Erika Lindquist

Erika Lindquist

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Erika Lindquist

Erika Lindquist

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Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

Authors:
John L Bowman Takayuki Kohchi Katsuyuki T Yamato Jerry Jenkins Shengqiang Shu Kimitsune Ishizaki Shohei Yamaoka Ryuichi Nishihama Yasukazu Nakamura Frédéric Berger Catherine Adam Shiori Sugamata Aki Felix Althoff Takashi Araki Mario A Arteaga-Vazquez Sureshkumar Balasubrmanian Kerrie Barry Diane Bauer Christian R Boehm Liam Briginshaw Juan Caballero-Perez Bruno Catarino Feng Chen Shota Chiyoda Mansi Chovatia Kevin M Davies Mihails Delmans Taku Demura Tom Dierschke Liam Dolan Ana E Dorantes-Acosta D Magnus Eklund Stevie N Florent Eduardo Flores-Sandoval Asao Fujiyama Hideya Fukuzawa Bence Galik Daniel Grimanelli Jane Grimwood Ueli Grossniklaus Takahiro Hamada Jim Haseloff Alexander J Hetherington Asuka Higo Yuki Hirakawa Hope N Hundley Yoko Ikeda Keisuke Inoue Shin-Ichiro Inoue Sakiko Ishida Qidong Jia Mitsuru Kakita Takehiko Kanazawa Yosuke Kawai Tomokazu Kawashima Megan Kennedy Keita Kinose Toshinori Kinoshita Yuji Kohara Eri Koide Kenji Komatsu Sarah Kopischke Minoru Kubo Junko Kyozuka Ulf Lagercrantz Shih-Shun Lin Erika Lindquist Anna M Lipzen Chia-Wei Lu Efraín De Luna Robert A Martienssen Naoki Minamino Masaharu Mizutani Miya Mizutani Nobuyoshi Mochizuki Isabel Monte Rebecca Mosher Hideki Nagasaki Hirofumi Nakagami Satoshi Naramoto Kazuhiko Nishitani Misato Ohtani Takashi Okamoto Masaki Okumura Jeremy Phillips Bernardo Pollak Anke Reinders Moritz Rövekamp Ryosuke Sano Shinichiro Sawa Marc W Schmid Makoto Shirakawa Roberto Solano Alexander Spunde Noriyuki Suetsugu Sumio Sugano Akifumi Sugiyama Rui Sun Yutaka Suzuki Mizuki Takenaka Daisuke Takezawa Hirokazu Tomogane Masayuki Tsuzuki Takashi Ueda Masaaki Umeda John M Ward Yuichiro Watanabe Kazufumi Yazaki Ryusuke Yokoyama Yoshihiro Yoshitake Izumi Yotsui Sabine Zachgo Jeremy Schmutz

Cell 2017 Oct;171(2):287-304.e15

Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.

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http://dx.doi.org/10.1016/j.cell.2017.09.030DOI Listing
October 2017

Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.

Appl Microbiol Biotechnol 2017 Mar 12;101(6):2603-2618. Epub 2017 Jan 12.

Biomass Science and Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94551, USA.

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http://dx.doi.org/10.1007/s00253-017-8091-1DOI Listing
March 2017

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

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

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.

Front Microbiol 2016 3;7:238. Epub 2016 Mar 3.

Department of Earth and Planetary Science, University of California, BerkeleyBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA.

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http://dx.doi.org/10.3389/fmicb.2016.00238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776211PMC
March 2016

Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode.

G3 (Bethesda) 2015 Nov 19;6(1):87-98. Epub 2015 Nov 19.

Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland

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http://dx.doi.org/10.1534/g3.115.023069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704728PMC
November 2015

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.

Proc Natl Acad Sci U S A 2015 Mar 2;112(11):3451-6. Epub 2015 Mar 2.

Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7;

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http://dx.doi.org/10.1073/pnas.1424293112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371944PMC
March 2015

The genome of Eucalyptus grandis.

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.

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http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Sci Rep 2014 Mar 31;4:4519. Epub 2014 Mar 31.

1] Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA [2] Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1038/srep04519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970191PMC
March 2014

MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1).

J Phycol 2012 Aug 12;48(4):883-96. Epub 2012 Apr 12.

Department of Biology, East Carolina University, Greenville, NC 27848, USADelaware Biotechnology Institute, Delaware Technology Park, Newark DE 19711, USADOE Joint Genomics Institute, Walnut Creek, CA 94598, USADepartment of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USADepartment of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, 06901, USADepartment of Marine Sciences, University of Connecticut, Groton, CT 06340, USASchool of Marine Science, University of Maine, Orono, ME 04469 USA.

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http://dx.doi.org/10.1111/j.1529-8817.2012.01138.xDOI Listing
August 2012

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

Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants.

Plant Cell Physiol 2011 Feb;52(2):317-32

Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.

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https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/
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http://dx.doi.org/10.1093/pcp/pcq188DOI Listing
February 2011

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.

Nat Methods 2010 Oct 19;7(10):807-12. Epub 2010 Sep 19.

Department of Energy Joint Genome Institute, Walnut Creek, California, USA.

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http://dx.doi.org/10.1038/nmeth.1507DOI Listing
October 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 porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.

PLoS One 2010 Feb 19;5(2):e9327. Epub 2010 Feb 19.

Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009327PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824831PMC
February 2010

Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey.

BMC Genomics 2009 Nov 30;10:567. Epub 2009 Nov 30.

Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166, A-1060 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2164-10-567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794292PMC
November 2009

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

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

Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes.

Integr Comp Biol 2006 Dec 3;46(6):919-30. Epub 2006 Jun 3.

Romberg Tiburon Center, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920 USA.

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http://dx.doi.org/10.1093/icb/icl007DOI Listing
December 2006

Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis.

Mol Biol Evol 2006 Nov 28;23(11):2026-38. Epub 2006 Jul 28.

The Roy J. Carver Center for Comparative Genomics, Department of Biological Sciences, University of Iowa, IA, USA.

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http://dx.doi.org/10.1093/molbev/msl074DOI Listing
November 2006

Recruitment of mammalian cell fibronectin to the surface of Chlamydia trachomatis.

Infect Immun 2002 Jul;70(7):3935-8

Division of Infectious Diseases, School of Public Health, University of California, Berkeley, California 94720, USA. .

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC128048PMC
http://dx.doi.org/10.1128/iai.70.7.3935-3938.2002DOI Listing
July 2002

Phage-display antibody detection of Chlamydia trachomatis-associated antigens.

Microbiology 2002 Feb;148(Pt 2):443-51

Division of Infectious Diseases, School of Public Health, 235 Earl Warren Hall, University of California, Berkeley, CA 94720-7360, USA.

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http://dx.doi.org/10.1099/00221287-148-2-443DOI Listing
February 2002