M
Michael F. Lin
Researcher at Massachusetts Institute of Technology
Publications - 44
Citations - 25299
Michael F. Lin is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 32, co-authored 44 publications receiving 23142 citations. Previous affiliations of Michael F. Lin include Broad Institute & Vassar College.
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Journal ArticleDOI
Comparative functional genomics of the fission yeasts
Nicholas Rhind,Zehua Chen,Moran Yassour,Moran Yassour,Dawn Thompson,Brian J. Haas,Naomi Habib,Ilan Wapinski,Ilan Wapinski,Sushmita Roy,Michael F. Lin,David I. Heiman,Sarah Young,Kanji Furuya,Yabin Guo,Alison L. Pidoux,Huei Mei Chen,Barbara Robbertse,Jonathan M. Goldberg,Keita Aoki,Elizabeth H. Bayne,Aaron M. Berlin,Christopher A. Desjardins,Edward Dobbs,Livio Dukaj,Lin Fan,Michael Fitzgerald,Courtney French,Sharvari Gujja,Klavs R. Hansen,Daniel Keifenheim,Joshua Z. Levin,Rebecca A. Mosher,Carolin A. Müller,Jenna Pfiffner,Margaret Priest,Carsten Russ,Agata Smialowska,Agata Smialowska,Peter Swoboda,Sean M. Sykes,Matthew W. Vaughn,Sonya Vengrova,Ryan J. Yoder,Qiandong Zeng,Robin C. Allshire,David C. Baulcombe,Bruce W. Birren,William Brown,Karl Ekwall,Karl Ekwall,Manolis Kellis,Janet Leatherwood,Henry L. Levin,Hanah Margalit,Robert A. Martienssen,Conrad A. Nieduszynski,Joseph W. Spatafora,Nir Friedman,Jacob Z. Dalgaard,Peter Baumann,Peter Baumann,Peter Baumann,Hironori Niki,Aviv Regev,Aviv Regev,Chad Nusbaum +66 more
TL;DR: Differences in gene content and regulation explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source and provide tools for investigation across the Schizosaccharomyces clade.
Journal ArticleDOI
Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison,Jouni Sirén,Adam M. Novak,Glenn Hickey,Jordan M. Eizenga,Eric T. Dawson,Eric T. Dawson,William J. Jones,Shilpa Garg,Charles Markello,Michael F. Lin,Benedict Paten,Richard Durbin,Richard Durbin +13 more
TL;DR: Vg as discussed by the authors is a toolkit of computational methods for creating, manipulating, and using these structures as references at the scale of the human genome, which provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference.
Journal ArticleDOI
Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone
Daniel J. Park,Gytis Dudas,Shirlee Wohl,Shirlee Wohl,Augustine Goba,Shannon L.M. Whitmer,Kristian G. Andersen,Rachel Sealfon,Rachel Sealfon,Jason T. Ladner,Jeffrey R. Kugelman,Christian B. Matranga,Sarah M. Winnicki,Sarah M. Winnicki,James Qu,Stephen K. Gire,Stephen K. Gire,Adrianne Gladden-Young,Simbirie Jalloh,Dolo Nosamiefan,Nathan L. Yozwiak,Nathan L. Yozwiak,Lina M. Moses,Pan Pan Jiang,Pan Pan Jiang,Aaron E. Lin,Aaron E. Lin,Stephen F. Schaffner,Stephen F. Schaffner,Brian H. Bird,Jonathan S. Towner,Mambu Mamoh,Michael Gbakie,Lansana Kanneh,David Kargbo,James L.B. Massally,Fatima K. Kamara,Edwin Konuwa,Josephine Sellu,Abdul A. Jalloh,Ibrahim Mustapha,Momoh Foday,Mohamed Yillah,Bobbie R. Erickson,Tara K. Sealy,Dianna M. Blau,Christopher D. Paddock,Aaron C. Brault,Brian R. Amman,Jane Basile,Scott W. Bearden,Jessica A. Belser,Eric Bergeron,Shelley Campbell,Ayan K. Chakrabarti,Kimberly A. Dodd,Mike Flint,Aridth Gibbons,Christin H. Goodman,John D. Klena,Laura K. Mcmullan,Laura Morgan,Brandy J. Russell,Johanna S. Salzer,Angela J. Sanchez,David Wang,Irwin Jungreis,Christopher Tomkins-Tinch,Andrey Kislyuk,Michael F. Lin,Sinéad B. Chapman,Bronwyn MacInnis,Ashley Matthews,Ashley Matthews,James Bochicchio,Lisa E. Hensley,Jens H. Kuhn,Chad Nusbaum,John S. Schieffelin,Bruce W. Birren,Marc Forget,Stuart T. Nichol,Gustavo Palacios,Daouda Ndiaye,Christian T. Happi,Sahr M. Gevao,Mohamed A. Vandi,Brima Kargbo,Edward C. Holmes,Trevor Bedford,Andreas Gnirke,Ute Ströher,Andrew Rambaut,Andrew Rambaut,Robert F. Garry,Pardis C. Sabeti,Pardis C. Sabeti +96 more
TL;DR: Analysis of sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic, confirms sustained human-to-human transmission within Sierra Leone and finds no evidence for import or export of EBOV across national borders after its initial introduction.
Journal ArticleDOI
Evidence of abundant stop codon readthrough in Drosophila and other metazoa.
Irwin Jungreis,Michael F. Lin,Rebecca Spokony,Clara S. Chan,Nicolas Nègre,Alec Victorsen,Kevin P. White,Manolis Kellis +7 more
TL;DR: An expanded set of 283 readthrough candidates is reported, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation.
Journal ArticleDOI
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
Katrina Kalantar,Tiago Carvalho,Charles F. A. de Bourcy,Boris Dimitrov,Greg Dingle,Rebecca Egger,Julie Han,Olivia B. Holmes,Yun Fang Juan,Ryan King,Andrey Kislyuk,Michael F. Lin,Maria Mariano,Todd Morse,Lucia V. Reynoso,David Rissato Cruz,Jonathan Sheu,Jennifer Tang,James H.-C. Wang,Mark A. Zhang,Emily Zhong,Vida Ahyong,Sreyngim Lay,Sophana Chea,Jennifer A. Bohl,Jessica E. Manning,Cristina M. Tato,Joseph L. DeRisi +27 more
TL;DR: Novel virus detection capability is benchmarked using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist infected with the recently emergent SARS-CoV-2.