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Method: Identification of complex genomic rearrangements in cancers using CouGaR
- Misko Dzamba,
- Arun K. Ramani,
- Pawel Buczkowicz,
- Yue Jiang,
- Man Yu,
- Cynthia Hawkins,
- and Michael Brudno
Genome Res. January 2017 27: 107-117; Published in Advance November 14, 2016, doi:10.1101/gr.211201.116
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
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Research: Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells
- Yan Gao,
- Xiaohui Ni,
- Hua Guo,
- Zhe Su,
- Yi Ba,
- Zhongsheng Tong,
- Zhi Guo,
- Xin Yao,
- Xixi Chen,
- Jian Yin,
- Zhao Yan,
- Lin Guo,
- Ying Liu,
- Fan Bai,
- X. Sunney Xie,
- and Ning Zhang
Genome Res. August 2017 27: 1312-1322; Published in Advance May 9, 2017, doi:10.1101/gr.216788.116
.... All authors were involved in writing and editing the paper. N.Z., X.S.X., and F.B. supervised all aspects of this work. References Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, et al. 2013. Punctuated evolution of prostate cancer s ...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
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Resource: Identification of protein features encoded by alternative exons using Exon Ontology
- Léon-Charles Tranchevent,
- Fabien Aubé,
- Louis Dulaurier,
- Clara Benoit-Pilven,
- Amandine Rey,
- Arnaud Poret,
- Emilie Chautard,
- Hussein Mortada,
- François-Olivier Desmet,
- Fatima Zahra Chakrama,
- Maira Alejandra Moreno-Garcia,
- Evelyne Goillot,
- Stéphane Janczarski,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. June 2017 27: 1087-1097; Published in Advance April 18, 2017, doi:10.1101/gr.212696.116
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Research: Developmental control of gene copy number by repression of replication initiation and fork progression
- Noa Sher,
- George W. Bell,
- Sharon Li,
- Jared Nordman,
- Thomas Eng,
- Matthew L. Eaton,
- David M. MacAlpine,
- and Terry L. Orr-Weaver
Genome Res. January 2012 22: 64-75; Published in Advance November 16, 2011, doi:10.1101/gr.126003.111
...origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 21: 14381449. Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL. 2002. Visualization of replication initiation and elongation in ...
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Research: Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
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Research: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma
- Winnie S. Liang,
- William Hendricks,
- Jeffrey Kiefer,
- Jessica Schmidt,
- Shobana Sekar,
- John Carpten,
- David W. Craig,
- Jonathan Adkins,
- Lori Cuyugan,
- Zarko Manojlovic,
- Rebecca F. Halperin,
- Adrienne Helland,
- Sara Nasser,
- Christophe Legendre,
- Laurence H. Hurley,
- Karthigayini Sivaprakasam,
- Douglas B. Johnson,
- Holly Crandall,
- Klaus J. Busam,
- Victoria Zismann,
- Valerie Deluca,
- Jeeyun Lee,
- Aleksandar Sekulic,
- Charlotte E. Ariyan,
- Jeffrey Sosman,
- and Jeffrey Trent
Genome Res. April 2017 27: 524-532; doi:10.1101/gr.213348.116
...A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, ChaissonM,Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 1521. Furney SJ, Turajlic S, Stamp G, Thomas JM, Hayes A, Strauss D, Gavrielides M, XingW, GoreM, Larkin J, et al. 2014. Themutational burden ...
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Research: High-throughput allele-specific expression across 250 environmental conditions
- Gregory A. Moyerbrailean,
- Allison L. Richards,
- Daniel Kurtz,
- Cynthia A. Kalita,
- Gordon O. Davis,
- Chris T. Harvey,
- Adnan Alazizi,
- Donovan Watza,
- Yoram Sorokin,
- Nancy Hauff,
- Xiang Zhou,
- Xiaoquan Wen,
- Roger Pique-Regi,
- and Francesca Luca
Genome Res. December 2016 26: 1627-1638; Published in Advance October 19, 2016, doi:10.1101/gr.209759.116
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Research: Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
- Peng Mao,
- Alexander J. Brown,
- Ewa P. Malc,
- Piotr A. Mieczkowski,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. October 2017 27: 1674-1684; Published in Advance September 14, 2017, doi:10.1101/gr.225771.117

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