Articles

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines

Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathoge...

Authors: Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett and Daniel S. Brewer

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA...

Authors: Brian J. Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet and Aviv Regev

DNA extraction for human microbiome studies: the issue of standardization

Among the laboratory and bioinformatic processing steps for human microbiome studies, a lack of consistency in DNA extraction methodologies is hindering the ability to compare results between studies and somet...

Authors: K. Leigh Greathouse, Rashmi Sinha and Emily Vogtmann

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algor...

Authors: Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu and Lana X. Garmire

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological var...

Authors: Ciara H. O’Flanagan, Kieran R. Campbell, Allen W. Zhang, Farhia Kabeer, Jamie L. P. Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham…

Global impact of somatic structural variation on the DNA methylome of human cancers

Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by...

Authors: Yiqun Zhang, Lixing Yang, Melanie Kucherlapati, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Eunjung Alice Lee, Harshad S. Mahadeshwar, Jiabin Tang, Jianhua Zhang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman…

Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome

Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a resul...

Authors: Wentao Shi, Andrea Massaia, Sandra Louzada, Juliet Handsaker, William Chow, Shane McCarthy, Joanna Collins, Pille Hallast, Kerstin Howe, Deanna M. Church, Fengtang Yang, Yali Xue and Chris Tyler-Smith

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We de...

Authors: Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz and Amos Tanay

Benchmarking comes of age

Authors: Mark D. Robinson and Olga Vitek

Correction to: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations

Following publication of the original article [1], a typographical error in the formula for calculating d_i in the “Scans for local adaptation” subsection in the Method section, was identified. The correct formula...

Authors: Shaohua Fan, Derek E. Kelly, Marcia H. Beltrame, Matthew E. B. Hansen, Swapan Mallick, Alessia Ranciaro, Jibril Hirbo, Simon Thompson, William Beggs, Thomas Nyambo, Sabah A. Omar, Dawit Wolde Meskel, Gurja Belay, Alain Froment, Nick Patterson, David Reich…

Identifying significantly impacted pathways: a comprehensive review and assessment

Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the import...

Authors: Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen and Sorin Draghici

Benchmark of computational methods for predicting microRNA-disease associations

A series of miRNA-disease association prediction methods have been proposed to prioritize potential disease-associated miRNAs. Independent benchmarking of these methods is warranted to assess their effectivene...

Authors: Zhou Huang, Leibo Liu, Yuanxu Gao, Jiangcheng Shi, Qinghua Cui, Jianwei Li and Yuan Zhou

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. ...

Authors: Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh and Rob Knight

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we pr...

Authors: Amanda J. Price, Leonardo Collado-Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger and Andrew E. Jaffe

How to meet your ‘silent partner’: tips for approaching editors at conferences

Authors: Yixin Yao

When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data

Considerable advances in genomics over the past decade have resulted in vast amounts of data being generated and deposited in global archives. The growth of these archives exceeds our ability to process their ...

Authors: Will P. M. Rowe

Quantitative MNase-seq accurately maps nucleosome occupancy levels

Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within ...

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

The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance

Robustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers.

Authors: Wei Song, Roded Sharan and Ivan Ovcharenko

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the dive...

Authors: Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros and Justin Guinney

A comparison of automatic cell identification methods for single-cell RNA sequencing data

Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotati...

Authors: Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders and Ahmed Mahfouz

scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data

Technical variation in feature measurements, such as gene expression and locus accessibility, is a key challenge of large-scale single-cell genomic datasets. We show that this technical variation in both scRNA...

Authors: Ruoxin Li and Gerald Quon

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cl...

Authors: Qian Zhu, Nan Liu, Stuart H. Orkin and Guo-Cheng Yuan

Expanding the scope and scale of microbiome research

Authors: Rob Knight, Ruth E. Ley, Jeroen Raes and Elizabeth A. Grice

TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis

In the analysis of high-throughput data from complex samples, cell composition is an important factor that needs to be accounted for. Except for a limited number of tissues with known pure cell type profiles, ...

Authors: Ziyi Li and Hao Wu

Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency

Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and t...

Authors: Taolan Zhao, Qing Huan, Jing Sun, Chunyan Liu, Xiuli Hou, Xiang Yu, Ian M. Silverman, Yi Zhang, Brian D. Gregory, Chun-Ming Liu, Wenfeng Qian and Xiaofeng Cao

Correction to: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Following publication of the original article [1], it was noticed that the incorrect Fig. 2 and Fig. 3. were processed during production. It was also noticed that Fig. 4a was processed with a superfluous “1e7”...

Authors: Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the ...

