Pond, Sergei K: search on Z-Library

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1

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes

Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 4.79 MB

english, 2018

2

Structure–function analysis of hepatitis C virus envelope glycoproteins E1 and E2

Nayak, Aparajita, Pattabiraman, Nagarajan, Fadra, Numrah, Goldman, Radoslav, Kosakovsky Pond, Sergei L., Mazumder, Raja

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 1.02 MB

english, 2015

3

Are All Subtypes Created Equal? The Effectiveness of Antiretroviral Therapy against Non–Subtype B HIV‐1

Kosakovsky Pond, Sergei L., Smith, Davey M.

Journal:

Clinical Infectious Diseases

Year:

2009

Language:

english

File:

PDF, 253 KB

english, 2009

4

Topologically massive higher spin gauge theories

Kuzenko, Sergei M., Ponds, Michael

Journal:

Journal of High Energy Physics

Year:

2018

Language:

english

File:

PDF, 824 KB

english, 2018

5

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Lemey, Philippe, Kosakovsky Pond, Sergei L., Drummond, Alexei J., Pybus, Oliver G., Shapiro, Beth, Barroso, Helena, Taveira, Nuno, Rambaut, Andrew

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 517 KB

english, 2007

6

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California

Dalai, Sudeb C., Junqueira, Dennis Maletich, Wilkinson, Eduan, Mehra, Renee, Kosakovsky Pond, Sergei L., Levy, Vivian, Israelski, Dennis, de Oliveira, Tulio, Katzenstein, David

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 3.43 MB

english, 2018

7

Spin projection operators and higher-spin Cotton tensors in three dimensions

Buchbinder, Evgeny I., Kuzenko, Sergei M., La Fontaine, James, Ponds, Michael

Journal:

Physics Letters B

Year:

2019

Language:

english

File:

PDF, 342 KB

english, 2019

8

Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: ignore at your own peril

Wisotsky, Sadie R, Kosakovsky Pond, Sergei L, Shank, Stephen D, Muse, Spencer V, Crandall, Keith

Journal:

Molecular Biology and Evolution

Year:

2020

File:

PDF, 1.96 MB

2020

9

Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania

Sanjay R. Mehta, Joel O. Wertheim, Wayne Delport, Luminita Ene, Gratiela Tardei, Dan Duiculescu, Sergei L. Kosakovsky Pond, Davey M. Smith

Journal:

Infection, Genetics and Evolution

Year:

2011

Language:

english

File:

PDF, 205 KB

english, 2011

10

Polymorphism data assist estimation of the non-synonymous over synonymous fixation rate ratio ω for closely related species

Mugal, Carina F, Kutschera, Verena E, Botero-Castro, Fidel, Wolf, Jochen B W, Kaj, Ingemar, Pond, Sergei Kosakovsky

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 866 KB

english, 2019

11

OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

Anand, Amitesh, Chen, Ke, Catoiu, Edward, Sastry, Anand V, Olson, Connor A, Sandberg, Troy E, Seif, Yara, Xu, Sibei, Szubin, Richard, Yang, Laurence, Feist, Adam M, Palsson, Bernhard O, Pond, Sergei K

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 5.01 MB

english, 2019

12

Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition

Moyano, Ana, Lustig, Gila, Rodel, Hylton E., Antal, Tibor, Sigal, Alex, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.56 MB

2020

13

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

Kosakovsky Pond, Sergei L., Posada, David, Stawiski, Eric, Chappey, Colombe, Poon, Art F.Y., Hughes, Gareth, Fearnhill, Esther, Gravenor, Mike B., Leigh Brown, Andrew J., Frost, Simon D.W., Fraser, Ch

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.19 MB

english, 2009

14

Column Sorting: Rapid Calculation of the Phylogenetic Likelihood Function

Kosakovsky Pond, Sergei, Muse, Spencer

Journal:

Systematic Biology

Year:

2004

Language:

english

File:

PDF, 263 KB

english, 2004

15

Network Analysis of Global Influenza Spread

Chan, Joseph, Holmes, Antony, Rabadan, Raul, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.46 MB

english, 2010

16

Bringing Molecules Back into Molecular Evolution

Wilke, Claus O., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 79 KB

english, 2012

17

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

Poon, Art F. Y., Kosakovsky Pond, Sergei L., Bennett, Phil, Richman, Douglas D., Leigh Brown, Andrew J., Frost, Simon D. W.

