J
Jeremy Johnson
Researcher at Broad Institute
Publications - 28
Citations - 4322
Jeremy Johnson is an academic researcher from Broad Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 19, co-authored 28 publications receiving 3454 citations. Previous affiliations of Jeremy Johnson include Science for Life Laboratory & University of California, Santa Cruz.
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Journal ArticleDOI
The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones,Manfred Grabherr,Manfred Grabherr,Yingguang Frank Chan,Pamela Russell,Evan Mauceli,Evan Mauceli,Jeremy Johnson,Ross Swofford,Mono Pirun,Mono Pirun,Michael C. Zody,Simon D. M. White,Ewan Birney,Stephen M. J. Searle,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Richard M. Myers,Craig Miller,Craig Miller,Brian R. Summers,Anne K. Knecht,Shannon D. Brady,Haili Zhang,Alex A. Pollen,Timothy R. Howes,Chris T. Amemiya,Eric S. Lander,Federica Di Palma,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,David M. Kingsley,David M. Kingsley +33 more
TL;DR: A high-quality reference genome assembly for threespine stickleback fish is developed and it is indicated that reuse of globally shared standing genetic variation has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation.
Journal ArticleDOI
The African coelacanth genome provides insights into tetrapod evolution
Chris T. Amemiya,Chris T. Amemiya,Jessica Alföldi,Alison P. Lee,Shaohua Fan,Hervé Philippe,Iain MacCallum,Ingo Braasch,Tereza Manousaki,Igor Schneider,Nicolas Rohner,Chris L. Organ,Domitille Chalopin,J. Joshua Smith,Mark Robinson,Rosemary A. Dorrington,Marco Gerdol,Bronwen Aken,Maria Assunta Biscotti,Marco Barucca,Denis Baurain,Aaron M. Berlin,Gregory L. Blatch,Gregory L. Blatch,Francesco Buonocore,Thorsten Burmester,Michael S. Campbell,Adriana Canapa,John P. Cannon,Alan Christoffels,Gianluca De Moro,Adrienne L. Edkins,Lin Fan,Anna Maria Fausto,Nathalie Feiner,Mariko Forconi,Junaid Gamieldien,Sante Gnerre,Andreas Gnirke,Jared V. Goldstone,Wilfried Haerty,Mark E. Hahn,Uljana Hesse,Steve Hoffmann,Jeremy Johnson,Sibel I. Karchner,Shigehiro Kuraku,Marcia Lara,Joshua Z. Levin,Gary W. Litman,Evan Mauceli,Evan Mauceli,Tsutomu Miyake,M. Gail Mueller,David R. Nelson,Anne Nitsche,Ettore Olmo,Tatsuya Ota,Alberto Pallavicini,Sumir Panji,Barbara Picone,Chris P. Ponting,Sonja J. Prohaska,Dariusz Przybylski,Nil Ratan Saha,Vydianathan Ravi,Filipe J. Ribeiro,Tatjana Sauka-Spengler,Giuseppe Scapigliati,Stephen M. J. Searle,Ted Sharpe,Oleg Simakov,Peter F. Stadler,John J. Stegeman,Kenta Sumiyama,Diana Tabbaa,Hakim Tafer,Jason Turner-Maier,Peter van Heusden,Simon D. M. White,Louise Williams,Mark Yandell,Henner Brinkmann,Jean Nicolas Volff,Clifford J. Tabin,Neil H. Shubin,Manfred Schartl,David B. Jaffe,John H. Postlethwait,Byrappa Venkatesh,Federica Di Palma,Eric S. Lander,Axel Meyer,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh +94 more
TL;DR: Through a phylogenomic analysis, it is concluded that the lungfish, and not the coelacanth, is the closest living relative of tetrapods.
Journal ArticleDOI
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Ingo Braasch,Andrew R. Gehrke,J. Joshua Smith,Kazuhiko Kawasaki,Tereza Manousaki,Jeremy Pasquier,Angel Amores,Thomas Desvignes,Peter Batzel,Julian M. Catchen,Aaron M. Berlin,Michael S. Campbell,Daniel Barrell,Daniel Barrell,Kyle J. Martin,John F Mulley,Vydianathan Ravi,Alison P. Lee,Tetsuya Nakamura,Domitille Chalopin,Shaohua Fan,Dustin J. Wcisel,Cristian Cañestro,Jason Sydes,Felix E.G. Beaudry,Yi Sun,Jana Hertel,Michael J. Beam,Mario Fasold,Mikio Ishiyama,Jeremy Johnson,Steffi Kehr,Marcia Lara,John H. Letaw,Gary W. Litman,Ronda T. Litman,Masato Mikami,Tatsuya Ota,Nil Ratan Saha,Louise Williams,Peter F. Stadler,Han Wang,John S. Taylor,Quenton C. Fontenot,Allyse M. Ferrara,Stephen M. J. Searle,Bronwen Aken,Bronwen Aken,Mark Yandell,Igor Schneider,Jeffrey A. Yoder,Jean-Nicolas Volff,Axel Meyer,Chris T. Amemiya,Byrappa Venkatesh,Peter W. H. Holland,Yann Guiguen,Julien Bobe,Neil H. Shubin,Federica Di Palma,Jessica Alföldi,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,John H. Postlethwait +63 more
TL;DR: In this article, the authors sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD).
Journal ArticleDOI
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
Valentin Wucher,Fabrice Legeai,Benoit Hedan,Guillaume Rizk,Laetitia Lagoutte,Tosso Leeb,Vidhya Jagannathan,Edouard Cadieu,Audrey David,Hannes Lohi,Susanna Cirera,Merete Fredholm,Nadine Botherel,Peter A. J. Leegwater,Céline Le Béguec,Hille Fieten,Jeremy Johnson,Jessica Alföldi,Catherine André,Kerstin Lindblad-Toh,Christophe Hitte,Thomas Derrien +21 more
TL;DR: FEELnc is presented, an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames and achieves similar or better classification performance on GENCODE and NONCODE data sets.
Journal ArticleDOI
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
Marc P. Hoeppner,Andrew L. Lundquist,Andrew L. Lundquist,Mono Pirun,Jennifer R. S. Meadows,Neda Zamani,Jeremy Johnson,Görel Sundström,April Cook,Michael Fitzgerald,Ross Swofford,Evan Mauceli,Behrooz Torabi Moghadam,Anna Greka,Jessica Alföldi,Amr Abouelleil,Lynne Aftuck,Daniel Bessette,Aaron M. Berlin,Adam Brown,Gary Gearin,Annie Lui,Pendexter Macdonald,Margaret Priest,Terrance Shea,Jason Turner-Maier,Andrew Zimmer,Eric S. Lander,Federica Di Palma,Federica Di Palma,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Manfred Grabherr,Manfred Grabherr +33 more
TL;DR: An improved genome build, canFam3.1, is presented and a much-improved annotation of the canine genome is provided and regulatory functions for several of the novel non-coding transcripts are suggested.