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    Schackwitz, Wendy

    TitleBusiness/Systems Analyst 4
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5634
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      Collapse Bibliographic 
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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. Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci Adv. 2017 Jul; 3(7):e1700239. PMID: 28695208.
        View in: PubMed
      2. Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz W, Lipzen AM, Duong PQ, Jones KC, Jiang L, Ruan D, Bauer D, Peng Y, Barry KW, Schmutz J, Ronald PC. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell. 2017 Jun; 29(6):1218-1231. PMID: 28576844.
        View in: PubMed
      3. 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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      4. McCarthy S, Johnson T, Pavlik BJ, Payne S, Schackwitz W, Martin J, Lipzen A, Keffeler E, Blum P. Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution. Appl Environ Microbiol. 2015 Nov 20; 82(3):857-67. PMID: 26590281; PMCID: PMC4725277.
      5. Ai C, McCarthy S, Schackwitz W, Martin J, Lipzen A, Blum P. Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains. Genome Announc. 2015 Oct 01; 3(5). PMID: 26430052; PMCID: PMC4591324.
      6. Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP. Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics. 2015 Sep 22; 16(1):725. PMID: 26395946; PMCID: PMC4580284.
      7. Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz W, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol. 2015; 6:604. PMID: 26157428; PMCID: PMC4477158.
      8. Singh R, Gradnigo J, White D, Lipzen A, Martin J, Schackwitz W, Moriyama E, Blum P. Complete Genome Sequence of an Evolved Thermotoga maritima Isolate. Genome Announc. 2015 May 28; 3(3). PMID: 26021931; PMCID: PMC4447916.
      9. McCarthy S, Gradnigo J, Johnson T, Payne S, Lipzen A, Martin J, Schackwitz W, Moriyama E, Blum P. Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives. Genome Announc. 2015 May 28; 3(3). PMID: 26021927; PMCID: PMC4447912.
      10. Chubukov V, Mingardon F, Schackwitz W, Baidoo EE, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, Mukhopadhyay A. Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC. Appl Environ Microbiol. 2015 Jul; 81(14):4690-6. PMID: 25934627; PMCID: PMC4551201.
      11. Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP. Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics. 2015 Apr 20; 16:326. PMID: 25909478; PMCID: PMC4409711.
      12. Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J. 2015 Nov; 9(11):2360-72. PMID: 25848870; PMCID: PMC4611501 [Available on 11/01/16].
      13. Baker SE, Schackwitz W, Lipzen A, Martin J, Haridas S, LaButti K, Grigoriev IV, Simmons BA, McCluskey K. Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announc. 2015 Apr 02; 3(2). PMID: 25838471; PMCID: PMC4384475.
      14. Muchero W, Guo J, DiFazio SP, Chen JG, Ranjan P, Slavov GT, Gunter LE, Jawdy S, Bryan AC, Sykes R, Ziebell A, Klápšte J, Porth I, Skyba O, Unda F, El-Kassaby YA, Douglas CJ, Mansfield SD, Martin J, Schackwitz W, Evans LM, Czarnecki O, Tuskan GA. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. BMC Genomics. 2015 Jan 23; 16:24. PMID: 25613058; PMCID: PMC4307895.
      15. Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics. 2014 Dec 13; 15:1103. PMID: 25494611; PMCID: PMC4378021.
      16. Kirby J, Nishimoto M, Chow RW, Baidoo EE, Wang G, Martin J, Schackwitz W, Chan R, Fortman JL, Keasling JD. Enhancing Terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate. Appl Environ Microbiol. 2015 Jan; 81(1):130-8. PMID: 25326299; PMCID: PMC4272731.
      17. Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz W, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP. Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biol Evol. 2014 Sep; 6(9):2557-66. PMID: 25364804; PMCID: PMC4202335.
      18. Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, Tuskan GA, DiFazio SP. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet. 2014 Oct; 46(10):1089-96. PMID: 25151358.
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      19. Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J. 2014 Aug; 79(3):361-74. PMID: 24888695.
