, discovered, and invented. The poems tell the story of Anna, a young woman born to Sicilian immigrants in Cleveland, Ohio, in the 1920s; Biagio, a petty thief with connections to the Mafia; and their daughter Cecilia. Cecilia is conceived while the couple is dating and shortly before Biagio is arrested and imprisoned, thus forcing Anna to confess her pregnancy to her parents who insist she give her daughter up for adoption. What follows is a family drama infused with shame and deception as the characters struggle to draw boundaries between their public and private lives. The poems are populated with items from the domestic realm—worn, feminine, familiar—and disrupted by violence just outside the frame.
Informed by and in conversation with contemporary poets such as Rita Dove, Claudia Emerson, A. Van Jordan, and Ted Genoways, my dissertation attempts to use the lyric tradition as a tool to excavate historical truth by marrying artifact and invention, developing a narrative from fragmented and incomplete records. In the narrative
sequence, individual poems may exhibit varying levels of lyric capacity—that is, the voice of a single speaker, the isolation of a moment—but ultimately, the
sequence as a whole, and many of the individual poems, are driven by my interest in telling a story that is deeply connected to its social context.
Advisors/Committee Members: Pugh, Christina (advisor), Ashton, Jennifer (committee member), Cintron, Ralph (committee member), Reeves, Roger (committee member), Muench, Simone (committee member).
Subjects/Keywords: poetry; lyric; narrative; poetic sequence
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APA (6th Edition):
Tracey, S. (2016). The Bullet In Her Pocket. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/20233
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Tracey, Sara. “The Bullet In Her Pocket.” 2016. Thesis, University of Illinois – Chicago. Accessed March 03, 2021.
http://hdl.handle.net/10027/20233.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Tracey, Sara. “The Bullet In Her Pocket.” 2016. Web. 03 Mar 2021.
Vancouver:
Tracey S. The Bullet In Her Pocket. [Internet] [Thesis]. University of Illinois – Chicago; 2016. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10027/20233.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Tracey S. The Bullet In Her Pocket. [Thesis]. University of Illinois – Chicago; 2016. Available from: http://hdl.handle.net/10027/20233
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Houston
28.
Luker, Austin 1985-.
A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA.
Degree: MS, Geology, 2012, University of Houston
URL: http://hdl.handle.net/10657/455
► A recent surge of interest has arisen concerning the Devonian organic-rich black shales native to the Appalachian Basin of the east coast of the United…
(more)
▼ A recent surge of interest has arisen concerning the Devonian organic-rich black shales native to the Appalachian Basin of the east coast of the United States and their potential as gas producers The Marcellus Shale Formation is part of the middle Devonian Hamilton Group (380 Ma) and is one of ten extensive black shale units in the Appalachian Basin deposited as part of a cyclic repetitive progression of three distinct rock types consisting of organic-rich shales, coarser clastics (silty shales, siltstones, and sandstones), and carbonates (Roen, 1984; Lash and Engelder, 2009). Gas production from these shales is widespread; with high versus low production rates not only controlled by the gas content in the shale, but also largely by the mineral content of the rock that makes the rock more conducive to fractures remaining open.
It is hypothesized that the ability of shale to fracture is controlled by the amount of silica and/or calcite in the rock, and that the variability in the occurrence of those minerals can be predicted by
sequence stratigraphy. The construction of a
sequence stratigraphic model on a basinwide scale over the state of Pennsylvania began with a correlation of 821 wireline well logs. Then, to tie the working
sequence stratigraphic model to mineralogy within individual zones of rock, analysis of 24 rotary sidewall cores was conducted using qualitative x-ray diffraction to determine the mineralogy of each sample.
This study determined that the mineralogy of the organic-rich shales within the Marcellus Formation can be predicted by
sequence stratigraphy, and also found there to be a relationship between mineralogy and total organic carbon (TOC). Now that a relationship is found between mineralogy, TOC, and its location within a
sequence stratigraphic framework specific zones may be identified in a predicable manner within certain sequences that are likely more productive than others.
Advisors/Committee Members: Wellner, Julia S. (advisor), Bhattacharya, Janok P. (committee member), Stewart, Robert R. (committee member), Rice, Derek (committee member).
Subjects/Keywords: Marcellus Formation; Sequence stratigraphy
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APA ·
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MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Luker, A. 1. (2012). A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA. (Masters Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/455
Chicago Manual of Style (16th Edition):
Luker, Austin 1985-. “A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA.” 2012. Masters Thesis, University of Houston. Accessed March 03, 2021.
http://hdl.handle.net/10657/455.
MLA Handbook (7th Edition):
Luker, Austin 1985-. “A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA.” 2012. Web. 03 Mar 2021.
Vancouver:
Luker A1. A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA. [Internet] [Masters thesis]. University of Houston; 2012. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10657/455.
