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Page 11 of 152

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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

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

  23. 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
  24. 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

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

  25. 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
  26. Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival....

    Authors: Tejaswi Iyyanki, Baozhen Zhang, Qixuan Wang, Ye Hou, Qiushi Jin, Jie Xu, Hongbo Yang, Tingting Liu, Xiaotao Wang, Fan Song, Yu Luan, Hironobu Yamashita, Ruby Chien, Huijue Lyu, Lijun Zhang, Lu Wang…
    Citation: Genome Biology 2021 22:105
  27. Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients w...

    Authors: Shuang Qu, Zichen Jiao, Geng Lu, Bing Yao, Ting Wang, Weiwei Rong, Jiahan Xu, Ting Fan, Xinlei Sun, Rong Yang, Jun Wang, Yongzhong Yao, Guifang Xu, Xin Yan, Tao Wang, Hongwei Liang…
    Citation: Genome Biology 2021 22:104
  28. Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address ...

    Authors: Gareth B. Gillard, Lars Grønvold, Line L. Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, John Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen R. Sandve and Torgeir R. Hvidsten
    Citation: Genome Biology 2021 22:103
  29. Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell tr...

    Authors: Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez-Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós and Jordi Solana
    Citation: Genome Biology 2021 22:89
  30. 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 2021 22:99

    The original article was published in Genome Biology 2021 22:98

  31. The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal...

    Authors: Maria Artesi, Vincent Hahaut, Basiel Cole, Laurens Lambrechts, Fereshteh Ashrafi, Ambroise Marçais, Olivier Hermine, Philip Griebel, Natasa Arsic, Frank van der Meer, Arsène Burny, Dominique Bron, Elettra Bianchi, Philippe Delvenne, Vincent Bours, Carole Charlier…
    Citation: Genome Biology 2021 22:97
  32. We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models...

    Authors: Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje and Julien Gagneur
    Citation: Genome Biology 2021 22:94

    The Publisher Correction to this article has been published in Genome Biology 2021 22:107

  33. The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cr...

    Authors: Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa and Georg Zeller
    Citation: Genome Biology 2021 22:93

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