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    Lindquist, Erika

    Title
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5612
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Warshan D, Espinoza JL, Stuart RK, Richter RA, Kim SY, Shapiro N, Woyke T, C Kyrpides N, Barry K, Singan V, Lindquist E, Ansong C, Purvine SO, M Brewer H, Weyman PD, Dupont CL, Rasmussen U. Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis. ISME J. 2017 Aug 11. PMID: 28800136.
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      2. Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist E, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci U S A. 2017 Aug 01; 114(31):E6361-E6370. PMID: 28716924.
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      3. Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. Widespread adenine N6-methylation of active genes in fungi. Nat Genet. 2017 Jun; 49(6):964-968. PMID: 28481340.
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      4. de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepcic K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol. 2017 Feb 14; 18(1):28. PMID: 28196534.
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      5. Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist E, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature. 2017 01 26; 541(7638):536-540. PMID: 28092920.
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      6. Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM. Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels. Appl Microbiol Biotechnol. 2017 Mar; 101(6):2603-2618. PMID: 28078400.
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      7. Fochi V, Chitarra W, Kohler A, Voyron S, Singan VR, Lindquist E, Barry KW, Girlanda M, Grigoriev IV, Martin F, Balestrini R, Perotto S. Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas. New Phytol. 2017 Jan; 213(1):365-379. PMID: 27859287.
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      8. Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist E, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 2016 Aug 30; 113(35):9882-7. PMID: 27535936; PMCID: PMC5024638 [Available on 02/28/17].
      9. Arango Isaza RE, Diaz-Trujillo C, Dhillon B, Aerts A, Carlier J, Crane CF, V de Jong T, de Vries I, Dietrich R, Farmer AD, Fortes Fereira C, Garcia S, Guzman M, Hamelin RC, Lindquist E, Mehrabi R, Quiros O, Schmutz J, Shapiro H, Reynolds E, Scalliet G, Souza M, Stergiopoulos I, Van der Lee TA, De Wit PJ, Zapater MF, Zwiers LH, Grigoriev IV, Goodwin SB, Kema GH. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control. PLoS Genet. 2016 Aug; 12(8):e1005876. PMID: 27512984; PMCID: PMC4981457.
      10. Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol. 2016 Jun 20; 26(12):1577-1584. PMID: 27238284.
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      11. Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist E, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Front Microbiol. 2016; 7:238. PMID: 26973616; PMCID: PMC4776211.
      12. de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE. Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLoS Genet. 2015 Dec; 11(12):e1005775. PMID: 26694319; PMCID: PMC4700972.
      13. Plaza DF, Schmieder SS, Lipzen A, Lindquist E, Künzler M. 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. PMID: 26585824; PMCID: PMC4704728.
      14. Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL. Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol. 2015; 6:978. PMID: 26441909; PMCID: PMC4585186.
      15. Doré J, Perraud M, Dieryckx C, Kohler A, Morin E, Henrissat B, Lindquist E, Zimmermann SD, Girard V, Kuo A, Grigoriev IV, Martin F, Marmeisse R, Gay G. Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytol. 2015 Dec; 208(4):1169-87. PMID: 26171947.
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      16. Young D, Rice J, Martin R, Lindquist E, Lipzen A, Grigoriev I, Hibbett D. Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation. PLoS One. 2015; 10(6):e0130381. PMID: 26111162; PMCID: PMC4482389.
      17. Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist E, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants. Genome Biol Evol. 2015 May 14; 7(6):1590-601. PMID: 25977457; PMCID: PMC4494064.
      18. Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist E, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):3451-6. PMID: 25733908; PMCID: PMC4371944.
      19. Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist E, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet. 2015 Apr; 47(4):410-5. PMID: 25706625.
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      20. Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Dueñas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutiérrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kües U, Berka RM, Martínez AT, Covert SF, Blanchette RA, Cullen D. Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood. PLoS Genet. 2014 Dec; 10(12):e1004759. PMID: 25474575; PMCID: PMC4256170.
      21. Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist E, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC. Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):16995-7002. PMID: 25362047; PMCID: PMC4260557.
      22. Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist E, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A. 2014 Jul 08; 111(27):9923-8. PMID: 24958869; PMCID: PMC4103376.
      23. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J. The genome of Eucalyptus grandis. Nature. 2014 Jun 19; 510(7505):356-62. PMID: 24919147.
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      24. Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep. 2014 Mar 31; 4:4519. PMID: 24682209; PMCID: PMC3970191.
      25. Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR. Insights into the maize pan-genome and pan-transcriptome. Plant Cell. 2014 Jan; 26(1):121-35. PMID: 24488960; PMCID: PMC3963563.
      26. Zhang JY, Lee YC, Torres-Jerez I, Wang M, Yin Y, Chou WC, He J, Shen H, Srivastava AC, Pennacchio C, Lindquist E, Grimwood J, Schmutz J, Xu Y, Sharma M, Sharma R, Bartley LE, Ronald PC, Saha MC, Dixon RA, Tang Y, Udvardi MK. Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant J. 2013 Apr; 74(1):160-73. PMID: 23289674.
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      27. Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet. 2013; 9(1):e1003233. PMID: 23357949; PMCID: PMC3554632.
      28. Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist E, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 2012; 8(12):e1003037. PMID: 23236275; PMCID: PMC3516569.
      29. Burow LC, Woebken D, Marshall IP, Lindquist E, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. ISME J. 2013 Apr; 7(4):817-29. PMID: 23190731; PMCID: PMC3603402.
      30. de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE. The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet. 2012; 8(11):e1003088. PMID: 23209441; PMCID: PMC3510045.
      31. Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Korený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 2012 Dec 06; 492(7427):59-65. PMID: 23201678.
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      32. Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist E, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17501-6. PMID: 23045686; PMCID: PMC3491501.
      33. Chan CX, Blouin NA, Zhuang Y, Zäuner S, Prochnik SE, Lindquist E, Lin S, Benning C, Lohr M, Yarish C, Gantt E, Grossman AR, Lu S, Müller K, W Stiller J, Brawley SH, Bhattacharya D. Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism. J Phycol. 2012 Dec; 48(6):1328-42. PMID: 27009986.
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      34. Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist E, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact. 2012 Oct; 25(10):1350-60. PMID: 22712506; PMCID: PMC3551261.
      35. Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, VanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics. 2012 Sep 02; 13:444. PMID: 22937793; PMCID: PMC3463431.
      36. Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012 Jun 29; 336(6089):1715-9. PMID: 22745431.
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      37. Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Pröschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol. 2012 May 25; 13(5):R39. PMID: 22630137; PMCID: PMC3446292.
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