Volume 23, issue 1, December 2022
271 articles in this issue
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Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes
Authors (first, second and last of 8)
- Eui-Hwan Choi
- Seobin Yoon
- Keun P. Kim
- Content type: Research
- Open Access
- Published: 03 March 2022
- Article: 70
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Enhanced protein isoform characterization through long-read proteogenomics
Authors (first, second and last of 16)
- Rachel M. Miller
- Ben T. Jordan
- Gloria M. Sheynkman
- Content type: Research
- Open Access
- Published: 03 March 2022
- Article: 69
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Towards accurate and reliable resolution of structural variants for clinical diagnosis
Authors (first, second and last of 6)
- Zhichao Liu
- Ruth Roberts
- Weida Tong
- Content type: Review
- Open Access
- Published: 03 March 2022
- Article: 68
This is part of 1 collection: -
TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs
Authors (first, second and last of 4)
- Jakob Hertzberg
- Stefan Mundlos
- Giuseppe Gallone
- Content type: Method
- Open Access
- Published: 01 March 2022
- Article: 67
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Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data
Authors (first, second and last of 10)
- Michael T. France
- Li Fu
- Jacques Ravel
- Content type: Research
- Open Access
- Published: 01 March 2022
- Article: 66
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The chromatin organization of a chlorarachniophyte nucleomorph genome
Authors (first, second and last of 7)
- Georgi K. Marinov
- Xinyi Chen
- William James Greenleaf
- Content type: Research
- Open Access
- Published: 01 March 2022
- Article: 65
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LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin
Authors (first, second and last of 15)
- Kaiwen Bao
- Qi Zhang
- Lei Shi
- Content type: Research
- Open Access
- Published: 28 February 2022
- Article: 64
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HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
Authors
- Yuxuan Du
- Fengzhu Sun
- Content type: Method
- Open Access
- Published: 28 February 2022
- Article: 63
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HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
Authors (first, second and last of 7)
- Haojie Chen
- Shiqi Tu
- Zhen Shao
- Content type: Method
- Open Access
- Published: 28 February 2022
- Article: 62
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Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal
Authors (first, second and last of 7)
- Haya Abbas-Egbariya
- Yael Haberman
- Amnon Amir
- Content type: Research
- Open Access
- Published: 23 February 2022
- Article: 61
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Contamination detection in genomic data: more is not enough
Authors
- Luc Cornet
- Denis Baurain
- Content type: Review
- Open Access
- Published: 21 February 2022
- Article: 60
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The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Authors (first, second and last of 27)
- Tomas Fitzgerald
- Ian Brettell
- Felix Loosli
- Content type: Research
- Open Access
- Published: 21 February 2022
- Article: 59
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Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Authors (first, second and last of 26)
- Adrien Leger
- Ian Brettell
- Tomas Fitzgerald
- Content type: Research
- Open Access
- Published: 21 February 2022
- Article: 58
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viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
Authors (first, second and last of 4)
- Dmitry Antipov
- Mikhail Rayko
- Pavel A. Pevzner
- Content type: Software
- Open Access
- Published: 21 February 2022
- Article: 57
This is part of 1 collection: -
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software
Authors (first, second and last of 8)
- Paul P. Gardner
- James M. Paterson
- Michael A. Black
- Content type: Research
- Open Access
- Published: 16 February 2022
- Article: 56
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Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
Authors (first, second and last of 16)
- Viacheslav Mylka
- Irina Matetovici
- Yvan Saeys
- Content type: Research
- Open Access
- Published: 16 February 2022
- Article: 55
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Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states
Authors (first, second and last of 17)
- Francisco Rodriguez-Algarra
- Robert A. E. Seaborne
- Vardhman K. Rakyan
- Content type: Research
- Open Access
- Published: 14 February 2022
- Article: 54
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Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Authors (first, second and last of 9)
- Shuai Cao
- Longfei Wang
- Z. Jeffrey Chen
- Content type: Research
- Open Access
- Published: 09 February 2022
- Article: 53
This is part of 1 collection: -
Susceptibility to hormone-mediated cancer is reflected by different tick rates of the epithelial and general epigenetic clock
Authors (first, second and last of 15)
- James E. Barrett
- Chiara Herzog
- Martin Widschwendter
- Content type: Research
- Open Access
- Published: 22 February 2022
- Article: 52
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A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants
Authors (first, second and last of 5)
- Shaofang Li
- Lang Liu
- Huanbin Zhou
- Content type: Research
- Open Access
- Published: 09 February 2022
- Article: 51
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An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development
Authors
- Chun-Kai Huang
- Wen-Dar Lin
- Shu-Hsing Wu
- Content type: Research
- Open Access
- Published: 09 February 2022
- Article: 50
This is part of 1 collection: -
Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
Authors (first, second and last of 4)
- Lijia Yu
- Yue Cao
- Pengyi Yang
- Content type: Research
- Open Access
- Published: 08 February 2022
- Article: 49
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Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation
Authors (first, second and last of 7)
- Yangping Li
- Feng Wang
- Bing Yao
- Content type: Research
- Open Access
- Published: 07 February 2022
- Article: 48
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Single-cell isoform analysis in human immune cells
Authors
- Roger Volden
- Christopher Vollmers
- Content type: Method
- Open Access
- Published: 07 February 2022
- Article: 47
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Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism
