Katherine S. Pollard

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 7

Top Topics

Gene Expression Data

Escherichia Coli

Top Venues

PLoS Comput. Biol.

Briefings Bioinform.

Publications

Chunyu Zhao, Boris Dimitrov, Miriam Goldman, Stephen Nayfach, Katherine S. Pollard
MIDAS2: Metagenomic Intra-species Diversity Analysis System. Bioinform. 39 (1) (2023)
Byron J. Smith, Xiangpeng Li, Zhou Jason Shi, Adam R. Abate, Katherine S. Pollard
Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. Frontiers Bioinform. 2 (2022)
Patrick H. Bradley, Katherine S. Pollard
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. Bioinform. 36 (4) (2020)
Stephen Nayfach, Zhou Jason Shi, Rekha Seshadri, Katherine S. Pollard, Nikos Kyrpides
New insights from uncultivated genomes of the global human gut microbiome. Nat. 568 (7753) (2019)
Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Comput. Biol. 14 (8) (2018)
Reuben Thomas, Sean Thomas, Alisha K. Holloway, Katherine S. Pollard
Features that define the best ChIP-seq peak calling algorithms. Briefings Bioinform. 18 (3) (2017)
Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard
Unboxing cluster heatmaps. BMC Bioinform. 18 (S-2) (2017)
Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alexander G. Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput. Biol. 11 (11) (2015)
Aram Avila-Herrera, Katherine S. Pollard
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinform. 16 (2015)
Stephen Nayfach, Michael A. Fischbach, Katherine S. Pollard
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinform. 31 (20) (2015)
Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra
Integrating Diverse Datasets Improves Developmental Enhancer Prediction. PLoS Comput. Biol. 10 (6) (2014)
Danielle G. Lemay, William F. Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian Korf, Katherine S. Pollard
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinform. 13 (2012)
John A. Capra, Alexander G. Williams, Katherine S. Pollard
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin. PLoS Comput. Biol. 8 (6) (2012)
Thomas J. Sharpton, Guillaume Jospin, Dongying Wu, Morgan G. I. Langille, Katherine S. Pollard, Jonathan A. Eisen
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinform. 13 (2012)
Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. PLoS Comput. Biol. 7 (1) (2011)
Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel
PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings Bioinform. 12 (1) (2011)
Xusheng Wang, Richa Agarwala, John A. Capra, Zugen Chen, Deanna M. Church, Daniel C. Ciobanu, Zhengsheng Li, Lu Lu, Khyobeni Mozhui, Megan K. Mulligan, Stanley F. Nelson, Katherine S. Pollard, William Taylor, Donald B. Thomason, Robert W. Williams
High-throughput sequencing of the DBA/2J mouse genome. BMC Bioinform. 11 (S-4) (2010)
Danielle G. Lemay, Margaret C. Neville, Michael Rudolph, Katherine S. Pollard, J. Bruce German
Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst. Biol. 1 (2007)
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe
The UCSC Archaeal Genome Browser. Nucleic Acids Res. 34 (Database-Issue) (2006)
Adam C. Siepel, Katherine S. Pollard, David Haussler
New Methods for Detecting Lineage-Specific Selection. RECOMB (2006)
Katherine S. Pollard, Mark J. van der Laan
Multiple Testing for Gene Expression Data: An Investigation of Null Distributions with Consequences for the Permutation Test. METMBS (2003)