Skip to main content

Articles

Page 1 of 142

  1. Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow f...

    Authors: Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin and Nathan C. Sheffield

    Citation: Genome Biology 2021 22:155

    Content type: Software

    Published on:

  2. The majority of pancreatic ductal adenocarcinomas (PDAC) are diagnosed at the metastatic stage, and standard therapies have limited activity with a dismal 5-year survival rate of only 8%. The liver and lung ar...

    Authors: Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas II, Soren Charmsaz, Nicole Gross, Skylar Woolman, Kayla Cruz, Rebecca M. Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan…

    Citation: Genome Biology 2021 22:154

    Content type: Research

    Published on:

  3. Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods,” but the veracity of such statements is questionable. Our manuscript discusses and ...

    Authors: Stefan Buchka, Alexander Hapfelmeier, Paul P. Gardner, Rory Wilson and Anne-Laure Boulesteix

    Citation: Genome Biology 2021 22:152

    Content type: Short Report

    Published on:

  4. The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely ...

    Authors: Naresh Loudya, Priyanka Mishra, Kotaro Takahagi, Yukiko Uehara-Yamaguchi, Komaki Inoue, Laszlo Bogre, Keiichi Mochida and Enrique López-Juez

    Citation: Genome Biology 2021 22:151

    Content type: Research

    Published on:

  5. The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chrom...

    Authors: Xian Hao, Jyotsana J. Parmar, Benoît Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber and Christophe Zimmer

    Citation: Genome Biology 2021 22:150

    Content type: Research

    Published on:

  6. Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there ...

    Authors: Chia-Chi Flora Huang, Shreyas Lingadahalli, Tunc Morova, Dogancan Ozturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altintas, Mohammadali Saffarzadeh, Stephane Le Bihan, Brian McConeghy, Bengul Gokbayrak…

    Citation: Genome Biology 2021 22:149

    Content type: Research

    Published on:

  7. In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we prese...

    Authors: Yingjie Xiao, Shuqin Jiang, Qian Cheng, Xiaqing Wang, Jun Yan, Ruyang Zhang, Feng Qiao, Chuang Ma, Jingyun Luo, Wenqiang Li, Haijun Liu, Wenyu Yang, Wenhao Song, Yijiang Meng, Marilyn L. Warburton, Jiuran Zhao…

    Citation: Genome Biology 2021 22:148

    Content type: Research

    Published on:

  8. Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal hu...

    Authors: Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner and Seth W. Cheetham

    Citation: Genome Biology 2021 22:146

    Content type: Short Report

    Published on:

  9. Cellular senescence is a permanent state of replicative arrest defined by a specific pattern of gene expression. The epigenome in senescent cells is sculptured in order to sustain the new transcriptional requi...

    Authors: Eros Di Giorgio, Harikrishnareddy Paluvai, Emiliano Dalla, Liliana Ranzino, Alessandra Renzini, Viviana Moresi, Martina Minisini, Raffaella Picco and Claudio Brancolini

    Citation: Genome Biology 2021 22:129

    Content type: Research

    Published on:

  10. Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship betwee...

    Authors: Jiazhen Shen, Dhaval Varshney, Angela Simeone, Xiaoyun Zhang, Santosh Adhikari, David Tannahill and Shankar Balasubramanian

    Citation: Genome Biology 2021 22:143

    Content type: Research

    Published on:

  11. Trans-acting expression quantitative trait loci (trans-eQTLs) account for ≥70% expression heritability and could therefore facilitate uncovering mechanisms underlying the origination of complex diseases. Identify...

    Authors: Saikat Banerjee, Franco L. Simonetti, Kira E. Detrois, Anubhav Kaphle, Raktim Mitra, Rahul Nagial and Johannes Söding

    Citation: Genome Biology 2021 22:142

    Content type: Method

    Published on:

  12. Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1

    Authors: Zhenxing Wang, Nicolas Butel, Juan Santos-González, Lauriane Simon, Cecilia Wärdig and Claudia Köhler

    Citation: Genome Biology 2021 22:141

    Content type: Research

    Published on:

  13. How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we lev...

    Authors: Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Gil Jr, Olivier Loudet, Vincent Colot and Leandro Quadrana

    Citation: Genome Biology 2021 22:138

    Content type: Research

    Published on:

  14. Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental...

    Authors: Michael F. Scott, Nick Fradgley, Alison R. Bentley, Thomas Brabbs, Fiona Corke, Keith A. Gardner, Richard Horsnell, Phil Howell, Olufunmilayo Ladejobi, Ian J. Mackay, Richard Mott and James Cockram

    Citation: Genome Biology 2021 22:137

    Content type: Research

    Published on:

  15. Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes alm...

    Authors: Federico Agostini, Julian Zagalak, Jan Attig, Jernej Ule and Nicholas M. Luscombe

    Citation: Genome Biology 2021 22:136

    Content type: Research

    Published on:

  16. Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human h...

