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
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy,Jason Ernst,Peter V. Kharchenko,Pouya Kheradpour,Nicolas Nègre,Matthew L. Eaton,Jane M. Landolin,Christopher A. Bristow,Lijia Ma,Michael F. Lin,Stefan Washietl,Bradley I. Arshinoff,Ferhat Ay,Patrick E. Meyer,Nicolas Robine,Nicole L. Washington,Luisa Di Stefano,Eugene Berezikov,Christopher D. Brown,Rogerio Candeias,Joseph W. Carlson,Adrian Carr,Irwin Jungreis,Daniel Marbach,Rachel Sealfon,Michael Y. Tolstorukov,Sebastian Will,Artyom A. Alekseyenko,Carlo G. Artieri,Benjamin W. Booth,Angela N. Brooks,Qi Dai,Carrie A. Davis,Michael O. Duff,X. Feng,Andrey A. Gorchakov,Tingting Gu,Jorja G. Henikoff,Philipp Kapranov,Renhua Li,Heather K. MacAlpine,John H. Malone,Aki Minoda,Jared T. Nordman,Katsutomo Okamura,Marc D. Perry,Sara K. Powell,Nicole C. Riddle,Akiko Sakai,Anastasia Samsonova,Jeremy E. Sandler,Yuri B. Schwartz,Noa Sher,Rebecca Spokony,David Sturgill,Marijke J. van Baren,Kenneth H. Wan,Li Yang,Charles Yu,Elise A. Feingold,Peter J. Good,Mark S. Guyer,Rebecca F. Lowdon,Kami Ahmad,Justen Andrews,Bonnie Berger,Steven E. Brenner,Michael R. Brent,Lucy Cherbas,Sarah C. R. Elgin,Thomas R. Gingeras,Robert L. Grossman,Roger A. Hoskins,Thomas C. Kaufman,W. J. Kent,Mitzi I. Kuroda,Terry L. Orr-Weaver,Norbert Perrimon,Vincenzo Pirrotta,James W. Posakony,Bing Ren,Steven Russell,Peter Cherbas,Brenton R. Graveley,Suzanna E. Lewis,Gos Micklem,Brian Oliver,Peter J. Park,Susan E. Celniker,Steven Henikoff,Gary H. Karpen,Eric C. Lai,David M. MacAlpine,Lincoln Stein,Kevin P. White,Manolis Kellis +95 more
TL;DR: The Drosophila Encyclopedia of DNA Elements (modENCODE) project as mentioned in this paper has been used to map transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines.
Journal ArticleDOI
A high-resolution map of human evolutionary constraint using 29 mammals.
Kerstin Lindblad-Toh,Manuel Garber,Or Zuk,Michael F. Lin,Michael F. Lin,Brian J. Parker,Stefan Washietl,Pouya Kheradpour,Pouya Kheradpour,Jason Ernst,Jason Ernst,Gregory E. Jordan,Evan Mauceli,Lucas D. Ward,Lucas D. Ward,Craig B. Lowe,Craig B. Lowe,Craig B. Lowe,Alisha K. Holloway,Michele Clamp,Sante Gnerre,Jessica Alföldi,Kathryn Beal,Jean Chang,Hiram Clawson,James Cuff,Federica Di Palma,Stephen Fitzgerald,Paul Flicek,Mitchell Guttman,Melissa J. Hubisz,David B. Jaffe,Irwin Jungreis,W. James Kent,Dennis Kostka,Marcia Lara,André L. Martins,Tim Massingham,Ida Moltke,Brian J. Raney,Matthew D. Rasmussen,James Robinson,Alexander Stark,Albert J. Vilella,Jiayu Wen,Xiaohui Xie,Michael C. Zody,Kim C. Worley,Christie Kovar,Donna M. Muzny,Richard A. Gibbs,Wesley C. Warren,Elaine R. Mardis,George M. Weinstock,George M. Weinstock,Richard K. Wilson,Ewan Birney,Elliott H. Margulies,Javier Herrero,Eric D. Green,David Haussler,David Haussler,Adam Siepel,Nick Goldman,Katherine S. Pollard,Jakob Skou Pedersen,Jakob Skou Pedersen,Eric S. Lander,Manolis Kellis,Manolis Kellis +69 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation and sequencing and comparative analysis of 29 eutherian genomes confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2%" of the genome.
Journal ArticleDOI
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters
Tiffany Hung,Yulei Wang,Michael F. Lin,Michael F. Lin,Ashley K. Koegel,Yojiro Kotake,Yojiro Kotake,Gavin D. Grant,Hugo M. Horlings,Nilay Shah,Christopher B. Umbricht,Pei Wang,Yu Wang,Benjamin Kong,Anita Langerød,Anne Lise Børresen-Dale,Seung K. Kim,Marc J. van de Vijver,Saraswati Sukumar,Michael L. Whitfield,Manolis Kellis,Manolis Kellis,Yue Xiong,David J. Wong,Howard Y. Chang +24 more
TL;DR: In this article, an ultra-high-density array that tiles the promoters of 56 cell-cycle genes was used to interrogate 108 samples representing diverse perturbations, identifying 216 transcribed regions that encode putative lncRNAs, many with RT-PCR-validated periodic expression during the cell cycle.
Journal ArticleDOI
Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
Geraldine Butler,Matthew D. Rasmussen,Michael F. Lin,Michael F. Lin,Manuel A. S. Santos,Sharadha Sakthikumar,Carol A. Munro,Esther Rheinbay,Esther Rheinbay,Manfred Grabherr,Anja Forche,Jennifer L. Reedy,Ino Agrafioti,Martha B. Arnaud,Steven Bates,Alistair J. P. Brown,Sascha Brunke,Maria C. Costanzo,David A. Fitzpatrick,Piet W. J. de Groot,David Harris,Lois L. Hoyer,Bernhard Hube,Frans M. Klis,Chinnappa D. Kodira,Nicola Lennard,Mary E. Logue,Ronny Martin,Aaron M. Neiman,Elissavet Nikolaou,Michael A. Quail,Janet Quinn,Maria C. Santos,Florian F. Schmitzberger,Gavin Sherlock,Prachi Shah,Kevin A. T. Silverstein,Marek S. Skrzypek,David R. Soll,Rodney Staggs,Ian Stansfield,Michael P. H. Stumpf,Peter E. Sudbery,Thyagarajan Srikantha,Qiandong Zeng,Judith Berman,Matthew Berriman,Joseph Heitman,Neil A. R. Gow,Michael C. Lorenz,Bruce W. Birren,Manolis Kellis,Manolis Kellis,Christina A. Cuomo +53 more
TL;DR: There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence in Candida albicans species.
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters
Tiffany Hung,Yulei Wang,Michael F. Lin,Michael F. Lin,Ashley K. Koegel,Yojiro Kotake,Yojiro Kotake,Gavin D. Grant,Hugo M. Horlings,Nilay Shah,Christopher B. Umbricht,Pei Wang,Yu Wang,Benjamin Kong,Anita Langerød,Anne Lise Børresen-Dale,Seung K. Kim,Marc J. van de Vijver,Saraswati Sukumar,Michael L. Whitfield,Manolis Kellis,Manolis Kellis,Yue Xiong,David J. Wong,Howard Y. Chang +24 more
TL;DR: This work uses an ultrahigh-density array that tiles the promoters of 56 cell-cycle genes to interrogate 108 samples representing diverse perturbations and identifies 216 transcribed regions that encode putative lncRNAs, many with RT-PCR–validated periodic expression during the cell cycle.