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Author Details

Uwe Ohler
Humboldt University
1999
130
50
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36474914Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19.Cell Genom2023
37956386Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing.J Cell Biol2023
37262323Toward Identification of Functional Sequences and Variants in Noncoding DNA.Annu Rev Biomed Data Sci2023
36996230Brassinosteroid gene regulatory networks at cellular resolution in the <i>Arabidopsis</i> root.Science2023
36814457A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.NAR Genom Bioinform2023
34273561SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy.Genomics Proteomics Bioinformatics2022
35831657Standardized annotation of translated open reading frames.Nat Biotechnol2022
35789323Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nat Genet2022
36777038Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.Cell Genom2022
36181683Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.STAR Protoc2022
35909238Cluster-independent marker feature identification from single-cell omics data using SEMITONES.Nucleic Acids Res2022
36096941Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.Genome Biol2022
35114978Deep learning for prediction of population health costs.BMC Med Inform Decis Mak2022
35294876The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.Cell Rep2022
34561102Intricacies of single-cell multi-omics data integration.Trends Genet2022
33357414Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.Mol Cell2021
33765284Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.Methods Mol Biol2021
33509077Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.BMC Genomics2021
34099733Spatio-temporal mRNA tracking in the early zebrafish embryo.Nat Commun2021
33428246Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.EMBO J2021
31128317Towards a deeper annotation of human lncRNAs.Biochim Biophys Acta Gene Regul Mech2020
31992613Deep neural networks for interpreting RNA-binding protein target preferences.Genome Res2020
31759823A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary.Mol Cell2020
33171098Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis.Dev Cell2020
32661261Deep learning for genomics using Janggu.Nat Commun2020
32601440Quantification of translation uncovers the functions of the alternative transcriptome.Nat Struct Mol Biol2020
32781615The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation.Int J Mol Sci2020
32157095Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.Nat Commun2020
30517751Deciphering human ribonucleoprotein regulatory networks.Nucleic Acids Res2019
31155234The Translational Landscape of the Human Heart.Cell2019
30824702Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.Nat Commun2019
30791920Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.Genome Biol2019
30967537Global identification of functional microRNA-mRNA interactions in Drosophila.Nat Commun2019
29028411Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP.RNA Biol2018
29893814SSMART: sequence-structure motif identification for RNA-binding proteins.Bioinformatics2018
30367057Determinants of promoter and enhancer transcription directionality in metazoans.Nat Commun2018
30337934Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation.Front Plant Sci2018
30384847omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.Genome Biol2018
29379186Redundant regulation.Nat Ecol Evol2018
29463232Finding RNA structure in the unstructured RBPome.BMC Genomics2018
27870833Integrative classification of human coding and noncoding genes through RNA metabolism profiles.Nat Struct Mol Biol2017
28087634Genome-wide identification of regulatory elements in Sertoli cells.Development2017
28334930RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.Nucleic Acids Res2017
29070071McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.Genome Biol2017
28977546ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.Nucleic Acids Res2017
28596291DDX54 regulates transcriptome dynamics during DNA damage response.Genome Res2017
28554830RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.J Biotechnol2017
28582575The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.Nucleic Acids Res2017
28928394RNA localization is a key determinant of neurite-enriched proteome.Nat Commun2017
28887026Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome.Trends Genet2017
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Collaborators

David L Corcoran
The University of North Carolina at Chapel Hill
Co-authored papers 14
Lorenzo Calviello
Functional Genomics Research Centre, Italy Computational Biology Research Centre
Co-authored papers 10
Altuna Akalin
Berlin Institute for Medical Systems Biology
Co-authored papers 7
Molly Megraw
Center for Quantitative Life Sciences, Oregon State University
Co-authored papers 5
Markus Hafner
National Institute of Arthritis and Musculoskeletal and Skin Diseases
Co-authored papers 5
Stoyan Georgiev
Stanford University
Co-authored papers 5
Galip G??rkan Yard??mc??
University of Washington
Co-authored papers 4
Gregory E Crawford
Center for Genomic & Computational Biology, Duke University
Co-authored papers 4
James T Kadonaga
University of California
Co-authored papers 4
Christopher B Burge
Co-authored papers 3
Anirudh Natarajan
University of California at Berkeley
Co-authored papers 3
Norbert H??bner
Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC)
Co-authored papers 2
Peter F Stadler
Co-authored papers 2
Michael Gotthardt
Co-authored papers 2
David A Wassarman
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Co-authored papers 2
Christopher K Glass
University of California San Diego
Co-authored papers 2
Gerald M Rubin
The University of Florida
Co-authored papers 2
Martin G Reese
Fabric Genomics Inc.
Co-authored papers 2
David A Garfield
Humboldt Universitat Berlin
Co-authored papers 2
Adam Frankish
Co-authored papers 2
Christopher Benner
Michigan State University College of Human Medicine
Co-authored papers 2
Yoichiro Shibata
Center for Genomic and Computational Biology, Duke University.
Co-authored papers 2
Sascha H Duttke
College of Veterinary Medicine, Washington State University
Co-authored papers 2
Lingyun Song
Center for Genomic & Computational Biology, Duke University
Co-authored papers 2
Sven Heinz
U.C. San Diego School of Medicine
Co-authored papers 2
Nathan Sheffield (CM4AI)
University of Virginia
Co-authored papers 2
Maria J Martin
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Erik van Nimwegen
University of Basel
Co-authored papers 1
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 1
Philipp Mertins
Co-authored papers 1
Release 1.2