Authors: Geoffrey M. Attardo, Adly M. M. Abd-Alla, Alvaro Acosta-Serrano, James E. Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jelle Caers, Guy Caljon, Mikkel B. Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson…

MITRE: inferring features from microbiota time-series data linked to host status

Longitudinal studies are crucial for discovering causal relationships between the microbiome and human disease. We present MITRE, the Microbiome Interpretable Temporal Rule Engine, a supervised machine learnin...

Authors: Elijah Bogart, Richard Creswell and Georg K. Gerber

Cytoscape Automation: empowering workflow-based network analysis

Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limite...

Authors: David Otasek, John H. Morris, Jorge Bouças, Alexander R. Pico and Barry Demchak

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing pat...

Authors: Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock and Nicholas R. Thomson

MPRAnalyze: statistical framework for massively parallel reporter assays

Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified ...

Authors: Tal Ashuach, David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis and Nir Yosef

Correction to: Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Following publication of the original article [1], the authors reported that Additional file 4, “Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses” had t...

Authors: Jordi Moreno-Romero, Gerardo Del Toro-De León, Vikash Kumar Yadav, Juan Santos-González and Claudia Köhler

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night.

Authors: Yun Sung Cho, Je Hoon Jun, Jung A Kim, Hak-Min Kim, Oksung Chung, Seung-Gu Kang, Jin-Young Park, Hwa-Jung Kim, Sunghyun Kim, Hee-Jong Kim, Jin-ho Jang, Ki-Jeong Na, Jeongho Kim, Seung Gu Park, Hwang-Yeol Lee, Andrea Manica…

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the ...

Authors: Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman and William Stafford Noble

Night science

Authors: Itai Yanai and Martin Lercher

The changing landscape of research funding: challenges for mid-career researchers

Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

Authors: Nick Wong

Funding research, a Chinese perspective

Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

Authors: Hui Yang

Of funding and finches

Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

Authors: Verena Jantsch and Michael Jantsch

Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes

Genomic global positioning system (GPS) applies the multilateration technique commonly used in the GPS to genomic data. In the framework we present here, investigators calculate genetic distances from their sa...

Authors: Kunhee Kim, Hyungryul Baik, Chloe Soohyun Jang, Jin Kyung Roh, Eleazer Eskin and Buhm Han

MetaCarvel: linking assembly graph motifs to biological variants

Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven dept...

Authors: Jay Ghurye, Todd Treangen, Marcus Fedarko, W. Judson Hervey IV and Mihai Pop

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease

Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota...

Authors: Nicholas Rhoades, Tasha Barr, Sara Hendrickson, Kamm Prongay, Andrew Haertel, Leanne Gill, Laura Garzel, Katrine Whiteson, Mark Slifka and Ilhem Messaoudi

Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation

CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study re...

Authors: Channabasavaiah B. Gurumurthy, Aidan R. O’Brien, Rolen M. Quadros, John Adams Jr, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K. Batra, Marie-Claude Beauchamp, Kathleen A. Becker, Guillaume Bernas, David Brough, Francisco Carrillo-Salinas, Wesley Chan, Hanying Chen, Ruby Dawson…

Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes

In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-...

Authors: Nilusha Malmuthuge, Guanxiang Liang and Le Luo Guan

Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis

Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circad...

Authors: Qingxin Song, Tien-Yu Huang, Helen H. Yu, Atsumi Ando, Paloma Mas, Misook Ha and Z. Jeffrey Chen

Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies

The combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the ...

Authors: Christos Vlachos, Claire Burny, Marta Pelizzola, Rui Borges, Andreas Futschik, Robert Kofler and Christian Schlötterer

An enhanced genetic model of colorectal cancer progression history

The classical genetic model of colorectal cancer presents APC mutations as the earliest genomic alterations, followed by KRAS and TP53 mutations. However, the timing and relative order of clonal expansion and oth...

Authors: Lixing Yang, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati and Peter J. Park

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable b...

Authors: Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin and Katherine S. Pollard

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data

scRNA-seq dataset integration occurs in different contexts, such as the identification of cell type-specific differences in gene expression across conditions or species, or batch effect correction. We present ...

Authors: Nelson Johansen and Gerald Quon

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1

Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process...

Authors: Daniel E. Martin-Herranz, Erfan Aref-Eshghi, Marc Jan Bonder, Thomas M. Stubbs, Sanaa Choufani, Rosanna Weksberg, Oliver Stegle, Bekim Sadikovic, Wolf Reik and Janet M. Thornton

The bio.tools registry of software tools and data resources for the life sciences

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European...

Authors: Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek…