Asaf Salamov

Asaf Salamov

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Asaf Salamov

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Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi.

Metab Eng Commun 2020 Jun 15;10:e00107. Epub 2019 Nov 15.

Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.

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http://dx.doi.org/10.1016/j.mec.2019.e00107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883316PMC
June 2020

Fungal Genome Annotation.

Methods Mol Biol 2018 ;1775:171-184

United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7804-5_15DOI Listing
February 2019

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

Authors:
Ronald P de Vries Robert Riley Ad Wiebenga Guillermo Aguilar-Osorio Sotiris Amillis Cristiane Akemi Uchima Gregor Anderluh Mojtaba Asadollahi Marion Askin Kerrie Barry Evy Battaglia Özgür Bayram Tiziano Benocci Susanna A Braus-Stromeyer Camila Caldana David Cánovas Gustavo C Cerqueira Fusheng Chen Wanping Chen Cindy Choi Alicia Clum Renato Augusto Corrêa Dos Santos André Ricardo de Lima Damásio George Diallinas Tamás Emri Erzsébet Fekete Michel Flipphi Susanne Freyberg Antonia Gallo Christos Gournas Rob Habgood Matthieu Hainaut María Laura Harispe Bernard Henrissat Kristiina S Hildén Ryan Hope Abeer Hossain Eugenia Karabika Levente Karaffa Zsolt Karányi Nada Kraševec Alan Kuo Harald Kusch Kurt LaButti Ellen L Lagendijk Alla Lapidus Anthony Levasseur Erika Lindquist Anna Lipzen Antonio F Logrieco Andrew MacCabe Miia R Mäkelä Iran Malavazi Petter Melin Vera Meyer Natalia Mielnichuk Márton Miskei Ákos P Molnár Giuseppina Mulé Chew Yee Ngan Margarita Orejas Erzsébet Orosz Jean Paul Ouedraogo Karin M Overkamp Hee-Soo Park Giancarlo Perrone Francois Piumi Peter J Punt Arthur F J Ram Ana Ramón Stefan Rauscher Eric Record Diego Mauricio Riaño-Pachón Vincent Robert Julian Röhrig Roberto Ruller Asaf Salamov Nadhira S Salih Rob A Samson Erzsébet Sándor Manuel Sanguinetti Tabea Schütze Kristina Sepčić Ekaterina Shelest Gavin Sherlock Vicky Sophianopoulou Fabio M Squina Hui Sun Antonia Susca Richard B Todd Adrian Tsang Shiela E Unkles Nathalie van de Wiele Diana van Rossen-Uffink Juliana Velasco de Castro Oliveira Tammi C Vesth Jaap Visser Jae-Hyuk Yu Miaomiao Zhou Mikael R Andersen David B Archer Scott E Baker Isabelle Benoit Axel A Brakhage Gerhard H Braus Reinhard Fischer Jens C Frisvad Gustavo H Goldman Jos Houbraken Berl Oakley István Pócsi Claudio Scazzocchio Bernhard Seiboth Patricia A vanKuyk Jennifer Wortman Paul S Dyer Igor V Grigoriev

Genome Biol 2017 02 14;18(1):28. Epub 2017 Feb 14.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

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http://dx.doi.org/10.1186/s13059-017-1151-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5307856PMC
February 2017

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Alternative splicing acting as a bridge in evolution.

Stem Cell Investig 2015 30;2:19. Epub 2015 Oct 30.

1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China.

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http://dx.doi.org/10.3978/j.issn.2306-9759.2015.10.01DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4923640PMC
June 2016

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Curr Biol 2016 06 26;26(12):1577-1584. Epub 2016 May 26.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089372PMC
http://dx.doi.org/10.1016/j.cub.2016.04.038DOI Listing
June 2016

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.

PLoS One 2015 15;10(7):e0132628. Epub 2015 Jul 15.

Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America; School of Natural Sciences, University of California at Merced, Merced, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132628PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503453PMC
May 2016

Genomics of wood-degrading fungi.

Fungal Genet Biol 2014 Nov 20;72:82-90. Epub 2014 May 20.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, United States. Electronic address:

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http://dx.doi.org/10.1016/j.fgb.2014.05.001DOI Listing
November 2014

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum.

Nat Commun 2014 May 9;5:3745. Epub 2014 May 9.

Institute of Evolution, University of Haifa, 199 Aba-Hushi Avenue Mount Carmel, Haifa 3498838, Israel.

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http://dx.doi.org/10.1038/ncomms4745DOI Listing
May 2014

Phylogenetic and phylogenomic overview of the Polyporales.

Mycologia 2013 Nov-Dec;105(6):1350-73. Epub 2013 Aug 11.

Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610, and CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.

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http://www.mycologia.org/content/105/6/1350.full.pdf
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http://www.mycologia.org/cgi/doi/10.3852/13-003
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http://dx.doi.org/10.3852/13-003DOI Listing
January 2014

MycoCosm portal: gearing up for 1000 fungal genomes.

Nucleic Acids Res 2014 Jan 1;42(Database issue):D699-704. Epub 2013 Dec 1.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkt1183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965089PMC
January 2014

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.

Science 2012 Jun;336(6089):1715-9

Biology Department, Clark University, Worcester, MA 01610, USA.

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http://as.vanderbilt.edu/rokaslab/pdfs/2012_Floudas_etal_Sci
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http://www.sciencemag.org/cgi/doi/10.1126/science.1221748
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http://dx.doi.org/10.1126/science.1221748DOI Listing
June 2012

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.

Proc Natl Acad Sci U S A 2012 Apr 20;109(14):5458-63. Epub 2012 Mar 20.

Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, E-28040 Madrid, Spain.

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http://www.treesearch.fs.fed.us/pubs/download/41647.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1119912109
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http://dx.doi.org/10.1073/pnas.1119912109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325662PMC
April 2012

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.

Genome Biol 2011 18;12(4):R40. Epub 2011 Apr 18.

Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-4-r40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218866PMC
February 2012

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Authors:
Jo Ann Banks Tomoaki Nishiyama Mitsuyasu Hasebe John L Bowman Michael Gribskov Claude dePamphilis Victor A Albert Naoki Aono Tsuyoshi Aoyama Barbara A Ambrose Neil W Ashton Michael J Axtell Elizabeth Barker Michael S Barker Jeffrey L Bennetzen Nicholas D Bonawitz Clint Chapple Chaoyang Cheng Luiz Gustavo Guedes Correa Michael Dacre Jeremy DeBarry Ingo Dreyer Marek Elias Eric M Engstrom Mark Estelle Liang Feng Cédric Finet Sandra K Floyd Wolf B Frommer Tomomichi Fujita Lydia Gramzow Michael Gutensohn Jesper Harholt Mitsuru Hattori Alexander Heyl Tadayoshi Hirai Yuji Hiwatashi Masaki Ishikawa Mineko Iwata Kenneth G Karol Barbara Koehler Uener Kolukisaoglu Minoru Kubo Tetsuya Kurata Sylvie Lalonde Kejie Li Ying Li Amy Litt Eric Lyons Gerard Manning Takeshi Maruyama Todd P Michael Koji Mikami Saori Miyazaki Shin-ichi Morinaga Takashi Murata Bernd Mueller-Roeber David R Nelson Mari Obara Yasuko Oguri Richard G Olmstead Naoko Onodera Bent Larsen Petersen Birgit Pils Michael Prigge Stefan A Rensing Diego Mauricio Riaño-Pachón Alison W Roberts Yoshikatsu Sato Henrik Vibe Scheller Burkhard Schulz Christian Schulz Eugene V Shakirov Nakako Shibagaki Naoki Shinohara Dorothy E Shippen Iben Sørensen Ryo Sotooka Nagisa Sugimoto Mamoru Sugita Naomi Sumikawa Milos Tanurdzic Günter Theissen Peter Ulvskov Sachiko Wakazuki Jing-Ke Weng William W G T Willats Daniel Wipf Paul G Wolf Lixing Yang Andreas D Zimmer Qihui Zhu Therese Mitros Uffe Hellsten Dominique Loqué Robert Otillar Asaf Salamov Jeremy Schmutz Harris Shapiro Erika Lindquist Susan Lucas Daniel Rokhsar Igor V Grigoriev

Science 2011 May 5;332(6032):960-3. Epub 2011 May 5.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

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http://sites.psu.edu/axtell/wp-content/uploads/sites/21458/2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1203810
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http://dx.doi.org/10.1126/science.1203810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216PMC
May 2011

The ecoresponsive genome of Daphnia pulex.

