Articles

Precise genome-wide mapping of single nucleosomes and linkers in vivo

We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our ...

Authors: Răzvan V. Chereji, Srinivas Ramachandran, Terri D. Bryson and Steven Henikoff

Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys

Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large ...

Authors: Yuanyuan Li, Hui Zheng, Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang and Wei Xie

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching ap...

Authors: Heewook Lee and Carl Kingsford

Correction to: A statistical framework for analyzing deep mutational scanning data

After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an ove...

Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale

Accurately selecting relevant alleles in large sequencing experiments remains technically challenging. Bystro (https://​bystro.​io/​) is the first online, cloud...

Authors: Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler and Thomas S. Wingo

SCANPY: large-scale single-cell gene expression data analysis

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing,...

Authors: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challe...

Authors: Gerben Menschaert, Xiaojing Wang, Andrew R. Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W. Deutsch, Tobias Ternent and Juan Antonio Vizcaíno

Focus on African diversity confirms complexity of skin pigmentation genetics

Renewed focus on African populations confirms the complexity of skin pigmentation genetics, and suggests future directions for pigmentation research.

Authors: Tina Lasisi and Mark D. Shriver

A panoramic view of RNA modifications: exploring new frontiers

Meeting report on the Cold Spring Harbor Asia conference on RNA Modifications and Epitranscriptomics, held in Suzhou, China, 13–17 November, 2017.

Authors: Zijun Zhang, Eddie Park, Lan Lin and Yi Xing

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protec...

Authors: Enrique Martin-Gayo, Michael B. Cole, Kellie E. Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W. Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D. Walker, Nir Yosef, Alex K. Shalek and Xu G. Yu

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha

In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur d...

Authors: Marc W. Schmid, Alejandro Giraldo-Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L. Bowman and Ueli Grossniklaus

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

The 3′ untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produce...

Authors: Sean M. West, Desirea Mecenas, Michelle Gutwein, David Aristizábal-Corrales, Fabio Piano and Kristin C. Gunsalus

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli throu...

Authors: Yufeng Qin, John D. Roberts, Sara A. Grimm, Fred B. Lih, Leesa J. Deterding, Ruifang Li, Kaliopi Chrysovergis and Paul A. Wade

SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells

Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential fo...

Authors: Özgen Deniz, Lorenzo de la Rica, Kevin C. L. Cheng, Dominik Spensberger and Miguel R. Branco

FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate ...

Authors: Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue and Chris Tyler-Smith

Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations

About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncate...

Authors: Lulu Huang, Audrey Low, Sagar S. Damle, Melissa M. Keenan, Steven Kuntz, Susan F. Murray, Brett P. Monia and Shuling Guo

Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells

Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mammalian epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well chara...

Authors: Arsham Ghahramani, Giacomo Donati, Nicholas M. Luscombe and Fiona M. Watt

Epigenetic supersimilarity of monozygotic twin pairs

Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to...

Authors: Timothy E. Van Baak, Cristian Coarfa, Pierre-Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Yun Gong…

RNA virus interference via CRISPR/Cas13a system in plants

CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleav...

Authors: Rashid Aman, Zahir Ali, Haroon Butt, Ahmed Mahas, Fatimah Aljedaani, Muhammad Zuhaib Khan, Shouwei Ding and Magdy Mahfouz

DotAligner: identification and clustering of RNA structure motifs

The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable natu...

Authors: Martin A. Smith, Stefan E. Seemann, Xiu Cheng Quek and John S. Mattick

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the...

Authors: Sabrina Krakau, Hugues Richard and Annalisa Marsico

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhanc...

Authors: Robert S. Young, Yatendra Kumar, Wendy A. Bickmore and Martin S. Taylor

Intergenic disease-associated regions are abundant in novel transcripts

Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS...

Authors: N. Bartonicek, M. B. Clark, X. C. Quek, J. R. Torpy, A. L. Pritchard, J. L. V. Maag, B. S. Gloss, J. Crawford, R. J. Taft, N. K. Hayward, G. W. Montgomery, J. S. Mattick, T. R. Mercer and M. E. Dinger

Adaptation of Arabidopsis thaliana to the Yangtze River basin

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...

Authors: Yu-Pan Zou, Xing-Hui Hou, Qiong Wu, Jia-Fu Chen, Zi-Wen Li, Ting-Shen Han, Xiao-Min Niu, Li Yang, Yong-Chao Xu, Jie Zhang, Fu-Min Zhang, Dunyan Tan, Zhixi Tian, Hongya Gu and Ya-Long Guo

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with ...

Authors: Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes and Daniel Gautheret

From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence

Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts...

