Articles

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of...

Authors: Yonghao Sun, Liang Dong, Ying Zhang, Da Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li and Fang Yang

Dynamic rewiring of the human interactome by interferon signaling

The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulate...

Authors: Craig H. Kerr, Michael A. Skinnider, Daniel D. T. Andrews, Angel M. Madero, Queenie W. T. Chan, R. Greg Stacey, Nikolay Stoynov, Eric Jan and Leonard J. Foster

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of da...

Authors: Fan Chen and Sündüz Keleş

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely rema...

Authors: Sharadha Sakthikumar, Ananya Roy, Lulu Haseeb, Mats E. Pettersson, Elisabeth Sundström, Voichita D. Marinescu, Kerstin Lindblad-Toh and Karin Forsberg-Nilsson

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been...

Authors: Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun D. Huang, Adrian Tett, Serena Manara, Federica Armanini, Debbie Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Valles-Colomer, Roberta Raffaetà, Omar Rota-Stabelli, Maria Carmen Collado…

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods...

Authors: Zijian Ni, Shuyang Chen, Jared Brown and Christina Kendziorski

Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen

CRISPR-based genome perturbation provides a new avenue to conveniently change DNA sequences, transcription, and epigenetic modifications in genetic screens. However, it remains challenging to assay the complex...

Authors: Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Yingzheng Liu, Zhenxing Yu, Yinyao Qi, Zhike Lu and Lijia Ma

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic vari...

Authors: Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser and Thomas Quertermous

MAUDE: inferring expression changes in sorting-based CRISPR screens

Improved methods are needed to model CRISPR screen data for interrogation of genetic elements that alter reporter gene expression readout. We create MAUDE (Mean Alterations Using Discrete Expression) for quant...

Authors: Carl G. de Boer, John P. Ray, Nir Hacohen and Aviv Regev

Author Correction: Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

An amendment to this paper has been published and can be accessed via the original article.

Authors: Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos and Jane A. Skok

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae

The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyc...

Authors: Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh…

The promise and challenge of cancer microbiome research

Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodo...

Authors: Sumeed Syed Manzoor, Annemiek Doedens and Michael B. Burns

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample ...

Authors: Elena Denisenko, Belinda B. Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, Olivier Clément, Rebecca K. Simmons, Ryan Lister and Alistair R. R. Forrest

Assembly and annotation of an Ashkenazi human reference genome

Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very sm...

Authors: Alaina Shumate, Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin M. Wagner, Nathan D. Olson, Mihaela Pertea, Marc L. Salit, Justin M. Zook and Steven L. Salzberg

Developmental regulation of canonical and small ORF translation from mRNAs

Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation ...

Authors: Pedro Patraquim, Muhammad Ali Shahzad Mumtaz, José Ignacio Pueyo, Julie Louise Aspden and Juan-Pablo Couso

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate r...

Authors: Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael C. Rusch, John Easton, Jing Ma, Eric Davis, Austyn Trull, J. Robert Michael, Karol Szlachta…

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucle...

Authors: Magali Hennion, Jean-Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stefan Engelen, Arnaud Lemainque, Benjamin Audit and Olivier Hyrien

Personalized and graph genomes reveal missing signal in epigenomic data

Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human ge...

Authors: Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen and Guillaume Bourque

Accounting for cell type hierarchy in evaluating single cell RNA-seq clustering

Cell clustering is one of the most common routines in single cell RNA-seq data analyses, for which a number of specialized methods are available. The evaluation of these methods ignores an important biological...

Authors: Zhijin Wu and Hao Wu

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microb...

Authors: Meagan A. Rubel, Arwa Abbas, Louis J. Taylor, Andrew Connell, Ceylan Tanes, Kyle Bittinger, Valantine N. Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman and Sarah A. Tishkoff

Gapless assembly of maize chromosomes using long-read technologies

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize...

Authors: Jianing Liu, Arun S. Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Victor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David A. Kudrna, Magdy Alabady, Candice N. Hirsch, Kevin A. Fengler, Doreen Ware, Todd P. Michael…

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structu...

Authors: Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu, Qiangfeng Cliff Zhang and Yun-Gui Yang

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isofor...

Authors: Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy R. B. Newman, Shunichi Kosugi, Lauren M. McIntyre, Victoria Moreno-Manzano and Ana Conesa

Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance

A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a g...

Authors: Isaac Kremsky and Victor G. Corces

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks

Non-canonical residues, caps, crosslinks, and nicks are important to many functions of DNAs, RNAs, proteins, and complexes. However, we do not fully understand how networks of such non-canonical macromolecules...

