Mutation effect estimation on protein–protein interactions using deep contextualized representation learning

JOURNAL ARTICLE published 1 June 2020 in NAR Genomics and Bioinformatics

Research funded by National Institutes of Health (U01HG008488,R01GM115833,U54GM114833) | National Science Foundation (IIS-1313606,DBI-1565137,DGE-1829071)

Authors: Guangyu Zhou | Muhao Chen | Chelsea J T Ju | Zheng Wang | Jyun-Yu Jiang | Wei Wang

ChEC-seq2: an improved chromatin endogenous cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein–DNA interactions

JOURNAL ARTICLE published 5 January 2024 in NAR Genomics and Bioinformatics

Research funded by National Institute of General Medical Sciences (R35GM136419)

Authors: Jake VanBelzen | Chengzhe Duan | Donna Garvey Brickner | Jason H Brickner

Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

JOURNAL ARTICLE published 1 June 2020 in NAR Genomics and Bioinformatics

Research funded by National Health and Medical Research Council (APP1132719,APP1083405,APP1107599) | NHMRC Practitioner Fellowship (1103329) | NHMRC Senior Research Fellowship (1154389) | Australian Research Council Future Fellowship (FT140100047)

Authors: Anne Senabouth | Stacey Andersen | Qianyu Shi | Lei Shi | Feng Jiang | Wenwei Zhang | Kristof Wing | Maciej Daniszewski | Samuel W Lukowski | Sandy S C Hung | Quan Nguyen | Lynn Fink | Anthony Beckhouse | Alice Pébay | Alex W Hewitt | Joseph E Powell

Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

JOURNAL ARTICLE published 1 June 2020 in NAR Genomics and Bioinformatics

Research funded by Fondation ARC (PGA1 RF20190208691)

Authors: Frédéric Pont | Marie Tosolini | Qing Gao | Marion Perrier | Miguel Madrid-Mencía | Tse Shun Huang | Pierre Neuvial | Maha Ayyoub | Kristopher Nazor | Jean-Jacques Fournié

Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data

JOURNAL ARTICLE published 1 September 2020 in NAR Genomics and Bioinformatics

Research funded by National Health and Medical Research Council (1147974,1156408) | Australian Government (wk73)

Authors: Phuc-Loi Luu | Phuc-Thinh Ong | Thanh-Phuoc Dinh | Susan J Clark

OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics

Research funded by Competitiveness, Entrepreneurship and Innovation (2014-2020,5002562) | Hellenic Foundation for Research and Innovation (1855-BOLOGNA) | General Secretariat for Research and Innovation (241) | Novo Nordisk Foundation (NNF14CC0001)

Authors: Fotis A Baltoumas | Sofia Zafeiropoulou | Evangelos Karatzas | Savvas Paragkamian | Foteini Thanati | Ioannis Iliopoulos | Aristides G Eliopoulos | Reinhard Schneider | Lars Juhl Jensen | Evangelos Pafilis | Georgios A Pavlopoulos

Tissue heterogeneity is prevalent in gene expression studies

JOURNAL ARTICLE published 23 June 2021 in NAR Genomics and Bioinformatics

Authors: Gregor Sturm | Markus List | Jitao David Zhang

Sequencing error profiles of Illumina sequencing instruments

JOURNAL ARTICLE published 6 January 2021 in NAR Genomics and Bioinformatics

Research funded by NHGRI (U41 HG006620) | NSF ABI Grant (1661497) | NIAID (R01 AI134384)

Authors: Nicholas Stoler | Anton Nekrutenko

A minimum reporting standard for multiple sequence alignments

JOURNAL ARTICLE published 1 June 2020 in NAR Genomics and Bioinformatics

Authors: Thomas K F Wong | Subha Kalyaanamoorthy | Karen Meusemann | David K Yeates | Bernhard Misof | Lars S Jermiin

Targeted DNA methylation from cell-free DNA using hybridization probe capture

JOURNAL ARTICLE published 6 October 2022 in NAR Genomics and Bioinformatics

Research funded by National Institutes of Health (R01CA201352)

