10 Papers
7 Citations
Lin Fan 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 7, co-authored 8 publications. Previous affiliations of Lin Fan include Broad Institute.
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Papers
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Andrea Pauli,Eivind Valen,Michael F. Lin,Manuel Garber,Nadine L. Vastenhouw,Joshua Z. Levin,Lin Fan,Albin Sandelin,John L. Rinn,Aviv Regev,Alexander F. Schier +10 more
TL;DR: This study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies.
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
Michal Rabani,Joshua Z. Levin,Lin Fan,Xian Adiconis,Raktima Raychowdhury,Manuel Garber,Andreas Gnirke,Chad Nusbaum,Nir Hacohen,Nir Friedman,Ido Amit,Aviv Regev,Aviv Regev +12 more
TL;DR: This study combines metabolic labeling of RNA at high temporal resolution with advanced RNA quantification and computational modeling to estimate RNA transcription and degradation rates during the response of mouse dendritic cells to lipopolysaccharide.
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.
The evolution, evolvability and engineering of gene regulatory DNA
Eeshit Dhaval Vaishnav,Carl G. de Boer,Jennifer Molinet,Moran Yassour,Lin Fan,Xian Adiconis,Dawn A. Thompson,Joshua Z. Levin,Francisco A. Cubillos,Aviv Regev +9 more
TL;DR: In this article , a sequence-to-expression model is proposed to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution.
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