Authors: Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale and Jonathan R. Karr

APEC: an accesson-based method for single-cell chromatin accessibility analysis

The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a...

Authors: Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin and Kun Qu

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

Genomic analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences. Here, we describe Conterminator, an efficient method to detect and remove incorrectly labe...

Authors: Martin Steinegger and Steven L. Salzberg

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in...

Authors: Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornes, Daria D. Nikolaeva, Benoit Ballester, Jan Grau, Ivo Grosse, Vsevolod Makeev, Ivan Kulakovskiy and Philipp Bucher

Effects of the COVID-19 pandemic on life scientists

Authors: Jan O. Korbel and Oliver Stegle

Sampling time-dependent artifacts in single-cell genomics studies

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample ...

Authors: Ramon Massoni-Badosa, Giovanni Iacono, Catia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodriguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elias Campo, Antonio Julià, José Ignacio Martín-Subero and Holger Heyn

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computati...

Authors: Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni and Oliver Stegle

Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia

Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis ...

Authors: Ping Wang, Zhonghui Tang, Byoungkoo Lee, Jacqueline Jufen Zhu, Liuyang Cai, Przemyslaw Szalaj, Simon Zhongyuan Tian, Meizhen Zheng, Dariusz Plewczynski, Xiaoan Ruan, Edison T. Liu, Chia-Lin Wei and Yijun Ruan

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

Unsupervised compression algorithms applied to gene expression data extract latent or hidden signals representing technical and biological sources of variation. However, these algorithms require a user to sele...

Authors: Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein and Casey S. Greene

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only present in the testis. However, it is...

Authors: Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos and Jane A. Skok

A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk

Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions betwee...

Authors: Andrew J. Gentles, Angela Bik-Yu Hui, Weiguo Feng, Armon Azizi, Ramesh V. Nair, Gina Bouchard, David A. Knowles, Alice Yu, Youngtae Jeong, Alborz Bejnood, Erna Forgó, Sushama Varma, Yue Xu, Amanda Kuong, Viswam S. Nair, Rob West…

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacteri...

Authors: Oguzhan Begik, Morghan C. Lucas, Huanle Liu, Jose Miguel Ramirez, John S. Mattick and Eva Maria Novoa

Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-specific effects of drug treatment in complex tissues. This application requires high levels of precision, robustness, and quantit...

Authors: Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock and Stefan Kubicek

What are innovations in peer review and editorial assessment for?

Authors: Willem Halffman and Serge P.J.M Horbach

Open access, open data and peer review

Authors: Jernej Ule

In memory of James Taylor: the birth of Galaxy

Authors: Anton Nekrutenko and Michael C. Schatz

Wheat chromatin architecture is organized in genome territories and transcription factories

Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major fa...

Authors: Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Severine Domenichini, Natalia Y. Rodriguez Granados, Soonkap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza-Mianza, Caroline Juery, Etienne Paux, Graham Moore…

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to...

Authors: Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell and Edward C. Holmes

ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in short-read sequ...

Authors: Egor Dolzhenko, Mark F. Bennett, Phillip A. Richmond, Brett Trost, Sai Chen, Joke J. F. A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew M. Gross, Bryan R. Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David R. Bentley…

CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes

Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integ...

Authors: Wanying Wu, Peifeng Ji and Fangqing Zhao

REPIC: a database for exploring the N⁶-methyladenosine methylome

The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m⁶A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples...

Authors: Shun Liu, Allen Zhu, Chuan He and Mengjie Chen

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection

Influenza is a severe respiratory illness that continually threatens global health. It has been widely known that gut microbiota modulates the host response to protect against influenza infection, but mechanis...

Authors: Qiang Zhang, Jin Hu, Jia-Wu Feng, Xiao-Tong Hu, Ting Wang, Wen-Xiao Gong, Kun Huang, Yi-Xiong Guo, Zhong Zou, Xian Lin, Run Zhou, Yu-Qi Yuan, An-Ding Zhang, Hong Wei, Gang Cao, Chen Liu…

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery

Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries ...

Authors: Johannes Köster, Louis J. Dijkstra, Tobias Marschall and Alexander Schönhuth

Open data in a deeply connected world

Authors: Barbara Cheifet

Hi-D: nanoscale mapping of nuclear dynamics in single living cells

Bulk chromatin motion has not been analyzed at high resolution. We present Hi-D, a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entir...

Authors: Haitham A. Shaban, Roman Barth, Ludmila Recoules and Kerstin Bystricky

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data

Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive...

Authors: Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen and Kai Tan