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  1. Content type: Method

    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

    Citation: Genome Biology 2019 20:211

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  2. Content type: Research

    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…

    Citation: Genome Biology 2019 20:210

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  3. Content type: Research

    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…

    Citation: Genome Biology 2019 20:209

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  4. Content type: Research

    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

    Citation: Genome Biology 2019 20:207

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  5. Content type: Method

    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

    Citation: Genome Biology 2019 20:206

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  6. Content type: Correction

    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...

    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…

    Citation: Genome Biology 2019 20:204

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    The original article was published in Genome Biology 2019 20:82

  7. Content type: Research

    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

    Citation: Genome Biology 2019 20:202

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  8. Content type: Research

    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

    Citation: Genome Biology 2019 20:201

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  9. Content type: Research

    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

    Citation: Genome Biology 2019 20:196

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  10. Content type: Method

    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

    Citation: Genome Biology 2019 20:198

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  11. Content type: Open Letter

    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

    Citation: Genome Biology 2019 20:195

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  12. Content type: Research

    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

    Citation: Genome Biology 2019 20:194

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  13. Content type: Research

    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

    Citation: Genome Biology 2019 20:189

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  14. Content type: Correction

    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

    Citation: Genome Biology 2019 20:188

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    The original article was published in Genome Biology 2019 20:148

  15. Content type: Research

    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…

    Citation: Genome Biology 2019 20:187

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  16. Content type: Software

    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

    Citation: Genome Biology 2019 20:185

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  17. Content type: Research

    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

    Citation: Genome Biology 2019 20:184

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  18. Content type: Method

    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

    Citation: Genome Biology 2019 20:183

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  19. Content type: Correction

    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

    Citation: Genome Biology 2019 20:182

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    The original article was published in Genome Biology 2019 20:41

  20. Content type: Research

    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…

    Citation: Genome Biology 2019 20:181

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  21. Content type: Database

    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

    Citation: Genome Biology 2019 20:180

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  22. Content type: Editorial

    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

    Citation: Genome Biology 2019 20:178

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    The Editorial to this article has been published in Genome Biology 2019 20:177

    The Editorial to this article has been published in Genome Biology 2019 20:176

  23. Content type: Editorial

    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

    Citation: Genome Biology 2019 20:177

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    The Editorial to this article has been published in Genome Biology 2019 20:176

    The Editorial to this article has been published in Genome Biology 2019 20:178

  24. Content type: Editorial

    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

    Citation: Genome Biology 2019 20:176

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    The Editorial to this article has been published in Genome Biology 2019 20:178

    The Editorial to this article has been published in Genome Biology 2019 20:177

  25. Content type: Short Report

    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

    Citation: Genome Biology 2019 20:175

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  26. Content type: Method

    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

    Citation: Genome Biology 2019 20:174

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  27. Content type: Research

    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

    Citation: Genome Biology 2019 20:173

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  28. Content type: Research

    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…

    Citation: Genome Biology 2019 20:171

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  29. Content type: Research

    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

    Citation: Genome Biology 2019 20:170

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  30. Content type: Research

    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

    Citation: Genome Biology 2019 20:169

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  31. Content type: Research

    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

    Citation: Genome Biology 2019 20:168

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  32. Content type: Method

    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

    Citation: Genome Biology 2019 20:167

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  33. Content type: Research

    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

    Citation: Genome Biology 2019 20:146

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  34. Content type: Method

    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....

    Authors: Tongxin Wang, Travis S. Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang and Kun Huang

    Citation: Genome Biology 2019 20:165

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  35. Content type: Open Letter

    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…

    Citation: Genome Biology 2019 20:164

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  36. Content type: Research

    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...

    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

    Citation: Genome Biology 2019 20:163

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  37. Content type: Correction

    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:

    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

    Citation: Genome Biology 2019 20:161

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    The original article was published in Genome Biology 2019 20:126