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      20. Wilson JG, French WT, Lipzen A, Martin J, Schackwitz W, Woyke T, Shapiro N, Bullard JW, Champlin FR, Donaldson JR. Draft Genome Sequence of Enterobacter cloacae Strain JD6301. Genome Announc. 2014 May 29; 2(3). PMID: 24874669; PMCID: PMC4038874.
      21. Byrne RT, Klingele AJ, Cabot EL, Schackwitz W, Martin JA, Martin J, Wang Z, Wood EA, Pennacchio C, Pennacchio LA, Perna NT, Battista JR, Cox MM. Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife. 2014 Mar 04; 3:e01322. PMID: 24596148; PMCID: PMC3939492.
      22. Hawley ER, Schackwitz W, Hess M. Metagenomic sequencing of two salton sea microbiomes. Genome Announc. 2014 Jan 23; 2(1). PMID: 24459270; PMCID: PMC3900902.
      23. Mukherjee S, Thompson LK, Godin S, Schackwitz W, Lipzen A, Martin J, Blanchard JL. Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One. 2014; 9(1):e86731. PMID: 24466216; PMCID: PMC3899296.
      24. 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.
      25. Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klápšte J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QC, Ehlting J, Douglas CJ, Tuskan GA. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour. 2013 Mar; 13(2):306-23. PMID: 23311503.
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      26. Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda). 2013 Jan; 3(1):41-63. PMID: 23316438; PMCID: PMC3538342.
      27. Kontur WS, Schackwitz W, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ. Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. J Bacteriol. 2012 Dec; 194(24):7016-7. PMID: 23209255; PMCID: PMC3510577.
      28. Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol. 2012 Nov; 196(3):713-25. PMID: 22861491.
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      29. Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One. 2012; 7(6):e38333. PMID: 22675544; PMCID: PMC3366947.
      30. Joshi HJ, Christiansen KM, Fitz J, Cao J, Lipzen A, Martin J, Smith-Moritz AM, Pennacchio LA, Schackwitz W, Weigel D, Heazlewood JL. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. Bioinformatics. 2012 May 15; 28(10):1303-6. PMID: 22451271.
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      31. McCluskey K, Wiest AE, Grigoriev IV, Lipzen A, Martin J, Schackwitz W, Baker SE. Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa. G3 (Bethesda). 2011 Sep; 1(4):303-16. PMID: 22384341; PMCID: PMC3276140.
      32. Techtmann SM, Colman AS, Murphy MB, Schackwitz W, Goodwin LA, Robb FT. Regulation of multiple carbon monoxide consumption pathways in anaerobic bacteria. Front Microbiol. 2011; 2:147. PMID: 21808633; PMCID: PMC3135865.
      33. Osbun N, Li J, O'Driscoll MC, Strominger Z, Wakahiro M, Rider E, Bukshpun P, Boland E, Spurrell CH, Schackwitz W, Pennacchio LA, Dobyns WB, Black GC, Sherr EH. Genetic and functional analyses identify DISC1 as a novel callosal agenesis candidate gene. Am J Med Genet A. 2011 Aug; 155A(8):1865-76. PMID: 21739582.
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      34. Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF. One bacterial cell, one complete genome. PLoS One. 2010 Apr 23; 5(4):e10314. PMID: 20428247; PMCID: PMC2859065.
      35. Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38):16151-6. PMID: 19805272; PMCID: PMC2752593.
      36. Cordeddu V, Di Schiavi E, Pennacchio LA, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, Flex E, Lepri F, Bartholdi D, Kutsche K, Ferrero GB, Anichini C, Selicorni A, Rossi C, Tenconi R, Zenker M, Merlo D, Dallapiccola B, Iyengar R, Bazzicalupo P, Gelb BD, Tartaglia M. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet. 2009 Sep; 41(9):1022-6. PMID: 19684605; PMCID: PMC2765465.
      37. Bickel RD, Schackwitz W, Pennacchio LA, Nuzhdin SV, Kopp A. Contrasting patterns of sequence evolution at the functionally redundant bric à brac paralogs in Drosophila melanogaster. J Mol Evol. 2009 Aug; 69(2):194-202. PMID: 19639236; PMCID: PMC2722720.
