Volume 21, issue 1, December 2020
306 articles in this issue
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In memory of James Taylor: the birth of Galaxy
Authors
- Anton Nekrutenko
- Michael C. Schatz
- Content type: Editorial
- Open Access
- Published: 30 April 2020
- Article: 105
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Wheat chromatin architecture is organized in genome territories and transcription factories
Authors (first, second and last of 26)
- Lorenzo Concia
- Alaguraj Veluchamy
- Moussa Benhamed
- Content type: Research
- Open Access
- Published: 29 April 2020
- Article: 104
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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Authors (first, second and last of 9)
- Vanessa R. Marcelino
- Philip T. L. C. Clausen
- Edward C. Holmes
- Content type: Software
- Open Access
- Published: 28 April 2020
- Article: 103
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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Authors (first, second and last of 19)
- Egor Dolzhenko
- Mark F. Bennett
- Michael A. Eberle
- Content type: Method
- Open Access
- Published: 28 April 2020
- Article: 102
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CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes
Authors
- Wanying Wu
- Peifeng Ji
- Fangqing Zhao
- Content type: Database
- Open Access
- Published: 28 April 2020
- Article: 101
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REPIC: a database for exploring the N6-methyladenosine methylome
Authors (first, second and last of 4)
- Shun Liu
- Allen Zhu
- Mengjie Chen
- Content type: Database
- Open Access
- Published: 28 April 2020
- Article: 100
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Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection
Authors (first, second and last of 18)
- Qiang Zhang
- Jin Hu
- Mei-Lin Jin
- Content type: Research
- Open Access
- Published: 28 April 2020
- Article: 99
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Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Authors (first, second and last of 4)
- Johannes Köster
- Louis J. Dijkstra
- Alexander Schönhuth
- Content type: Method
- Open Access
- Published: 28 April 2020
- Article: 98
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Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures
Authors (first, second and last of 6)
- Oguzhan Begik
- Morghan C. Lucas
- Eva Maria Novoa
- Content type: Research
- Open Access
- Published: 07 May 2020
- Article: 97
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Open data in a deeply connected world
Authors
- Barbara Cheifet
- Content type: Editorial
- Open Access
- Published: 20 April 2020
- Article: 96
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Hi-D: nanoscale mapping of nuclear dynamics in single living cells
Authors (first, second and last of 4)
- Haitham A. Shaban
- Roman Barth
- Kerstin Bystricky
- Content type: Method
- Open Access
- Published: 20 April 2020
- Article: 95
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scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Authors (first, second and last of 5)
- Wenbao Yu
- Yasin Uzun
- Kai Tan
- Content type: Software
- Open Access
- Published: 20 April 2020
- Article: 94
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Reverse-genetics studies of lncRNAs—what we have learnt and paths forward
Authors (first, second and last of 4)
- Fan Gao
- Ye Cai
- Dongyang Xu
- Content type: Review
- Open Access
- Published: 14 April 2020
- Article: 93
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Inference of single-cell phylogenies from lineage tracing data using Cassiopeia
Authors (first, second and last of 9)
- Matthew G Jones
- Alex Khodaverdian
- Nir Yosef
- Content type: Method
- Open Access
- Published: 14 April 2020
- Article: 92
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A multidimensional systems biology analysis of cellular senescence in aging and disease
Authors (first, second and last of 16)
- Roberto A. Avelar
- Javier Gómez Ortega
- João Pedro de Magalhães
- Content type: Research
- Open Access
- Published: 07 April 2020
- Article: 91
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Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
Authors (first, second and last of 17)
- Eric L. Van Nostrand
- Gabriel A. Pratt
- Gene W. Yeo
- Content type: Research
- Open Access
- Published: 06 April 2020
- Article: 90
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The preceding root system drives the composition and function of the rhizosphere microbiome
Authors (first, second and last of 12)
- Yi Zhou
- David R. Coventry
- Matthew D. Denton
- Content type: Research
- Open Access
- Published: 06 April 2020
- Article: 89
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Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing
Authors (first, second and last of 10)
- Jinyan Huang
- Ling Bai
- Jun Chen
- Content type: Research
- Open Access
- Published: 06 April 2020
- Article: 88
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What are innovations in peer review and editorial assessment for?
