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Method: Increased taxon sampling reveals thousands of hidden orthologs in flatworms
- José M. Martín-Durán,
- Joseph F. Ryan,
- Bruno C. Vellutini,
- Kevin Pang,
- and Andreas Hejnol
Genome Res. July 2017 27: 1263-1272; Published in Advance April 11, 2017, doi:10.1101/gr.216226.116
...Res 43: D470D478. Conesa A, Gtz S, Garca-Gmez JM, Terol J, Taln M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 36743676. DalquenDA, Dessimoz C. 2013. Bidirectional best hitsmissmany orthologs ...
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Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
- Lili Wang,
- Jean Fan,
- Joshua M. Francis,
- George Georghiou,
- Sarah Hergert,
- Shuqiang Li,
- Rutendo Gambe,
- Chensheng W. Zhou,
- Chunxiao Yang,
- Sheng Xiao,
- Paola Dal Cin,
- Michaela Bowden,
- Dylan Kotliar,
- Sachet A. Shukla,
- Jennifer R. Brown,
- Donna Neuberg,
- Dario R. Alessi,
- Cheng-Zhong Zhang,
- Peter V. Kharchenko,
- Kenneth J. Livak,
- and Catherine J. Wu
Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
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Research: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Young Seok Ju,
- Jose M.C. Tubio,
- William Mifsud,
- Beiyuan Fu,
- Helen R. Davies,
- Manasa Ramakrishna,
- Yilong Li,
- Lucy Yates,
- Gunes Gundem,
- Patrick S. Tarpey,
- Sam Behjati,
- Elli Papaemmanuil,
- Sancha Martin,
- Anthony Fullam,
- Moritz Gerstung,
- ICGC Prostate Cancer Working Group,
- ICGC Bone Cancer Working Group,
- ICGC Breast Cancer Working Group,
- Jyoti Nangalia,
- Anthony R. Green,
- Carlos Caldas,
- Åke Borg,
- Andrew Tutt,
- Ming Ta Michael Lee,
- Laura J. van't Veer,
- Benita K.T. Tan,
- Samuel Aparicio,
- Paul N. Span,
- John W.M. Martens,
- Stian Knappskog,
- Anne Vincent-Salomon,
- Anne-Lise Børresen-Dale,
- Jórunn Erla Eyfjörd,
- Ola Myklebost,
- Adrienne M. Flanagan,
- Christopher Foster,
- David E. Neal,
- Colin Cooper,
- Rosalind Eeles,
- G. Steven Bova,
- Sunil R. Lakhani,
- Christine Desmedt,
- Gilles Thomas,
- Andrea L. Richardson,
- Colin A. Purdie,
- Alastair M. Thompson,
- Ultan McDermott,
- Fengtang Yang,
- Serena Nik-Zainal,
- Peter J. Campbell,
- and Michael R. Stratton
Genome Res. June 2015 25: 814-824; Published in Advance May 11, 2015, doi:10.1101/gr.190470.115
...Atlas (TCGA) Project Team and their specimen donors for providing sequencing data used in this study. Thisworkwas supported by theWellcome Trust. Y.S.J is supported by a EuropeanMolecular Biology Organization long-term fellowship (LTF 1203_2012). J.M. C.T. is supported by Marie Curie Fellowship FP7 ...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
...Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity Natalia J. Martinez 1 , 2 , 3 , Maria C. Ow 2 , 3 , John S. Reece-Hoyes 1 , 2 , M. Inmaculada Barrasa 1 , 2 , Victor R. Ambros 2 , 4 , and Albertha J.M. Walhout 1 , 2 , 4 1 Program in Gene Function ...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
... or UTR truncations is defined as a novel isoform involving changes only in the UTR relative to an existing transcript. (JM) Novel isoform involving the exon change within the gene body. Note that straightforward assignment of an exon combination constitutes the main advantage of the long reads (J ...
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Method: Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis
- Steve Swinnen,
- Kristien Schaerlaekens,
- Thiago Pais,
- Jürgen Claesen,
- Georg Hubmann,
- Yudi Yang,
- Mekonnen Demeke,
- María R. Foulquié-Moreno,
- Annelies Goovaerts,
- Kris Souvereyns,
- Lieven Clement,
- Françoise Dumortier,
- and Johan M. Thevelein
Genome Res. May 2012 22: 975-984; Published in Advance March 7, 2012, doi:10.1101/gr.131698.111
...mutations on tolerance to low and high ethanol levels and to other stress conditions (S Swinnen, A Goovaerts, K Schaerlaekens, F Dumortier, P Verdyck, K Souvereyns, M. Foulqui-Moreno, and JM Thevelein, in prep.).In conclusion, we have shown that pooled-segregant whole- sequencing using relatively low ...
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LETTER: Defining the mammalian CArGome
- Qiang Sun,
- Guang Chen,
- Jeffrey W. Streb,
- Xiaochun Long,
- Yumei Yang,
- Christian J. Stoeckert, Jr.,
- and Joseph M. Miano
Genome Res. February 2006 16: 197-207; Published in Advance December 19, 2005, doi:10.1101/gr.4108706
...-mail j.m.miano@rochester.edu ; fax (585) 273-1497. Accepted November 1, 2005. Received May 6, 2005. Cold Spring Harbor Laboratory Press Jeffrey Miano Streb Jeffrey W. Christian J, Stoeckert Long, X JM Miano Christian Stoeckert Sun, Qiang Xiaochun Long Sun Qiang Miano, JM ...
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LETTER: Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1
- Nitin S. Baliga,
- Sarah J. Bjork,
- Richard Bonneau,
- Min Pan,
- Chika Iloanusi,
- Molly C.H. Kottemann,
- Leroy Hood,
- and Jocelyne DiRuggiero
Genome Res. June 2004 14: 1025-1035; Published in Advance May 12, 2004, doi:10.1101/gr.1993504
...a remarkably high UV-radiation resistance in the extremely halophilic archaeon Halobacterium NRC-1 withstanding up to 110 J/m 2 with no loss of viability. Gene knockout analysis in two putative photolyase-like genes ( phr1 and phr2 ) implicated only phr2 in photoreactivation. The UV-response was further ...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118

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