Science 2011 Feb;331(6017):555-61

Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.

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http://www3.nd.edu/~mpfrende/PDFs/Science-2011-Colbourne-555
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http://www.sciencemag.org/cgi/doi/10.1126/science.1197761
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http://dx.doi.org/10.1126/science.1197761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199PMC
February 2011

Identification of promoter regions and regulatory sites.

Methods Mol Biol 2010 ;674:57-83

Department of Computer Science, Royal Holloway, London, UK.

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http://link.springer.com/10.1007/978-1-60761-854-6_5
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http://dx.doi.org/10.1007/978-1-60761-854-6_5DOI Listing
December 2010

The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.

Plant Cell 2010 Sep 17;22(9):2943-55. Epub 2010 Sep 17.

Centre National de la Recherche Scientifique, Laboratoire Information Génomique et Structurale UPR2589, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France.

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http://www.plantcell.org/lookup/doi/10.1105/tpc.110.076406
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http://dx.doi.org/10.1105/tpc.110.076406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965543PMC
September 2010

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Nature 2008 Nov 15;456(7219):239-44. Epub 2008 Oct 15.

CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France.

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http://dx.doi.org/10.1038/nature07410DOI Listing
November 2008

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Authors:
Sabeeha S Merchant Simon E Prochnik Olivier Vallon Elizabeth H Harris Steven J Karpowicz George B Witman Astrid Terry Asaf Salamov Lillian K Fritz-Laylin Laurence Maréchal-Drouard Wallace F Marshall Liang-Hu Qu David R Nelson Anton A Sanderfoot Martin H Spalding Vladimir V Kapitonov Qinghu Ren Patrick Ferris Erika Lindquist Harris Shapiro Susan M Lucas Jane Grimwood Jeremy Schmutz Pierre Cardol Heriberto Cerutti Guillaume Chanfreau Chun-Long Chen Valérie Cognat Martin T Croft Rachel Dent Susan Dutcher Emilio Fernández Hideya Fukuzawa David González-Ballester Diego González-Halphen Armin Hallmann Marc Hanikenne Michael Hippler William Inwood Kamel Jabbari Ming Kalanon Richard Kuras Paul A Lefebvre Stéphane D Lemaire Alexey V Lobanov Martin Lohr Andrea Manuell Iris Meier Laurens Mets Maria Mittag Telsa Mittelmeier James V Moroney Jeffrey Moseley Carolyn Napoli Aurora M Nedelcu Krishna Niyogi Sergey V Novoselov Ian T Paulsen Greg Pazour Saul Purton Jean-Philippe Ral Diego Mauricio Riaño-Pachón Wayne Riekhof Linda Rymarquis Michael Schroda David Stern James Umen Robert Willows Nedra Wilson Sara Lana Zimmer Jens Allmer Janneke Balk Katerina Bisova Chong-Jian Chen Marek Elias Karla Gendler Charles Hauser Mary Rose Lamb Heidi Ledford Joanne C Long Jun Minagawa M Dudley Page Junmin Pan Wirulda Pootakham Sanja Roje Annkatrin Rose Eric Stahlberg Aimee M Terauchi Pinfen Yang Steven Ball Chris Bowler Carol L Dieckmann Vadim N Gladyshev Pamela Green Richard Jorgensen Stephen Mayfield Bernd Mueller-Roeber Sathish Rajamani Richard T Sayre Peter Brokstein Inna Dubchak David Goodstein Leila Hornick Y Wayne Huang Jinal Jhaveri Yigong Luo Diego Martínez Wing Chi Abby Ngau Bobby Otillar Alexander Poliakov Aaron Porter Lukasz Szajkowski Gregory Werner Kemin Zhou Igor V Grigoriev Daniel S Rokhsar Arthur R Grossman

Science 2007 Oct;318(5848):245-50

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1126/science.1143609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087PMC
October 2007

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.

