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Author Details

Katherine S Pollard
Gladstone Institutes
2002
182
61
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36321886MIDAS2: Metagenomic Intra-species Diversity Analysis System.Bioinformatics2023
36321886MIDAS2: Metagenomic Intra-species Diversity Analysis System.Bioinformatics2023
37563669Maast: genotyping thousands of microbial strains efficiently.Genome Biol2023
37961712Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.bioRxiv2023
37961123SuPreMo: a computational tool for streamlining <i>in silico</i> perturbation using sequence-based predictive models.bioRxiv2023
37961120Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv2023
37868032<i>In silico</i> discovery of repetitive elements as key sequence determinants of 3D genome folding.Cell Genom2023
36711864Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis.bioRxiv2023
36824845Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.bioRxiv2023
37017090Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy.Circ Genom Precis Med2023
36640767Machine learning dissection of human accelerated regions in primate neurodevelopment.Neuron2023
36945630Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.medRxiv2023
37316519Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.Nat Commun2023
37066196Comparing chromatin contact maps at scale: methods and insights.bioRxiv2023
37104607Three-dimensional genome rewiring in loci with human accelerated regions.Science2023
37104599Evolutionary constraint and innovation across hundreds of placental mammals.Science2023
36856771Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.STAR Protoc2023
37419111Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Mol Cell2023
37292728Comparing chromatin contact maps at scale: methods and insights.Res Sq2023
36657438Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell Syst2023
37961712Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.bioRxiv2023
37961123SuPreMo: a computational tool for streamlining <i>in silico</i> perturbation using sequence-based predictive models.bioRxiv2023
37961120Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv2023
37868032<i>In silico</i> discovery of repetitive elements as key sequence determinants of 3D genome folding.Cell Genom2023
37563669Maast: genotyping thousands of microbial strains efficiently.Genome Biol2023
37292728Comparing chromatin contact maps at scale: methods and insights.Res Sq2023
37419111Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Mol Cell2023
37316519Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.Nat Commun2023
37017090Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy.Circ Genom Precis Med2023
36945630Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.medRxiv2023
37104607Three-dimensional genome rewiring in loci with human accelerated regions.Science2023
37104599Evolutionary constraint and innovation across hundreds of placental mammals.Science2023
37066196Comparing chromatin contact maps at scale: methods and insights.bioRxiv2023
36856771Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.STAR Protoc2023
36711864Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis.bioRxiv2023
36640767Machine learning dissection of human accelerated regions in primate neurodevelopment.Neuron2023
36824845Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.bioRxiv2023
36657438Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell Syst2023
34837041Navigating the pitfalls of applying machine learning in genomics.Nat Rev Genet2022
36304283Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.Front Bioinform2022
35967929Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis.Bioinform Adv2022
35649376Differential Etv2 threshold requirement for endothelial and erythropoietic development.Cell Rep2022
35938400Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.Circulation2022
36138165Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism.Nat Microbiol2022
36070559Enhancer Function and Evolutionary Roles of Human Accelerated Regions.Annu Rev Genet2022
35484242Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.Mol Psychiatry2022
35365713Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.Sci Rep2022
35417481Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.PLoS One2022
35718796Correction to: Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.Mol Psychiatry2022
36469554Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.Curr Protoc2022
  • 1 - 50 of 364

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Collaborators

John A Capra
Bakar Computational Health Sciences Institute, University of California san francisco
Co-authored papers 16
Benoit G Bruneau
Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes
Co-authored papers 15
Nadav Ahituv
University of California san francisco
Co-authored papers 11
Joshua Ladau
Lawrence Berkeley National Laboratory
Co-authored papers 10
Pawel F Przytycki
Co-authored papers 9
Deepak Srivastava
Gladstone Institutes San Francisco
Co-authored papers 8
Kathleen C Keough
University of California San Francisco
Co-authored papers 8
Adam Siepel
Co-authored papers 8
Jack A Gilbert
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 7
Rob Knight
University of California
Co-authored papers 7
Melissa J Hubisz
Co-authored papers 6
Reuben Thomas
Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes
Co-authored papers 6
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 6
Peter J Turnbaugh
University of California san francisco
Co-authored papers 5
Kerstin Lindblad-Toh
Uppsala University
Co-authored papers 5
Abigail L Lind
Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes
Co-authored papers 5
Jonathan A Eisen
McLean Hospital
Co-authored papers 5
Joseph L DeRisi
University of California San Francisco
Co-authored papers 4
Oliver A Ryder
Co-authored papers 4
Sol Katzman
Co-authored papers 4
Jay Shendure
University of Washington
Co-authored papers 4
Rebecca Truty
Invitae Corporation
Co-authored papers 4
Elinor K Karlsson
Co-authored papers 4
Casey A Gifford
Gladstone Institutes, USA Roddenberry Center for Stem Cell Biology at Gladstone
Co-authored papers 4
Yu Huang
Gladstone Institutes San Francisco
Co-authored papers 4
Bruce R Conklin
Gladstone Institutes
Co-authored papers 4
Arun Padmanabhan
Gladstone Institutes San Francisco
Co-authored papers 4
Daniel He
Co-authored papers 4
Brian L Black
Cardiovascular Research Institute, University of California san francisco
Co-authored papers 4
Pieter C Dorrestein
Co-authored papers 4
Release 1.2