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Author Details

Benedict Paten
UC Santa Cruz Genomics Institute, University of California
2005
129
51
PMIDPaper TitleJournal TitlePublished Year
36413377LungMAP Portal Ecosystem: Systems-level Exploration of the Lung.Am J Respir Cell Mol Biol2024
36413377LungMAP Portal Ecosystem: Systems-level Exploration of the Lung.Am J Respir Cell Mol Biol2024
38030727Identification of constrained sequence elements across 239 primate genomes.Nature2024
37165083Pangenome graph construction from genome alignments with Minigraph-Cactus.Nat Biotechnol2024
38030727Identification of constrained sequence elements across 239 primate genomes.Nature2024
37165083Pangenome graph construction from genome alignments with Minigraph-Cactus.Nat Biotechnol2024
36200899Toward a data infrastructure for the Plant Cell Atlas.Plant Physiol2023
36200899Toward a data infrastructure for the Plant Cell Atlas.Plant Physiol2023
36420896GENCODE: reference annotation for the human and mouse genomes in 2023.Nucleic Acids Res2023
37745389Local read haplotagging enables accurate long-read small variant calling.bioRxiv2023
37719153A unified pipeline for FISH spatial transcriptomics.Cell Genom2023
38077089The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.bioRxiv2023
37710018Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.Nat Methods2023
37614242Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease.Alzheimers Dement (N Y)2023
36909548Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.bioRxiv2023
36646895Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.Nat Methods2023
37205357A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in <i>AFF3</i> as a significant cause of intellectual disability.medRxiv2023
37192819Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research.J Am Med Inform Assoc2023
36945442Structurally divergent and recurrently mutated regions of primate genomes.bioRxiv2023
36749013Optimal gap-affine alignment in O(s) space.Bioinformatics2023
37122002Inversion polymorphism in a complete human genome assembly.Genome Biol2023
36865218Phased nanopore assembly with Shasta and modular graph phasing with GFAse.bioRxiv2023
37104599Evolutionary constraint and innovation across hundreds of placental mammals.Science2023
37164484Gaps and complex structurally variant loci in phased genome assemblies.Genome Res2023
37719153A unified pipeline for FISH spatial transcriptomics.Cell Genom2023
38077089The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.bioRxiv2023
37710018Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.Nat Methods2023
37745389Local read haplotagging enables accurate long-read small variant calling.bioRxiv2023
37614242Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease.Alzheimers Dement (N Y)2023
37192819Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research.J Am Med Inform Assoc2023
37122002Inversion polymorphism in a complete human genome assembly.Genome Biol2023
36945442Structurally divergent and recurrently mutated regions of primate genomes.bioRxiv2023
37205357A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in <i>AFF3</i> as a significant cause of intellectual disability.medRxiv2023
37104599Evolutionary constraint and innovation across hundreds of placental mammals.Science2023
37164484Gaps and complex structurally variant loci in phased genome assemblies.Genome Res2023
36749013Optimal gap-affine alignment in O(s) space.Bioinformatics2023
36646895Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.Nat Methods2023
36909548Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.bioRxiv2023
36420896GENCODE: reference annotation for the human and mouse genomes in 2023.Nucleic Acids Res2023
36865218Phased nanopore assembly with Shasta and modular graph phasing with GFAse.bioRxiv2023
35020984Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting.N Engl J Med2022
36179091GBZ file format for pangenome graphs.Bioinformatics2022
35444317The Human Pangenome Project: a global resource to map genomic diversity.Nature2022
35384842Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.Elife2022
35483961A complete pedigree-based graph workflow for rare candidate variant analysis.Genome Res2022
35361931Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.Nat Methods2022
35357935A complete reference genome improves analysis of human genetic variation.Science2022
36195648Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer.Sci Rep2022
35720974PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.Cell Genom2022
35020984Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting.N Engl J Med2022
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Collaborators

David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 40
Mark Diekhans
Genomics Institute, University of California Santa Cruz
Co-authored papers 24
Miten Jain
Northeastern University
Co-authored papers 23
Adam M Novak
UC Santa Cruz Genomics Institute, University of California
Co-authored papers 19
Ian T Fiddes
Liver Center and Diabetes Center, University of California san francisco
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Evan E Eichler
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William James Kent
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Adam M Phillippy
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Paul Flicek
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Daniel R Zerbino
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Mark Akeson
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Jean Monlong
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Sergey Koren
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Hiram Clawson
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Tobias Marschall
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Ewan Birney
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Andrew Carroll
Google LLC
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Fritz J Sedlazeck
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Richard E Green
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Mark Gerstein
Yale University
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Oliver A Ryder
Co-authored papers 6
Mark J P Chaisson
University of Southern California
Co-authored papers 6
Guojie Zhang
University of Copenhagen, Universitetsparken 15
Co-authored papers 6
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 6
Ann S Zweig
Co-authored papers 6
Donna Karolchik
Co-authored papers 6
Richard Durbin
University of Cambridge
Co-authored papers 6
Jan O Korbel
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 5
Adam Frankish
Co-authored papers 5
Tina Graves
McDonnell Genome Institute, Washington University
Co-authored papers 5
Release 1.2