Authors: David N Buckley | Gerald Gooden | Kuan Feng | Jacob Enk | Bodour Salhia

How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis

JOURNAL ARTICLE published 5 January 2024 in NAR Genomics and Bioinformatics

Research funded by German Research Foundation (442077441)

Authors: Louisa Wessels Perelo | Gisela Gabernet | Daniel Straub | Sven Nahnsen

scAIDE: clustering of large-scale single-cell RNA-seq data reveals putative and rare cell types

JOURNAL ARTICLE published 1 December 2020 in NAR Genomics and Bioinformatics

Research funded by National Natural Science Foundation of China (61872218,61721003,61673241,61906105) | National Key Research and Development Program of China (2019YFB1404804)

Authors: Kaikun Xie | Yu Huang | Feng Zeng | Zehua Liu | Ting Chen

OLOGRAM-MODL: mining enrichedn-wise combinations of genomic features with Monte Carlo and dictionary learning

JOURNAL ARTICLE published 4 October 2021 in NAR Genomics and Bioinformatics

Authors: Quentin Ferré | Cécile Capponi | Denis Puthier

In silicoanalysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity

JOURNAL ARTICLE published 28 January 2021 in NAR Genomics and Bioinformatics

Research funded by European Research Council (ERC-StG 281851,ERC-PoC 755284) | Bioimaging-GR (MIS 5002755) | Competitiveness, Entrepreneurship and Innovation (NSRF 2014-2020)

Authors: Maria Anna Rapsomaniki | Stella Maxouri | Patroula Nathanailidou | Manuel Ramirez Garrastacho | Nickolaos Nikiforos Giakoumakis | Stavros Taraviras | John Lygeros | Zoi Lygerou

An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency

JOURNAL ARTICLE published 13 January 2022 in NAR Genomics and Bioinformatics

Research funded by EU horizon 2020 (714731) | LLS and rising tide foundation (RTF6005-19) | ISF-NSFC (2427/18) | ISF-IPMP-Israel Precision Medicine Program (3165/19,BIRAX 713023)

Authors: Tamir Biezuner | Yardena Brilon | Asaf Ben Arye | Barak Oron | Aditee Kadam | Adi Danin | Nili Furer | Mark D Minden | Dennis Dong Hwan Kim | Shiran Shapira | Nadir Arber | John Dick | Paaladinesh Thavendiranathan | Yoni Moskovitz | Nathali Kaushansky | Noa Chapal-Ilani | Liran I Shlush

Spinach genomes reveal migration history and candidate genes for important crop traits

JOURNAL ARTICLE published 4 April 2024 in NAR Genomics and Bioinformatics

Research funded by Austrian Science Fund (P 32860-B)

Authors: An Nguyen-Hoang | Felix L Sandell | Heinz Himmelbauer | Juliane C Dohm

Inferring structural and dynamical properties of gene networks from data with deep learning

JOURNAL ARTICLE published 9 July 2022 in NAR Genomics and Bioinformatics

Research funded by National Key Research and Development Program of China (2019YFA0709502) | National Natural Science Foundation of China (12171102)

Authors: Feng Chen | Chunhe Li

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

JOURNAL ARTICLE published 13 January 2022 in NAR Genomics and Bioinformatics

Research funded by Deutsche Forschungsgemeinschaft (EXC 2124 - 390838134,ZUK63,398967434 - TRR 261,EXC 2180 - 390900677) | German Federal Ministry of Education and Research (01ZX1301F) | Chan Zuckerberg Initiative (EOSS2-0000000270)

Authors: Sabrina Krakau | Daniel Straub | Hadrien Gourlé | Gisela Gabernet | Sven Nahnsen

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

JOURNAL ARTICLE published 1 June 2020 in NAR Genomics and Bioinformatics

Authors: Lars S Jermiin | Renee A Catullo | Barbara R Holland

Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome

JOURNAL ARTICLE published 6 October 2022 in NAR Genomics and Bioinformatics

Research funded by National Institute of General Medical Sciences (R01GM133810,F31CA257090)

Authors: Collin A O’Leary | Van S Tompkins | Warren B Rouse | Gijong Nam | Walter N Moss