Council of Science Editors:
Luker A1. A COMPARISON OF SEQUENCE STRATIGRAPHY AND MINERALOGICAL VARIATIONS ASSOCIATED WITH TOTAL ORGANIC CARBON IN THE MARCELLUS FORMATION: WASHINGTON COUNTY, PENNSYLVANIA. [Masters Thesis]. University of Houston; 2012. Available from: http://hdl.handle.net/10657/455
Columbia University
29.
Ding, Hongxu.
Understand Biology Using Single Cell RNA-Sequencing.
Degree: 2018, Columbia University
URL: https://doi.org/10.7916/D8Z04S0R
► This dissertation summarizes the development of experimental and analytical tools for single cell RNA sequencing (scRNA-Seq), including 1) scPLATE-Seq, a FACS- and plate-based scRNASeq platform,…
(more)
▼ This dissertation summarizes the development of experimental and analytical tools for single cell RNA sequencing (scRNA-Seq), including 1) scPLATE-Seq, a FACS- and plate-based scRNASeq platform, which is accurate, robust, fully automated and cost-efficient; 2) metaVIPER, an algorithm for transcriptional regulator activity inference based on scRNA-Seq profiles; and 3) iterClust, a statistical framework for iterative clustering analysis, especially suitable for dissecting hierarchy of heterogeneity among single cells. Further this dissertation summarizes biological questions answered by combining these tools, including 1) understanding inter- and intra-tumor heterogeneity of human glioblastoma; 2) elucidating regulators of β-cell de-differentiation in type-2 diabetes; and 3) developing novel therapeutics targeting cell-state regulators of breast cancer stem cells.
Subjects/Keywords: Biology; Nucleotide sequence; Systems biology
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APA ·
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Export
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APA (6th Edition):
Ding, H. (2018). Understand Biology Using Single Cell RNA-Sequencing. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8Z04S0R
Chicago Manual of Style (16th Edition):
Ding, Hongxu. “Understand Biology Using Single Cell RNA-Sequencing.” 2018. Doctoral Dissertation, Columbia University. Accessed March 03, 2021.
https://doi.org/10.7916/D8Z04S0R.
MLA Handbook (7th Edition):
Ding, Hongxu. “Understand Biology Using Single Cell RNA-Sequencing.” 2018. Web. 03 Mar 2021.
Vancouver:
Ding H. Understand Biology Using Single Cell RNA-Sequencing. [Internet] [Doctoral dissertation]. Columbia University; 2018. [cited 2021 Mar 03].
Available from: https://doi.org/10.7916/D8Z04S0R.
Council of Science Editors:
Ding H. Understand Biology Using Single Cell RNA-Sequencing. [Doctoral Dissertation]. Columbia University; 2018. Available from: https://doi.org/10.7916/D8Z04S0R
University of California – San Francisco
30.
Yunes, Jeffrey.
ShareMSA: real time collaboration on multiple sequence alignments.
Degree: Bioengineering, 2017, University of California – San Francisco
URL: http://www.escholarship.org/uc/item/25m055cn
► A Multiple Sequence Alignment (MSA) is a widely used data structure in bioinformatics for applications ranging from evolutionary analyses to protein engineering. ShareMSA is a…
(more)
▼ A Multiple Sequence Alignment (MSA) is a widely used data structure in bioinformatics for applications ranging from evolutionary analyses to protein engineering. ShareMSA is a website that allows users to visualize, share, and collaborate on MSAs. ShareMSA makes MSAs more accessible by allowing collaborators one-click access to the MSA and annotations without the need to install software. In addition, when those with requisite permissions change the annotations or legend, all viewers of the MSA see the changes in real time. A Chimera plugin is available via the ShareMSA website, allowing Chimera users to publish MSAs from within this sequence-structure visualization software.
Subjects/Keywords: Bioinformatics; collaboration; multiple sequence alignments
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APA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Yunes, J. (2017). ShareMSA: real time collaboration on multiple sequence alignments. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/25m055cn
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Yunes, Jeffrey. “ShareMSA: real time collaboration on multiple sequence alignments.” 2017. Thesis, University of California – San Francisco. Accessed March 03, 2021.
http://www.escholarship.org/uc/item/25m055cn.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Yunes, Jeffrey. “ShareMSA: real time collaboration on multiple sequence alignments.” 2017. Web. 03 Mar 2021.
Vancouver:
Yunes J. ShareMSA: real time collaboration on multiple sequence alignments. [Internet] [Thesis]. University of California – San Francisco; 2017. [cited 2021 Mar 03].
Available from: http://www.escholarship.org/uc/item/25m055cn.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Yunes J. ShareMSA: real time collaboration on multiple sequence alignments. [Thesis]. University of California – San Francisco; 2017. Available from: http://www.escholarship.org/uc/item/25m055cn
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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. 
Open Access Theses and Dissertations