Katherine S. Pollard

26 papers B 1Journal 24Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop.
CoRR
Elizabeth Fahsbender, Alma Andersson, Jeremy Ash, Polina Binder, Daniel Burkhardt, Benjamin Chang, Georg K. Gerber, Anthony Gitter, Patrick Godau, Ankit Gupta, Genevieve Haliburton, Siyu He, Trey Ideker, Ivana Jelic, Aly Khan, Yang-Joon Kim, Aditi Krishnapriyan, Jon M. Laurent, Tianyu Liu, Emma Lundberg, Shalin B. Mehta, Rob Moccia, Angela Oliveira Pisco, Katherine S. Pollard, Suresh Ramani, Julio Saez-Rodriguez, Yasin Senbabaoglu, Elana Simon, Srinivasan Sivanandan, Gustavo Stolovitzky, Marc Valer, Bo Wang, Xikun Zhang, James Zou, Katrina Kalantar
2025 J jnl
ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.
PLoS Comput. Biol.
Laura M. Gunsalus, Michael J. Keiser, Katherine S. Pollard
2025 J jnl
Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).
PLoS Comput. Biol.
Miriam Goldman, Chunyu Zhao, Katherine S. Pollard
2024 J jnl
SuPreMo: a computational tool for streamlining
Bioinform.
Ketrin Gjoni, Katherine S. Pollard
2023 J jnl
MIDAS2: Metagenomic Intra-species Diversity Analysis System.
Bioinform.
Chunyu Zhao, Boris Dimitrov, Miriam Goldman, Stephen Nayfach, Katherine S. Pollard
2022 J jnl
CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.
Bioinform.
Pawel F. Przytycki, Katherine S. Pollard
2022 J jnl
Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.
Frontiers Bioinform.
Byron J. Smith, Xiangpeng Li, Zhou Jason Shi, Adam R. Abate, Katherine S. Pollard
2020 J jnl
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
Bioinform.
Patrick H. Bradley, Katherine S. Pollard
2019 J jnl
New insights from uncultivated genomes of the global human gut microbiome.
Nat.
Stephen Nayfach, Zhou Jason Shi, Rekha Seshadri, Katherine S. Pollard, Nikos Kyrpides
2018 J jnl
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
PLoS Comput. Biol.
Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
2017 J jnl
Features that define the best ChIP-seq peak calling algorithms.
Briefings Bioinform.
Reuben Thomas, Sean Thomas, Alisha K. Holloway, Katherine S. Pollard
2017 J jnl
Unboxing cluster heatmaps.
BMC Bioinform.
Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard
2015 J jnl
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
PLoS Comput. Biol.
Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alexander G. Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton
2015 J jnl
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species.
BMC Bioinform.
Aram Avila-Herrera, Katherine S. Pollard
2015 J jnl
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Bioinform.
Stephen Nayfach, Michael A. Fischbach, Katherine S. Pollard
2014 J jnl
Integrating Diverse Datasets Improves Developmental Enhancer Prediction.
PLoS Comput. Biol.
Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra
2012 J jnl
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.
BMC Bioinform.
Danielle G. Lemay, William F. Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian Korf, Katherine S. Pollard
2012 J jnl
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin.
PLoS Comput. Biol.
John A. Capra, Alexander G. Williams, Katherine S. Pollard
2012 J jnl
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.
BMC Bioinform.
Thomas J. Sharpton, Guillaume Jospin, Dongying Wu, Morgan G. I. Langille, Katherine S. Pollard, Jonathan A. Eisen
2011 J jnl
PHAST and RPHAST: phylogenetic analysis with space/time models.
Briefings Bioinform.
Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel
2011 J jnl
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data.
PLoS Comput. Biol.
Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard
2010 J jnl
High-throughput sequencing of the DBA/2J mouse genome.
BMC Bioinform.
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
2007 J jnl
Gene regulatory networks in lactation: identification of global principles using bioinformatics.
BMC Syst. Biol.
Danielle G. Lemay, Margaret C. Neville, Michael Rudolph, Katherine S. Pollard, J. Bruce German
2006 B conf
New Methods for Detecting Lineage-Specific Selection.
RECOMB
Adam C. Siepel, Katherine S. Pollard, David Haussler
2006 J jnl
The UCSC Archaeal Genome Browser.
Nucleic Acids Res.
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe
2003 — conf
Multiple Testing for Gene Expression Data: An Investigation of Null Distributions with Consequences for the Permutation Test.
METMBS
Katherine S. Pollard, Mark J. van der Laan