Nat Methods 2007 Jun 29;4(6):495-500. Epub 2007 Apr 29.

Department of Energy Joint Genome Institute (DOE-JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nmeth1043DOI Listing
June 2007

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.

Nat Biotechnol 2007 Mar 4;25(3):319-26. Epub 2007 Mar 4.

US Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin 53705, USA.

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http://dx.doi.org/10.1038/nbt1290DOI Listing
March 2007

Comparative metagenomics of microbial communities.

Science 2005 Apr;308(5721):554-7

Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1107851DOI Listing
April 2005

The sequence and analysis of duplication-rich human chromosome 16.

Authors:
Joel Martin Cliff Han Laurie A Gordon Astrid Terry Shyam Prabhakar Xinwei She Gary Xie Uffe Hellsten Yee Man Chan Michael Altherr Olivier Couronne Andrea Aerts Eva Bajorek Stacey Black Heather Blumer Elbert Branscomb Nancy C Brown William J Bruno Judith M Buckingham David F Callen Connie S Campbell Mary L Campbell Evelyn W Campbell Chenier Caoile Jean F Challacombe Leslie A Chasteen Olga Chertkov Han C Chi Mari Christensen Lynn M Clark Judith D Cohn Mirian Denys John C Detter Mark Dickson Mira Dimitrijevic-Bussod Julio Escobar Joseph J Fawcett Dave Flowers Dea Fotopulos Tijana Glavina Maria Gomez Eidelyn Gonzales David Goodstein Lynne A Goodwin Deborah L Grady Igor Grigoriev Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Carl E Hildebrand Wayne Huang Sanjay Israni Jamie Jett Phillip B Jewett Kristen Kadner Heather Kimball Arthur Kobayashi Marie-Claude Krawczyk Tina Leyba Jonathan L Longmire Frederick Lopez Yunian Lou Steve Lowry Thom Ludeman Chitra F Manohar Graham A Mark Kimberly L McMurray Linda J Meincke Jenna Morgan Robert K Moyzis Mark O Mundt A Christine Munk Richard D Nandkeshwar Sam Pitluck Martin Pollard Paul Predki Beverly Parson-Quintana Lucia Ramirez Sam Rash James Retterer Darryl O Ricke Donna L Robinson Alex Rodriguez Asaf Salamov Elizabeth H Saunders Duncan Scott Timothy Shough Raymond L Stallings Malinda Stalvey Robert D Sutherland Roxanne Tapia Judith G Tesmer Nina Thayer Linda S Thompson Hope Tice David C Torney Mary Tran-Gyamfi Ming Tsai Levy E Ulanovsky Anna Ustaszewska Nu Vo P Scott White Albert L Williams Patricia L Wills Jung-Rung Wu Kevin Wu Joan Yang Pieter Dejong David Bruce Norman A Doggett Larry Deaven Jeremy Schmutz Jane Grimwood Paul Richardson Daniel S Rokhsar Evan E Eichler Paul Gilna Susan M Lucas Richard M Myers Edward M Rubin Len A Pennacchio

Nature 2004 Dec;432(7020):988-94

DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature03187DOI Listing
December 2004

The DNA sequence and biology of human chromosome 19.

Nature 2004 Apr;428(6982):529-35

Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nature02399DOI Listing
April 2004

The Pedant Human Genome Database ? Functional Annotation of the Human Genome.

ScientificWorldJournal 2002 5;2:82-83. Epub 2002 Feb 5.

Institut für Bioinformatik, GSF-Forschungszentrum für Umwelt und Gesundheit, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1100/tsw.2002.39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009325PMC
February 2002