Journal:

Year:

2007

Language:

english

File:

PDF, 580 KB

english, 2007

18

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.

Nickle, David C., Jojic, Nebojsa, Heckerman, David, Jojic, Vladimir, Kirovski, Darko, Rolland, Morgane, Kosakovsky Pond, Sergei, Mullins, James I.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 403 KB

english, 2008

19

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men With and Without STI-Associated Urethritis

Council, Olivia D., Zhou, Shuntai, McCann, Chase D., Hoffman, Irving, Tegha, Gerald, Kamwendo, Deborah, Matoga, Mitch, Kosakovsky Pond, Sergei L., Cohen, Myron S., Swanstrom, Ronald

Journal:

Journal of Virology

Year:

2020

File:

PDF, 3.50 MB

2020

20

A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex

Avanzato, Victoria A., Oguntuyo, Kasopefoluwa Y., Escalera-Zamudio, Marina, Gutierrez, Bernardo, Golden, Michael, Kosakovsky Pond, Sergei L., Pryce, Rhys, Walter, Thomas S., Seow, Jeffrey, Doores, Kat

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

File:

PDF, 2.26 MB

2019

21

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

Dhar, Amrit, Ralph, Duncan K., Minin, Vladimir N., Matsen, Frederick A., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.70 MB

2020

22

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Hepler, N. Lance, Scheffler, Konrad, Weaver, Steven, Murrell, Ben, Richman, Douglas D., Burton, Dennis R., Poignard, Pascal, Smith, Davey M., Kosakovsky Pond, Sergei L., Murphy, Robert F.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 578 KB

english, 2014

23

HPV Clearance and the Neglected Role of Stochasticity

Ryser, Marc D., Myers, Evan R., Durrett, Rick, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

24

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope

Poon, Art F. Y., Lewis, Fraser I., Pond, Sergei L. Kosakovsky, Frost, Simon D. W.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 321 KB

english, 2007

25

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

Shank, Stephen D., Weaver, Steven, Kosakovsky Pond, Sergei L.

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

26

Coping with Viral Diversity in HIV Vaccine Design

Nickle, David C., Rolland, Morgane, Jensen, Mark A., Pond, Sergei L. Kosakovsky, Deng, Wenjie, Seligman, Mark, Heckerman, David, Mullins, James I., Jojic, Nebojsa

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.22 MB

english, 2007

27

Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures

Huang, Yi-Fei, Golding, G. Brian, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 557 KB

english, 2014

28

Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men

Pacold, Mary E., Pond, Sergei L. Kosakovsky, Wagner, Gabriel A., Delport, Wayne, Bourque, Daniel L., Richman, Douglas D., Little, Susan J., Smith, Davey M.

Journal:

Year:

2012

Language:

english

File:

PDF, 295 KB

english, 2012

29

Inference of Ancestral Recombination Graphs through Topological Data Analysis

Cámara, Pablo G., Levine, Arnold J., Rabadán, Raúl, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 4.15 MB

english, 2016

30

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts

Rife Magalis, Brittany, Kosakovsky Pond, Sergei L, Summers, Michael F, Salemi, Marco

Journal:

Virus Evolution

Year:

2018

Language:

english

File:

PDF, 1.55 MB

english, 2018

31

Inferring the ancestry of parents and grandparents from genetic data

Pei, Jingwen, Zhang, Yiming, Nielsen, Rasmus, Wu, Yufeng, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.34 MB

2020

32

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines

Raja Mazumder, Zhang-Zhi Hu, C. R. Vinayaka, Jose-Luis Sagripanti, Simon D. W. Frost, Sergei L. Kosakovsky Pond, Cathy H. Wu

Journal:

Year:

2007

Language:

english

File:

PDF, 621 KB

english, 2007

33

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

Smith, Stephen A., Brown, Joseph W., Hinchliff, Cody E., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.90 MB

english, 2013

34

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

Hutchison, Alan L., Maienschein-Cline, Mark, Chiang, Andrew H., Tabei, S. M. Ali, Gudjonson, Herman, Bahroos, Neil, Allada, Ravi, Dinner, Aaron R., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.97 MB

english, 2015

35

Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study

Canini, Laetitia, Conway, Jessica M., Perelson, Alan S., Carrat, Fabrice, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 458 KB

english, 2014

36

SnIPRE: Selection Inference Using a Poisson Random Effects Model

Eilertson, Kirsten E., Booth, James G., Bustamante, Carlos D., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