Authors (first, second and last of 25)
- Yihui Zhu
- J. Antonio Gomez
- Janine M. LaSalle
- Content type: Research
- Open Access
- Published: 16 February 2022
- Article: 46
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Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation
Authors (first, second and last of 11)
- Liuling Pei
- Xianhui Huang
- Maojun Wang
- Content type: Research
- Open Access
- Published: 03 February 2022
- Article: 45
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Comparison of confound adjustment methods in the construction of gene co-expression networks
Authors
- Alanna C. Cote
- Hannah E. Young
- Laura M. Huckins
- Content type: Short Report
- Open Access
- Published: 03 February 2022
- Article: 44
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Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything
Authors
- Tanjina Kader
- Magnus Zethoven
- Kylie L. Gorringe
- Content type: Review
- Open Access
- Published: 02 February 2022
- Article: 43
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MUON: multimodal omics analysis framework
Authors
- Danila Bredikhin
- Ilia Kats
- Oliver Stegle
- Content type: Software
- Open Access
- Published: 01 February 2022
- Article: 42
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Universal prediction of cell-cycle position using transfer learning
Authors (first, second and last of 10)
- Shijie C. Zheng
- Genevieve Stein-O’Brien
- Kasper D. Hansen
- Content type: Research
- Open Access
- Published: 31 January 2022
- Article: 41
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FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering
Authors (first, second and last of 7)
- Chunling Wang
- Junbo Yang
- Guifang Jia
- Content type: Research
- Open Access
- Published: 31 January 2022
- Article: 40
This is part of 1 collection: -
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Authors (first, second and last of 7)
- Giorgos Skoufos
- Fatemeh Almodaresi
- Ioannis S. Vlachos
- Content type: Method
- Open Access
- Published: 31 January 2022
- Article: 39
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VirStrain: a strain identification tool for RNA viruses
Authors
- Herui Liao
- Dehan Cai
- Yanni Sun
- Content type: Method
- Open Access
- Published: 31 January 2022
- Article: 38
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CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
Authors (first, second and last of 4)
- Alexey Kozlov
- Joao M. Alves
- David Posada
- Content type: Method
- Open Access
- Published: 26 January 2022
- Article: 37
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Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M
Authors (first, second and last of 16)
- Zheng Sun
- Shi Huang
- Jian Xu
- Content type: Method
- Open Access
- Published: 26 January 2022
- Article: 36
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Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource
Authors (first, second and last of 16)
- Lisa Dressler
- Michele Bortolomeazzi
- Francesca D. Ciccarelli
- Content type: Research
- Open Access
- Published: 26 January 2022
- Article: 35
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Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution
Authors (first, second and last of 12)
- Jingya Yuan
- Haojie Sun
- Qingxin Song
- Content type: Research
- Open Access
- Published: 24 January 2022
- Article: 34
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IDEAS: individual level differential expression analysis for single-cell RNA-seq data
Authors (first, second and last of 6)
- Mengqi Zhang
- Si Liu
- Wei Sun
- Content type: Method
- Open Access
- Published: 24 January 2022
- Article: 33
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
Authors (first, second and last of 15)
- Reza Nasirigerdeh
- Reihaneh Torkzadehmahani
- Jan Baumbach
- Content type: Method
- Open Access
- Published: 24 January 2022
- Article: 32
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Statistics or biology: the zero-inflation controversy about scRNA-seq data
Authors (first, second and last of 4)
- Ruochen Jiang
- Tianyi Sun
- Jingyi Jessica Li
- Content type: Review
- Open Access
- Published: 21 January 2022
- Article: 31
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Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
Authors (first, second and last of 4)
- Li Tang
- Matthew C. Hill
- Min Li
- Content type: Method
- Open Access
- Published: 21 January 2022
- Article: 30
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Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
Authors
- Xiao Luo
- Xiongbin Kang
- Alexander Schönhuth
- Content type: Method
- Open Access
- Published: 20 January 2022
- Article: 29
This is part of 1 collection: -
Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration
Authors (first, second and last of 13)
- Yu-Chan Zhang
- Yan-Fei Zhou
- Yue-Qin Chen
- Content type: Research
- Open Access
- Published: 19 January 2022
- Article: 28
This is part of 1 collection: -
Comparison and evaluation of statistical error models for scRNA-seq
Authors
- Saket Choudhary
- Rahul Satija
- Content type: Research
- Open Access
- Published: 18 January 2022
- Article: 27
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Blood-based epigenome-wide analyses of cognitive abilities
Authors (first, second and last of 24)
- Daniel L. McCartney
- Robert F. Hillary
- Riccardo E. Marioni
- Content type: Research
- Open Access
- Published: 17 January 2022
- Article: 26
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DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA
Authors (first, second and last of 7)
- Hang Qin
- Liang Ou
- Xuan Li
- Content type: Method
- Open Access
- Published: 17 January 2022
- Article: 25
This is part of 1 collection: -
Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression
Authors (first, second and last of 12)
- Thomas H. Jonkman
- Koen F. Dekkers
- Bastiaan T. Heijmans
- Content type: Research
- Open Access
- Published: 14 January 2022
- Article: 24
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Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries
Authors (first, second and last of 7)
- Yanyu Liang
- Milton Pividori
- Hae Kyung Im
- Content type: Research
- Open Access
- Published: 13 January 2022
- Article: 23
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An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim
Authors (first, second and last of 10)
- Meriam Guellil
- Marcel Keller
- Christiana L. Scheib
- Content type: Research
- Open Access
- Published: 03 February 2022
- Article: 22