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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...High resolution s of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis Yuan Lu1,9, Edward Rice2,9, Kang Du1, Susanne Kneitz3, Magali Naville4, Corentin Dechaud4, Jean-Nicolas Volff4, Mikki Boswell1, William Boswell1, LaDeana Hillier5, Chad...
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Research: Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci
- Ted Hong,
- Sreeja Parameswaran,
- Omer A. Donmez,
- Daniel Miller,
- Carmy Forney,
- Michael Lape,
- Mariana Saint Just Ribeiro,
- Jun Liang,
- Lee E. Edsall,
- Albert F. Magnusen,
- William Miller,
- Iouri Chepelev,
- John B. Harley,
- Bo Zhao,
- Leah C. Kottyan,
- and Matthew T. Weirauch
Genome Res. December 2021 31: 2185-2198; Published in Advance November 19, 2021, doi:10.1101/gr.264705.120
...in autoimmune diseases such as rheumatoid arthritis (RA) (Balandraud and Roudier 2018), inflammatory bowel disease (IBD) (Dimitroulia et al. 2013), SLE (Harley and James 2006), and MS (Bagert 2009). Despite extensive epidemiologic and serological evidence, the molecular mechanisms through which EBV...
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Letter: Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
- Robert A. Kingsley,
- Chisomo L. Msefula,
- Nicholas R. Thomson,
- Samuel Kariuki,
- Kathryn E. Holt,
- Melita A. Gordon,
- David Harris,
- Louise Clarke,
- Sally Whitehead,
- Vartul Sangal,
- Kevin Marsh,
- Mark Achtman,
- Malcolm E. Molyneux,
- Martin Cormican,
- Julian Parkhill,
- Calman A. MacLennan,
- Robert S. Heyderman,
- and Gordon Dougan
Genome Res. December 2009 19: 2279-2287; Published in Advance November 9, 2009, doi:10.1101/gr.091017.109
...Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype Robert A. Kingsley 1 , 9 , 10 , Chisomo L. Msefula 2 , 9 , Nicholas R. Thomson 1 , 9 , Samuel Kariuki 1 , 3...
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Research: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
- Amine Namouchi,
- Xavier Didelot,
- Ulrike Schöck,
- Brigitte Gicquel,
- and Eduardo P.C. Rocha
Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111
...tuberculosis complex (MTBC) (Smith et al. 2006). Recent works even suggested that MTBC evolves essentially under genetic drift (Hershberg et al. 2008). Yet, the s ofM. tuberculosis havemoderate numbers of Insertion Sequences, few pseudogenes, and no obvious other signals of extensive degradation (Cole 1998...
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LETTER: Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography
- Igor Mokrousov,
- Ho Minh Ly,
- Tatiana Otten,
- Nguyen Ngoc Lan,
- Boris Vyshnevskyi,
- Sven Hoffner,
- and Olga Narvskaya
Genome Res. October 2005 15: 1357-1364; Published in Advance September 16, 2005, doi:10.1101/gr.3840605
..., Russia 2 Research Institute of Phthisiopulmonology, St. Petersburg, 193063, Russia 3 National Institute of Hygiene and Epidemiology, Hanoi 10000, Vietnam 4 Pham Ngoc Thach Tuberculosis and Lung Diseases Centre, Ho Chi Minh City, Vietnam 5 Swedish Institute for Infectious Disease Control, Solna 17182...
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LETTER: Comparing Genomes within the Species Mycobacterium tuberculosis
- Midori Kato-Maeda,
- Jeanne T. Rhee,
- Thomas R. Gingeras,
- Hugh Salamon,
- Jorg Drenkow,
- Nat Smittipat,
- and Peter M. Small
Genome Res. April 1, 2001 11: 547-554; doi:10.1101/gr166401
...in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. 94 : 9869 – 9874 . ↵ Valway S.E. , Sanchez M.P. , Shinnick T.F. , Orme I. , Agerton T. , Hoy D. , Jones J.S. , Westmoreland H. , Onorato I.M. ( 1998 ) An outbreak involving extensive transmission...
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LETTER: Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
- Timothy P. Stinear,
- Torsten Seemann,
- Paul F. Harrison,
- Grant A. Jenkin,
- John K. Davies,
- Paul D.R. Johnson,
- Zahra Abdellah,
- Claire Arrowsmith,
- Tracey Chillingworth,
- Carol Churcher,
- Kay Clarke,
- Ann Cronin,
- Paul Davis,
- Ian Goodhead,
- Nancy Holroyd,
- Kay Jagels,
- Angela Lord,
- Sharon Moule,
- Karen Mungall,
- Halina Norbertczak,
- Michael A. Quail,
- Ester Rabbinowitsch,
- Danielle Walker,
- Brian White,
- Sally Whitehead,
- Pamela L.C. Small,
- Roland Brosch,
- Lalita Ramakrishnan,
- Michael A. Fischbach,
- Julian Parkhill,
- and Stewart T. Cole
Genome Res. May 2008 18: 729-741; Published in Advance April 10, 2008, doi:10.1101/gr.075069.107
...paratuberculosis and Mycobacterium smegmatis reveal how an ancestral generalist mycobacterium evolved into M. tuberculosis and M. marinum . M. tuberculosis has undergone genome downsizing and extensive lateral gene transfer to become a specialized pathogen of humans and other primates without retaining...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
....zwart@nki.nlAbstractEstrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...sequences, contribute to evolutionary adaptation but can also confer deleterious effects and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs...
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ARTICLE: Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis
- Lee Ann McCue,
- Kathleen A. McDonough,
- and Charles E. Lawrence
Genome Res. February 1, 2000 10: 204-219; doi:10.1101/gr.10.2.204
...Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis Lee Ann McCue , Kathleen A. McDonough , and Charles E. Lawrence 1 The Wadsworth Center...

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