      38. Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, Schackwitz W, Martin J, Eggington J, Durfee TJ, Middle CM, Norton JE, Popelars MC, Li H, Klugman SA, Hamilton LL, Bane LB, Pennacchio LA, Albert TJ, Perna NT, Cox MM, Battista JR. Directed evolution of ionizing radiation resistance in Escherichia coli. J Bacteriol. 2009 Aug; 191(16):5240-52. PMID: 19502398; PMCID: PMC2725583.
      39. Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, Sabol SL, Cui C, Bai Y, Koriabine M, Yoshinaga Y, Cheng JF, Chen F, Martin J, Schackwitz W, Gunn TM, Kramer KL, De Jong PJ, Pennacchio LA, Lo CW. Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci U S A. 2009 Mar 03; 106(9):3219-24. PMID: 19218456; PMCID: PMC2651267.
      40. Alvarez Retuerto AI, Cantor RM, Gleeson JG, Ustaszewska A, Schackwitz W, Pennacchio LA, Geschwind DH. Association of common variants in the Joubert syndrome gene (AHI1) with autism. Hum Mol Genet. 2008 Dec 15; 17(24):3887-96. PMID: 18782849; PMCID: PMC2638573.
      41. Costford SR, Kavaslar N, Ahituv N, Chaudhry SN, Schackwitz W, Dent R, Pennacchio LA, McPherson R, Harper ME. Gain-of-function R225W mutation in human AMPKgamma(3) causing increased glycogen and decreased triglyceride in skeletal muscle. PLoS One. 2007 Sep 19; 2(9):e903. PMID: 17878938; PMCID: PMC1964808.
      42. Pandit B, Sarkozy A, Pennacchio LA, Carta C, Oishi K, Martinelli S, Pogna EA, Schackwitz W, Ustaszewska A, Landstrom A, Bos JM, Ommen SR, Esposito G, Lepri F, Faul C, Mundel P, López Siguero JP, Tenconi R, Selicorni A, Rossi C, Mazzanti L, Torrente I, Marino B, Digilio MC, Zampino G, Ackerman MJ, Dallapiccola B, Tartaglia M, Gelb BD. Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet. 2007 Aug; 39(8):1007-12. PMID: 17603483.
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      43. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007 Apr; 80(4):779-91. PMID: 17357083; PMCID: PMC1852707.
      44. Tartaglia M, Pennacchio LA, Zhao C, Yadav KK, Fodale V, Sarkozy A, Pandit B, Oishi K, Martinelli S, Schackwitz W, Ustaszewska A, Martin J, Bristow J, Carta C, Lepri F, Neri C, Vasta I, Gibson K, Curry CJ, Siguero JP, Digilio MC, Zampino G, Dallapiccola B, Bar-Sagi D, Gelb BD. Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet. 2007 Jan; 39(1):75-9. PMID: 17143282.
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      45. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Collier JM, Hébert S, Doelle H, Dent R, Pennacchio LA, McPherson R. A PYY Q62P variant linked to human obesity. Hum Mol Genet. 2006 Feb 01; 15(3):387-91. PMID: 16368708.
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      46. Weng L, Kavaslar N, Ustaszewska A, Doelle H, Schackwitz W, Hébert S, Cohen JC, McPherson R, Pennacchio LA. Lack of MEF2A mutations in coronary artery disease. J Clin Invest. 2005 Apr; 115(4):1016-20. PMID: 15841183; PMCID: PMC1070426.
      47. Schackwitz W, Inoue T, Thomas JH. Chemosensory neurons function in parallel to mediate a pheromone response in C. elegans. Neuron. 1996 Oct; 17(4):719-28. PMID: 8893028.
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      48. Starich TA, Herman RK, Kari CK, Yeh WH, Schackwitz W, Schuyler MW, Collet J, Thomas JH, Riddle DL. Mutations affecting the chemosensory neurons of Caenorhabditis elegans. Genetics. 1995 Jan; 139(1):171-88. PMID: 7705621; PMCID: PMC1206316.

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