37

HIV-1 Clade B pol Evolution following Primary Infection

Hightower, George K., May, Susanne J., Pérez-Santiago, Josué, Pacold, Mary E., Wagner, Gabriel A., Little, Susan J., Richman, Douglas D., Mehta, Sanjay R., Smith, Davey M., Pond, Sergei L. Kosakovsky,

Journal:

Year:

2013

Language:

english

File:

PDF, 216 KB

english, 2013

38

Contrast-FEL â a test for differences in selective pressures at individual sites among clades and sets of branches

Kosakovsky Pond, Sergei L, Wisotsky, Sadie R, Escalante, Ananias, Magalis, Brittany Rife, Weaver, Steven, Crandall, Keith

Journal:

Molecular Biology and Evolution

Year:

2020

File:

PDF, 3.03 MB

2020

39

The Relatedness of HIV Epidemics in the United States–Mexico Border Region

Mehta, Sanjay R., Delport, Wayne, Brouwer, Kimberly C., Espitia, Stephen, Patterson, Thomas, Pond, Sergei Kosakovsky, Strathdee, Steffanie A., Smith, Davey M.

Journal:

AIDS Research and Human Retroviruses

Year:

2010

Language:

english

File:

PDF, 103 KB

english, 2010

40

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics

Chowdhury, Salim Akhter, Shackney, Stanley E., Heselmeyer-Haddad, Kerstin, Ried, Thomas, Schäffer, Alejandro A., Schwartz, Russell, Pond, Sergei L. Kosakovsky.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

41

Phylodynamic Inference for Structured Epidemiological Models

Rasmussen, David A., Volz, Erik M., Koelle, Katia, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.46 MB

english, 2014

42

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

Arnold, Brian, Sohail, Mashaal, Wadsworth, Crista, Corander, Jukka, Hanage, William P, Sunyaev, Shamil, Grad, Yonatan H, Pond, Sergei Kosakovsky

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 2.99 MB

english, 2019

43

Phylogenetic modeling of regulatory element turnover based on epigenomic data

Dukler, Noah, Huang, Yi-Fei, Siepel, Adam, Pond, Sergei Kosakovsky

Journal:

Molecular Biology and Evolution

Year:

2020

Language:

english

File:

PDF, 1.84 MB

english, 2020

44

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Chen, Gary K., Chi, Eric C., Ranola, John Michael O., Lange, Kenneth, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 8.21 MB

english, 2015

45

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses

Kosakovsky Pond, Sergei L., Frost, Simon D. W., Grossman, Zehava, Gravenor, Michael B., Richman, Douglas D., Brown, Andrew J. Leigh

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 573 KB

english, 2006

46

Benchmarking Multi-Rate Codon Models

Delport, Wayne, Scheffler, Konrad, Gravenor, Mike B., Muse, Spencer V., Kosakovsky Pond, Sergei, Poon, Art F. Y.

Journal:

Year:

2010

Language:

english

File:

PDF, 161 KB

english, 2010

47

Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure

Fisher, Randall G., Smith, Davey M., Murrell, Ben, Slabbert, Ruhan, Kirby, Bronwyn M., Edson, Clair, Cotton, Mark F., Haubrich, Richard H., Kosakovsky Pond, Sergei L., Van Zyl, Gert U.

Journal:

Journal of Clinical Virology

Year:

2015

Language:

english

File:

PDF, 587 KB

english, 2015

48

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

Archer, John, Rambaut, Andrew, Taillon, Bruce E., Harrigan, P. Richard, Lewis, Marilyn, Robertson, David L., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.32 MB

english, 2010

49

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data

Gopalakrishnan, Sathej, Montazeri, Hesam, Menz, Stephan, Beerenwinkel, Niko, Huisinga, Wilhelm, Pond, Sergei L kosakovsky.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 983 KB

english, 2014

50

HIV-associated neurocognitive disorder is associated with HIV-1 dual infection

Wagner, Gabriel A., Chaillon, Antoine, Liu, Siqi, Franklin, Donald R., Caballero, Gemma, Kosakovsky Pond, Sergei L., Vaida, Florin, Heaton, Robert K., Letendre, Scott L., Grant, Igor, Richman, Douglas

Journal:

Year:

2016

Language:

english

File:

PDF, 248 KB

english, 2016

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