Authors: Athina Vidaki and Manfred Kayser

Single-cell RNA-seq study determines the ontogeny of macrophages in glioblastomas

A large-scale single-cell RNA-seq analysis of tumor-associated macrophages in gliomas has unveiled a new aspect of the complex tumor microenvironment and new biomarkers.

Authors: Chenghang (Chuck) Zong

Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylatio...

Authors: Yuting Chen, Martin Widschwendter and Andrew E. Teschendorff

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex

Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and n...

Authors: Lorena Verduci, Maria Ferraiuolo, Andrea Sacconi, Federica Ganci, Jlenia Vitale, Teresa Colombo, Paola Paci, Sabrina Strano, Giuseppe Macino, Nikolaus Rajewsky and Giovanni Blandino

Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment

Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt th...

Authors: Sören Müller, Gary Kohanbash, S. John Liu, Beatriz Alvarado, Diego Carrera, Aparna Bhaduri, Payal B. Watchmaker, Garima Yagnik, Elizabeth Di Lullo, Martina Malatesta, Nduka M. Amankulor, Arnold R. Kriegstein, Daniel A. Lim, Manish Aghi, Hideho Okada and Aaron Diaz

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline,...

Authors: Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert and David Hot

Stranger in a strange land: the experiences of immigrant researchers

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

Authors: Sophien Kamoun, Rosa Lozano-Durán and Luay Nakhleh

Balancing selection and trans-specific polymorphisms

Balancing selection maintains variation for evolution. A recent study investigated the extent of balancing selection in two Brassicaceae species and highlighted its importance for adaptation.

Authors: Baosheng Wang and Thomas Mitchell-Olds

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, a...

Authors: Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu…

Experimental design and quantitative analysis of microbial community multiomics

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the res...

Authors: Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan and Curtis Huttenhower

Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species

Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3′-sequencing data in this species precludes comprehensive ...

Authors: Piero Sanfilippo, Jiayu Wen and Eric C. Lai

RNAs: dynamic and mutable

Authors: Mihaela Zavolan and Brenton R. Graveley

The 3′ end of the story: deciphering combinatorial interactions that control mRNA fate

A new study investigates how microRNAs affect the binding of proteins to RNA.

Authors: Jeremy R. Sanford and Luiz O. F. Penalva

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

The American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpre...

Authors: Rajarshi Ghosh, Ninad Oak and Sharon E. Plon

CRISPR/Cas9-mediated targeted chromosome elimination

The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an en...

Authors: Erwei Zuo, Xiaona Huo, Xuan Yao, Xinde Hu, Yidi Sun, Jianhang Yin, Bingbing He, Xing Wang, Linyu Shi, Jie Ping, Yu Wei, Wenqin Ying, Wei Wei, Wenjia Liu, Cheng Tang, Yixue Li…

Computational biologists: moving to the driver's seat

The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by ...

Authors: Itai Yanai and Eva Chmielnicki

Functional assessment of human enhancer activities using whole-genome STARR-sequencing

Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, be...

Authors: Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya Brunetti, Heather Eckart and Kevin P. White

Forebrain-specific, conditional silencing of Staufen2 alters synaptic plasticity, learning, and memory in rats

Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution...

Authors: Stefan M. Berger, Iván Fernández-Lamo, Kai Schönig, Sandra M. Fernández Moya, Janina Ehses, Rico Schieweck, Stefano Clementi, Thomas Enkel, Sascha Grothe, Oliver von Bohlen und Halbach, Inmaculada Segura, José María Delgado-García, Agnès Gruart, Michael A. Kiebler and Dusan Bartsch

Intron retention enhances gene regulatory complexity in vertebrates

While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of ...

Authors: Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J. Lieschke, Justin J-L Wong and John E. J. Rasko

Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives

In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...

Authors: Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu and Ya-Long Guo

xCell: digitally portraying the tissue cellular heterogeneity landscape

Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for ...

Authors: Dvir Aran, Zicheng Hu and Atul J. Butte

Rescue of high-specificity Cas9 variants using sgRNAs with matched 5’ nucleotides

We report that engineered Cas9 variants with improved specificity—eCas9-1.1 and Cas9-HF1—are often poorly active in human cells, when complexed with single guide RNAs (sgRNAs) with a mismatch at the 5’ terminu...

Authors: Sojung Kim, Taegeun Bae, Jaewoong Hwang and Jin-Soo Kim

Early career researchers want Open Science

Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it i...

Authors: Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann…

The interplay of demography and selection during maize domestication and expansion

The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...

Authors: Li Wang, Timothy M. Beissinger, Anne Lorant, Claudia Ross-Ibarra, Jeffrey Ross-Ibarra and Matthew B. Hufford

Correction to: Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.

Authors: Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…