Authors
- Willem Halffman
- Serge P.J.M Horbach
- Content type: Editorial
- Open Access
- Published: 04 May 2020
- Article: 87
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Open access, open data and peer review
Authors
- Jernej Ule
- Content type: Editorial
- Open Access
- Published: 04 May 2020
- Article: 86
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Lamina-associated domains: peripheral matters and internal affairs
Authors
- Nolwenn Briand
- Philippe Collas
- Content type: Review
- Open Access
- Published: 02 April 2020
- Article: 85
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TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
Authors (first, second and last of 12)
- Guangyu Wang
- Qingshu Meng
- Kaifu Chen
- Content type: Method
- Open Access
- Published: 02 April 2020
- Article: 84
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CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma
Authors (first, second and last of 21)
- S. John Liu
- Martina Malatesta
- Daniel A. Lim
- Content type: Research
- Open Access
- Published: 31 March 2020
- Article: 83
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Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples
Authors
- Jacob Schreiber
- Jeffrey Bilmes
- William Stafford Noble
- Content type: Method
- Open Access
- Published: 30 March 2020
- Article: 82
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Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome
Authors (first, second and last of 4)
- Jacob Schreiber
- Timothy Durham
- William Stafford Noble
- Content type: Method
- Open Access
- Published: 30 March 2020
- Article: 81
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Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts
Authors (first, second and last of 12)
- Benjamin H. Mullin
- Jennifer Tickner
- Scott G. Wilson
- Content type: Research
- Open Access
- Published: 26 March 2020
- Article: 80
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DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure
Authors
- Tuan Trieu
- Alexander Martinez-Fundichely
- Ekta Khurana
- Content type: Method
- Open Access
- Published: 26 March 2020
- Article: 79
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A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing
Authors (first, second and last of 13)
- Peng Chen
- Jin Zhou
- Lei Yin
- Content type: Research
- Open Access
- Published: 25 March 2020
- Article: 78
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Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome
Authors (first, second and last of 8)
- Takuro Horii
- Sumiyo Morita
- Izuho Hatada
- Content type: Research
- Open Access
- Published: 01 April 2020
- Article: 77
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High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells
Authors
- Peiyao A. Zhao
- Takayo Sasaki
- David M. Gilbert
- Content type: Research
- Open Access
- Published: 24 March 2020
- Article: 76
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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Authors (first, second and last of 6)
- Zhilian Jia
- Jingwei Li
- Qiang Wu
- Content type: Research
- Open Access
- Published: 23 March 2020
- Article: 75
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Obstacles to detecting isoforms using full-length scRNA-seq data
Authors (first, second and last of 4)
- Jennifer Westoby
- Pavel Artemov
- Anne Ferguson-Smith
- Content type: Research
- Open Access
- Published: 23 March 2020
- Article: 74
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HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Authors (first, second and last of 9)
- Su Wang
- Soohyun Lee
- Peter J. Park
- Content type: Method
- Open Access
- Published: 23 March 2020
- Article: 73
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VALOR2: characterization of large-scale structural variants using linked-reads
Authors (first, second and last of 6)
- Fatih KaraoÄŸlanoÄŸlu
- Camir Ricketts
- Can Alkan
- Content type: Method
- Open Access
- Published: 19 March 2020
- Article: 72
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Benchmarking of computational error-correction methods for next-generation sequencing data
Authors (first, second and last of 26)
- Keith Mitchell
- Jaqueline J. Brito
- Serghei Mangul
- Content type: Research
- Open Access
- Published: 17 March 2020
- Article: 71
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Diverse genetic mechanisms underlie worldwide convergent rice feralization
Authors (first, second and last of 20)
- Jie Qiu
- Lei Jia
- Longjiang Fan
- Content type: Research
- Open Access
- Published: 26 March 2020
- Article: 70
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BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty
Authors
- Simone Tiberi
- Mark D. Robinson
- Content type: Method
- Open Access
- Published: 16 March 2020
- Article: 69
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Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
Authors
- Alexander T. Dilthey
- Sebastian A. Meyer
- Achim J. Kaasch
- Content type: Software
- Open Access
- Published: 14 March 2020
- Article: 68
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Renaissance minds in 21st century science
Authors
- Itai Yanai
- Martin Lercher
- Content type: Editorial
- Open Access
- Published: 13 March 2020
- Article: 67
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Decode-seq: a practical approach to improve differential gene expression analysis
Authors (first, second and last of 8)
- Yingshu Li
- Hang Yang
- Qiang Tu
- Content type: Short Report
- Open Access
- Published: 23 March 2020
- Article: 66
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CHOP: haplotype-aware path indexing in population graphs
Authors (first, second and last of 5)
- Tom Mokveld
- Jasper Linthorst
- Marcel Reinders
- Content type: Method
- Open Access
- Published: 11 March 2020
- Article: 65
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Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium
Authors (first, second and last of 16)
- Juri Kazakevych
- Jérémy Denizot
- Patrick Varga-Weisz
- Content type: Research
- Open Access
- Published: 11 March 2020
- Article: 64
This is part of 1 collection: -
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life
Authors
- Michael Peeri
- Tamir Tuller
- Content type: Research
- Open Access
- Published: 09 March 2020
- Article: 63
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A benchmark of algorithms for the analysis of pooled CRISPR screens
Authors (first, second and last of 5)
- Sunil Bodapati
- Timothy P. Daley
- Lei S. Qi
- Content type: Review
- Open Access
- Published: 09 March 2020
- Article: 62
This is part of 1 collection: -
Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Authors (first, second and last of 8)
- Peipei Li
- Elizabeth Ensink
- Viviane Labrie
- Content type: Research
- Open Access
- Published: 09 March 2020
- Article: 61
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The genome evolution and domestication of tropical fruit mango
Authors (first, second and last of 29)
- Peng Wang
- Yingfeng Luo
- Yeyuan Chen
- Content type: Research
- Open Access
- Published: 06 March 2020
- Article: 60
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Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Authors (first, second and last of 10)
- Xin Liu
- Yong Chen
- Jian Xu
- Content type: Method
- Open Access
- Published: 05 March 2020
- Article: 59
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WhatsGNU: a tool for identifying proteomic novelty
Authors
- Ahmed M. Moustafa
- Paul J. Planet
- Content type: Short Report
- Open Access
- Published: 05 March 2020
- Article: 58
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Decontamination of ambient RNA in single-cell RNA-seq with DecontX
Authors (first, second and last of 7)
- Shiyi Yang
- Sean E. Corbett
- Joshua D. Campbell
- Content type: Method
- Open Access
- Published: 05 March 2020
- Article: 57