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... (Source: Genome Biology)
Source: Genome Biology - October 17, 2019 Category: Genetics & Stem Cells 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 & Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - October 15, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - October 14, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - October 11, 2019 Category: Genetics & Stem Cells Authors: Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz and Amos Tanay Tags: Method Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - October 9, 2019 Category: Genetics & Stem Cells Authors: Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen and Sorin Draghici Tags: Research Source Type: research

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 di in the “Scans for local adaptation” subsection in the Method section, was identified. The correct formula... (Source: Genome Biology)
Source: Genome Biology - October 9, 2019 Category: Genetics & Stem Cells 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 Tags: Correction Source Type: research

Benchmarking comes of age
(Source: Genome Biology)
Source: Genome Biology - October 9, 2019 Category: Genetics & Stem Cells Authors: Mark D. Robinson and Olga Vitek Tags: Editorial Source Type: research

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. ... (Source: Genome Biology)
Source: Genome Biology - October 8, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - October 8, 2019 Category: Genetics & Stem Cells Authors: Zhou Huang, Leibo Liu, Yuanxu Gao, Jiangcheng Shi, Qinghua Cui, Jianwei Li and Yuan Zhou Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 26, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

How to meet your ‘silent partner’: tips for approaching editors at conferences
(Source: Genome Biology)
Source: Genome Biology - September 17, 2019 Category: Genetics & Stem Cells Authors: Yixin Yao Tags: Editorial Source Type: research

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 ... (Source: Genome Biology)
Source: Genome Biology - September 13, 2019 Category: Genetics & Stem Cells Authors: R ăzvan V. Chereji, Terri D. Bryson and Steven Henikoff Tags: Method Source Type: research

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 ... (Source: Genome Biology)
Source: Genome Biology - September 13, 2019 Category: Genetics & Stem Cells Authors: Will P. M. Rowe Tags: Review Source Type: research

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. (Source: Genome Biology)
Source: Genome Biology - September 12, 2019 Category: Genetics & Stem Cells Authors: Wei Song, Roded Sharan and Ivan Ovcharenko Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 10, 2019 Category: Genetics & Stem Cells 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 Tags: Open Letter Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 9, 2019 Category: Genetics & Stem Cells Authors: Qian Zhu, Nan Liu, Stuart H. Orkin and Guo-Cheng Yuan Tags: Software Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 9, 2019 Category: Genetics & Stem Cells Authors: Ruoxin Li and Gerald Quon Tags: Method Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 9, 2019 Category: Genetics & Stem Cells Authors: Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders and Ahmed Mahfouz Tags: Research Source Type: research

Expanding the scope and scale of microbiome research
(Source: Genome Biology)
Source: Genome Biology - September 5, 2019 Category: Genetics & Stem Cells Authors: Rob Knight, Ruth E. Ley, Jeroen Raes and Elizabeth A. Grice Tags: Editorial Source Type: research

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, ... (Source: Genome Biology)
Source: Genome Biology - September 4, 2019 Category: Genetics & Stem Cells Authors: Ziyi Li and Hao Wu Tags: Method Source Type: research

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”... (Source: Genome Biology)
Source: Genome Biology - September 3, 2019 Category: Genetics & Stem Cells Authors: Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski Tags: Correction Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 3, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 2, 2019 Category: Genetics & Stem Cells Authors: Jordi Moreno-Romero, Gerardo Del Toro-De Le ón, Vikash Kumar Yadav, Juan Santos-González and Claudia Köhler Tags: Correction Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 2, 2019 Category: Genetics & Stem Cells 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. Est ée Török, Sharon Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - September 2, 2019 Category: Genetics & Stem Cells Authors: David Otasek, John H. Morris, Jorge Bou ças, Alexander R. Pico and Barry Demchak Tags: Software Source Type: research

MITRE: inferring features from microbiota time-series data linked to host status
We present MITRE, the Microbiome Interpretable Temporal Rule Engine, a supervised machine learnin... (Source: Genome Biology)
Source: Genome Biology - September 2, 2019 Category: Genetics & Stem Cells Authors: Elijah Bogart, Richard Creswell and Georg K. Gerber Tags: Method Source Type: research

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 ... (Source: Genome Biology)
Source: Genome Biology - September 2, 2019 Category: Genetics & Stem Cells 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, Aur élie Hua-Van, Emily C. Jennings, D Tags: Research Source Type: research

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. (Source: Genome Biology)
Source: Genome Biology - August 29, 2019 Category: Genetics & Stem Cells 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 & hellip; Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 28, 2019 Category: Genetics & Stem Cells Authors: Verena Jantsch and Michael Jantsch Tags: Editorial Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 28, 2019 Category: Genetics & Stem Cells Authors: Hui Yang Tags: Editorial Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 28, 2019 Category: Genetics & Stem Cells Authors: Nick Wong Tags: Editorial Source Type: research

