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Research: Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
- David H. Gutmann,
- Michael D. McLellan,
- Ibrahim Hussain,
- John W. Wallis,
- Lucinda L. Fulton,
- Robert S. Fulton,
- Vincent Magrini,
- Ryan Demeter,
- Todd Wylie,
- Cyriac Kandoth,
- Jeffrey R. Leonard,
- Abhijit Guha,
- Christopher A. Miller,
- Li Ding,
- and Elaine R. Mardis
Genome Res. March 2013 23: 431-439; Published in Advance December 5, 2012, doi:10.1101/gr.142604.112
...JR, Perry A, Hernandez MR, Gutmann DH. 2005. Natural history of neurofibromatosis 1-associated optic nerve glioma in mice. Ann Neurol 57: 119127. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. 2011. High density DNA methylation array ...
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Research: mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
- Matthieu Legendre,
- Stéphane Audic,
- Olivier Poirot,
- Pascal Hingamp,
- Virginie Seltzer,
- Deborah Byrne,
- Audrey Lartigue,
- Magali Lescot,
- Alain Bernadac,
- Julie Poulain,
- Chantal Abergel,
- and Jean-Michel Claverie
Genome Res. May 2010 20: 664-674; Published in Advance April 1, 2010, doi:10.1101/gr.102582.109
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Research: Genome-wide evidence for selection acting on single amino acid repeats
- Wilfried Haerty and
- G. Brian Golding
Genome Res. June 2010 20: 755-760; Published in Advance January 7, 2010, doi:10.1101/gr.101246.109
...and a Natural Science and Engineering Research Council grant to G.B.G. References Al-Shahrour F, Minguez P, Tarraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J, et al. 2006. BABELOMICS: A systems biology perspective in the functional annotation of scale experiments. Nucleic ...
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Research: Signatures of positive selection apparent in a small sample of human exomes
- Jacob A. Tennessen,
- Jennifer Madeoy,
- and Joshua M. Akey
Genome Res. October 2010 20: 1327-1334; Published in Advance August 6, 2010, doi:10.1101/gr.106161.110
.... Accepted August 2, 2010. Copyright 2010 by Cold Spring Harbor Laboratory Press Joshua Akey JoshuaM Akey Jacob A Tennessen, JA Madeoy J.A. Tennessen JA Tennessen JM Akey Tennessen, J Tennessen Akey, J J Akey J.M. Akey Tennessen, Jacob A Joshua M Madeoy, J Jennifer, Madeoy Joshua M Akey ...
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Research: Aberrant firing of replication origins potentially explains intragenic nonrecurrent rearrangements within genes, including the human DMD gene
- Arunkanth Ankala,
- Jordan N. Kohn,
- Anisha Hegde,
- Arjun Meka,
- Chin Lip Hon Ephrem,
- Syed H. Askree,
- Shruti Bhide,
- and Madhuri R. Hegde
Genome Res. January 2012 22: 25-34; Published in Advance November 16, 2011, doi:10.1101/gr.123463.111
...486. Borowiec JA, Schildkraut CL. 2011. Open sesame: Activating dormant replication origins in the mouse immunoglobulin heavy chain (igh) locus. Curr Opin Cell Biol 23: 284292. Branzei D, Foiani M. 2010. Maintaining stability at the replication fork. Nat Rev Mol Cell Biol 11: 208219. Chen JM, Chuzhanova N ...
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Research: Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease
- Claudio Casola,
- Ugne Zekonyte,
- Andrew D. Phillips,
- David N. Cooper,
- and Matthew W. Hahn
Genome Res. March 2012 22: 429-435; Published in Advance November 16, 2011, doi:10.1101/gr.127738.111
.... Ectopic gene conversions in the human . Genomics 93: 2732. Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA. 2006. Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat 27: 545 552. Chen P, Xie LJ, Huang GY, Zhao XQ, Chang C. 2005 ...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...Luis F. Paulin1,7, Jeremy Fan2,7, Kieran O'Neill2, Erin Pleasance2, Vanessa L. Porter2,3,4, Steven J.M. Jones2,3 and Fritz J. Sedlazeck1,5,6 1Human Genome Sequencing Center Baylor College of Medicine, Houston, Texas 77030, USA; 2Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver ...
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Research: Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures
- Giuliana Giannuzzi,
- Eugenia Migliavacca,
- and Alexandre Reymond
Genome Res. September 2014 24: 1455-1468; Published in Advance June 10, 2014, doi:10.1101/gr.167742.113
.... Detecting differential usage of exons from RNA-seq data. Genome Res 22: 20082017. Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, Alkan C, Campbell CD, Vives L, Malig M, et al. 2010. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat ...
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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118

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