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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium; 7Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium; 8Department of Pharmaceutics, Ghent University, Ghent 9000, Belgium; 9Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...and Harvard, Cambridge, Massachusetts 02142, USA; 2Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA; 3Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; 4Perelman School...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...of the most thoroughly studied nonhuman primate species. However, little is known about -wide genetic variation in this species. A detailed understanding of extant genomic variation among rhesus macaques has implications for the use of this species as a model for studies of human health and disease, as well...
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Research: The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease
- Laure K. Case,
- Emma H. Wall,
- Julie A. Dragon,
- Naresha Saligrama,
- Dimitry N. Krementsov,
- Mohamad Moussawi,
- James F. Zachary,
- Sally A. Huber,
- Elizabeth P. Blankenhorn,
- and Cory Teuscher
Genome Res. September 2013 23: 1474-1485; Published in Advance June 25, 2013, doi:10.1101/gr.156703.113
...Abstract Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J (B6) background, we show that susceptibility to two diverse animal...
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Research: Personal and population genomics of human regulatory variation
- Benjamin Vernot,
- Andrew B. Stergachis,
- Matthew T. Maurano,
- Jeff Vierstra,
- Shane Neph,
- Robert E. Thurman,
- John A. Stamatoyannopoulos,
- and Joshua M. Akey
Genome Res. September 2012 22: 1689-1697; doi:10.1101/gr.134890.111
..., regulatory variation has been linked to the susceptibility of a wide variety of human diseases, including infectious, autoimmune, psychiatric, neoplastic, and neurodegenerative disorders (for review, see Skelly et al. 2009). In addition, regulatory variation is an important substrate for evolutionary change...
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PERSPECTIVE: Using Mouse Genetics to Understand Infectious Disease Pathogenesis
- William F. Dietrich
Genome Res. March 1, 2001 11: 325-331; doi:10.1101/gr.173101
.... Opin. Microbiol. 2 : 30 – 34 . ↵ Weatherall D. , Clegg J. , Kwiatkowski D. ( 1997 ) The role of genomics in studying genetic susceptibility to infectious disease. Genome Res. 7 : 967 – 973 . ↵ Weinrauch Y. , Zychlinsky A. ( 1999 ) The induction of apoptosis by bacterial pathogens. Annu. Rev. Microbiol...
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Research: Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes
- Jeremy R.B. Newman,
- Ana Conesa,
- Matthew Mika,
- Felicia N. New,
- Suna Onengut-Gumuscu,
- Mark A. Atkinson,
- Stephen S. Rich,
- Lauren M. McIntyre,
- and Patrick Concannon
Genome Res. November 2017 27: 1807-1815; Published in Advance October 12, 2017, doi:10.1101/gr.217984.116
...by grants from the National Institutes of Health (DP3DK085678/DK/NIDDK, AI42288/NIAID, GM1022 27/NIGMS) and utilizes resources provided by the Type 1 Diabetes Genetics Consortium, a collaborative clinical study sponsored by NIDDK, National Institute of Allergy and Infectious Diseases, National Human Genome...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
....] Laboratorymice are importantmodels formany infectious diseases, and inbred strains ofmice often showdifferences in susceptibility to infection, revealing the host mechanisms that perceive and clear pathogens.Geneticmapping of host–pathogen interactions inmice has identified many loci conferring resistance...
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PERSPECTIVE: Advances in livestock genomics: Opening the barn door
- James E. Womack
Genome Res. December 2005 15: 1699-1705; doi:10.1101/gr.3809105
...as livestock genomics enters its sequencing era. The Human Genome Project is properly credited with accelerating the discovery of disease genes and providing a totally new paradigm for medical research. It has sharpened our approach to the study of development, behavior, cancer, and infectious diseases...
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Perspective: Human genomic disease variants: A neutral evolutionary explanation
- Joel T. Dudley,
- Yuseob Kim,
- Li Liu,
- Glenn J. Markov,
- Kristyn Gerold,
- Rong Chen,
- Atul J. Butte,
- and Sudhir Kumar
Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111
...Human genomic disease variants: A neutral evolutionary explanation Joel T. Dudley 1 , 2 , 3 , Yuseob Kim 4 , 5 , Li Liu 5 , Glenn J. Markov 5 , 6 , Kristyn Gerold 5 , Rong Chen 2 , Atul J. Butte 1 , 2 , 3...

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