    Authors: Samuel S. Minot, Kevin C. Barry, Caroline Kasman, Jonathan L. Golob and Amy D. Willis

    Citation: Genome Biology 2021 22:135

    Content type: Method

    Published on:

  17. The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth betwe...

    Authors: Simon Yuan Wang, Elizabeth Ann Pollina, I-Hao Wang, Lindsay Kristina Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin Aaron Garcia, Paul Lieberman Greer and Eric Lieberman Greer

    Citation: Genome Biology 2021 22:134

    Content type: Research

    Published on:

  18. Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing splicing pathways cannot be determined by...

    Authors: Carrie Kovalak, Scott Donovan, Alicia A. Bicknell, Mihir Metkar and Melissa J. Moore

    Citation: Genome Biology 2021 22:132

    Content type: Research

    Published on:

  19. While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. W...

    Authors: Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich and Joseph Schacherer

    Citation: Genome Biology 2021 22:126

    Content type: Method

    Published on:

  20. Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB hig...

    Authors: Hyerim Kim, Yunhee Kang, Yujing Li, Li Chen, Li Lin, Nicholas D. Johnson, Dan Zhu, M. Hope Robinson, Leon McSwain, Benjamin G. Barwick, Xianrui Yuan, Xinbin Liao, Jie Zhao, Zhiping Zhang, Qiang Shu, Jianjun Chen…

    Citation: Genome Biology 2021 22:125

    Content type: Research

    Published on:

  21. To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. Howe...

    Authors: Dongyuan Song and Jingyi Jessica Li

    Citation: Genome Biology 2021 22:124

    Content type: Method

    Published on:

  22. Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptom...

    Authors: Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol C. Shetty, Anup Mahurkar and Julie C. Dunning Hotopp

    Citation: Genome Biology 2021 22:121

    Content type: Review

    Published on:

  23. Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

    Authors: Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge…

    Citation: Genome Biology 2021 22:120

    Content type: Research

    Published on:

  24. Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation...

    Authors: Jianying Li, Daojun Yuan, Pengcheng Wang, Qiongqiong Wang, Mengling Sun, Zhenping Liu, Huan Si, Zhongping Xu, Yizan Ma, Boyang Zhang, Liuling Pei, Lili Tu, Longfu Zhu, Ling-Ling Chen, Keith Lindsey, Xianlong Zhang…

    Citation: Genome Biology 2021 22:119

    Content type: Research

    Published on:

  25. Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional...

    Authors: Audrey Montigny, Patrizia Tavormina, Carine Duboe, Hélène San Clémente, Marielle Aguilar, Philippe Valenti, Dominique Lauressergues, Jean-Philippe Combier and Serge Plaza

    Citation: Genome Biology 2021 22:118

    Content type: Research

    Published on:

  26. The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many qu...

    Authors: Jochen Spiegel, Sergio Martínez Cuesta, Santosh Adhikari, Robert Hänsel-Hertsch, David Tannahill and Shankar Balasubramanian

    Citation: Genome Biology 2021 22:117

    Content type: Research

    Published on:

  27. DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation diff...

    Authors: Lindsay F. Rizzardi, Peter F. Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, Kimberly E. Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen and Andrew P. Feinberg

    Citation: Genome Biology 2021 22:116

    Content type: Research

    Published on:

  28. Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the...

    Authors: Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh and Richard Michelmore

    Citation: Genome Biology 2021 22:115

    Content type: Method

    Published on:

  29. High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this t...

    Authors: Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti and Catalina A. Vallejos

    Citation: Genome Biology 2021 22:114

    Content type: Method

    Published on:

  30. Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for p...

    Authors: Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu and De-Zhu Li

    Citation: Genome Biology 2021 22:113

    Content type: Research

    Published on:

  31. Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromo...

    Authors: Ruqian Lyu, Vanessa Tsui, Davis J. McCarthy and Wayne Crismani

    Citation: Genome Biology 2021 22:112

    Content type: Review

    Published on:

  32. Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference...

    Authors: Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann Jr, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas…

    Citation: Genome Biology 2021 22:111

    Content type: Research

    Published on:

    The Research to this article has been published in Genome Biology 2021 22:109

  33. X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem ...

    Authors: Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher and Edda G. Schulz

    Citation: Genome Biology 2021 22:110

    Content type: Research

    Published on:

  34. Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and ...

    Authors: Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann Jr…

    Citation: Genome Biology 2021 22:109

    Content type: Research

    Published on:

    The Research to this article has been published in Genome Biology 2021 22:111

  35. Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs ar...

    Authors: Anil Panigrahi and Bert W. O’Malley

    Citation: Genome Biology 2021 22:108

    Content type: Review

    Published on:

Annual Journal Metrics