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  1. Method

    CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

    We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously inf...

    Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang, Frank Alber, Fengzhu Sun, Steven M. Dubinett, Wenyuan Li and Xianghong Jasmine Zhou

    Genome Biology 2017 18:53

    Published on: 24 March 2017

  2. Method

    cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

    It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitativ...

    Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A. Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S. Liu and Junwen Wang

    Genome Biology 2017 18:52

    Published on: 16 March 2017

  3. Software

    IRFinder: assessing the impact of intron retention on mammalian gene expression

    Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing dat...

    Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Au, Justin J-L Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E. J. Rasko and William Ritchie

    Genome Biology 2017 18:51

    Published on: 15 March 2017

  4. Research

    Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

    The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific g...

    Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt…

    Genome Biology 2017 18:50

    Published on: 10 March 2017

  5. Research

    The birth of a human-specific neural gene by incomplete duplication and gene fusion

    Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The hu...

    Max L. Dougherty, Xander Nuttle, Osnat Penn, Bradley J. Nelson, John Huddleston, Carl Baker, Lana Harshman, Michael H. Duyzend, Mario Ventura, Francesca Antonacci, Richard Sandstrom, Megan Y. Dennis and Evan E. Eichler

    Genome Biology 2017 18:49

    Published on: 9 March 2017

  6. Research

    Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

    Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the dista...

    Hongsheng Gui, Duco Schriemer, William W. Cheng, Rajendra K. Chauhan, Guillermo Antiňolo, Courtney Berrios, Marta Bleda, Alice S. Brooks, Rutger W. W. Brouwer, Alan J. Burns, Stacey S. Cherny, Joaquin Dopazo, Bart J. L. Eggen, Paola Griseri, Binta Jalloh, Thuy-Linh Le…

    Genome Biology 2017 18:48

    Published on: 8 March 2017

  7. Research

    Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

    Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies.

    Ryan L. Collins, Harrison Brand, Claire E. Redin, Carrie Hanscom, Caroline Antolik, Matthew R. Stone, Joseph T. Glessner, Tamara Mason, Giulia Pregno, Naghmeh Dorrani, Giorgia Mandrile, Daniela Giachino, Danielle Perrin, Cole Walsh, Michelle Cipicchio, Maura Costello…

    Genome Biology 2017 18:36

    Published on: 6 March 2017

  8. Erratum

    Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

    Yasin Şenbabaoğlu, Ron S. Gejman, Andrew G. Winer, Ming Liu, Eliezer M. Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J. Manley, Danny N. Khalil, Samuel D. Kaffenberger, Yingbei Chen…

    Genome Biology 2017 18:46

    Published on: 1 March 2017

    The original article was published in Genome Biology 2016 17:231

  9. Method

    Single-cell transcriptome conservation in cryopreserved cells and tissues

    A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains t...

    Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A. Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut and Holger Heyn

    Genome Biology 2017 18:45

    Published on: 1 March 2017

  10. METHOD

    BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most me...

    Ines de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A. J. Ponder, Kerstin B. Meyer and Florian Markowetz

    Genome Biology 2017 18:39

    Published on: 24 February 2017

  11. METHOD

    epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

    The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We dev...

    Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A. Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen and Carsten Wiuf

    Genome Biology 2017 18:38

    Published on: 21 February 2017

  12. Research

    Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage

    Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains ...

    Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng and Xiao-Bing Zhang

    Genome Biology 2017 18:35

    Published on: 20 February 2017

  13. Research

    Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

    Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyplo...

    Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D. Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu…

    Genome Biology 2017 18:33

    Published on: 20 February 2017

  14. Research

    RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

    Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s e...

    Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani and Riccardo Zecchina

    Genome Biology 2017 18:37

    Published on: 20 February 2017

  15. Research

    The genome landscape of indigenous African cattle

    The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step...

    Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun Sung, Minseok Seo, Hyeonsoo Jeong, Taehyung Kwon, Mengistie Taye, Ki-Duk Song, Dajeong Lim…

    Genome Biology 2017 18:34

    Published on: 20 February 2017

  16. Research Highlight

    Mouse genomic screen reveals novel host regulator of metastasis

    Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of...

    Toni Celià-Terrassa and Yibin Kang

    Genome Biology 2017 18:31

    Published on: 16 February 2017

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