Night science
(Source: Genome Biology)
Source: Genome Biology - August 28, 2019 Category: Genetics & Stem Cells Authors: Itai Yanai and Martin Lercher Tags: Editorial Source Type: research

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 ... (Source: Genome Biology)
Source: Genome Biology - August 28, 2019 Category: Genetics & Stem Cells Authors: Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman and William Stafford Noble Tags: Database Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 27, 2019 Category: Genetics & Stem Cells Authors: Kunhee Kim, Hyungryul Baik, Chloe Soohyun Jang, Jin Kyung Roh, Eleazer Eskin and Buhm Han Tags: Short Report Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 26, 2019 Category: Genetics & Stem Cells 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, Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 26, 2019 Category: Genetics & Stem Cells Authors: Nicholas Rhoades, Tasha Barr, Sara Hendrickson, Kamm Prongay, Andrew Haertel, Leanne Gill, Laura Garzel, Katrine Whiteson, Mark Slifka and Ilhem Messaoudi Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 26, 2019 Category: Genetics & Stem Cells Authors: Jay Ghurye, Todd Treangen, Marcus Fedarko, W. Judson Hervey IV and Mihai Pop Tags: Method Source Type: research

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-... (Source: Genome Biology)
Source: Genome Biology - August 23, 2019 Category: Genetics & Stem Cells Authors: Nilusha Malmuthuge, Guanxiang Liang and Le Luo Guan Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 20, 2019 Category: Genetics & Stem Cells Authors: Qingxin Song, Tien-Yu Huang, Helen H. Yu, Atsumi Ando, Paloma Mas, Misook Ha and Z. Jeffrey Chen Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 15, 2019 Category: Genetics & Stem Cells Authors: Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin and Katherine S. Pollard Tags: Method Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 15, 2019 Category: Genetics & Stem Cells Authors: Lixing Yang, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati and Peter J. Park Tags: Research Source Type: research

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 ... (Source: Genome Biology)
Source: Genome Biology - August 15, 2019 Category: Genetics & Stem Cells Authors: Christos Vlachos, Claire Burny, Marta Pelizzola, Rui Borges, Andreas Futschik, Robert Kofler and Christian Schl ötterer Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 14, 2019 Category: Genetics & Stem Cells 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 Tags: Research Source Type: research

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
We present ... (Source: Genome Biology)
Source: Genome Biology - August 14, 2019 Category: Genetics & Stem Cells Authors: Nelson Johansen and Gerald Quon Tags: Method Source Type: research

Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters
Like many bacteria, Vibrio cholerae deploys a harpoon-like type VI secretion system (T6SS) to compete against other microbes in environmental and host settings. The T6SS punctures adjacent cells and delivers toxi... (Source: Genome Biology)
Source: Genome Biology - August 12, 2019 Category: Genetics & Stem Cells Authors: Cristian V. Crisan, Aroon T. Chande, Kenneth Williams, Vishnu Raghuram, Lavanya Rishishwar, Gabi Steinbach, Samit S. Watve, Peter Yunker, I. King Jordan and Brian K. Hammer Tags: Research Source Type: research

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... (Source: Genome Biology)
Source: Genome Biology - August 12, 2019 Category: Genetics & Stem Cells Authors: Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Herv é Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondr Tags: Open Letter Source Type: research

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments.... (Source: Genome Biology)
Source: Genome Biology - August 12, 2019 Category: Genetics & Stem Cells Authors: Tongxin Wang, Travis S. Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang and Kun Huang Tags: Method Source Type: research

Is it time to change the reference genome?
The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, prop... (Source: Genome Biology)
Source: Genome Biology - August 9, 2019 Category: Genetics & Stem Cells Authors: Sara Ballouz, Alexander Dobin and Jesse A. Gillis Tags: Opinion Source Type: research

Correction to: Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm
Following publication of the original article [1], the following error was reported: The actin control panel in Fig. 3 of this paper is reproduced from Fig. 7 of Tour é et al, 2004 [2] by kind permission of the... (Source: Genome Biology)
Source: Genome Biology - August 9, 2019 Category: Genetics & Stem Cells Authors: Aminata Tour é, Emily J. Clemente, Peter J. I. Ellis, Shantha K. Mahadevaiah, Obah A. Ojarikre, Penny A. F. Ball, Louise Reynard, Kate L. Loveland, Paul S. Burgoyne and Nabeel A. Affara Tags: Correction Source Type: research

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Following publication of the original article [1], the authors reported that the Availability of data and materials section required updating. The updated text reads as follows: (Source: Genome Biology)
Source: Genome Biology - August 9, 2019 Category: Genetics & Stem Cells Authors: Baosheng Wang, Julius P. Mojica, Nadeesha Perera, Cheng-Ruei Lee, John T. Lovell, Aditi Sharma, Catherine Adam, Anna Lipzen, Kerrie Barry, Daniel S. Rokhsar, Jeremy Schmutz and Thomas Mitchell-Olds Tags: Correction Source Type: research