PUB - Publikationen an der Universität Bielefeld

The 1001 genomes project for Arabidopsis thaliana.
Weigel D, Mott R., Genome Biol. 10(5), 2009
PMID: 19519932

ATTED-II provides coexpressed gene networks for Arabidopsis.
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953027

agriGO: a GO analysis toolkit for the agricultural community.
Du Z, Zhou X, Ling Y, Zhang Z, Su Z., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20435677

An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.
Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ., PLoS ONE 2(8), 2007
PMID: 17684564

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z., BMC Bioinformatics 10(), 2009
PMID: 19192299

Cytoscape 2.8: new features for data integration and network visualization.
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T., Bioinformatics 27(3), 2010
PMID: 21149340

MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data.
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL., Plant Physiol. 155(1), 2010
PMID: 21075962

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962307

MetaCyc and AraCyc. Metabolic pathway databases for plant research.
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY., Plant Physiol. 138(1), 2005
PMID: 15888675

Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P., Adv Bioinformatics 2008(), 2008
PMID: 19956698

VirtualPlant: a software platform to support systems biology research.
Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutierrez RA., Plant Physiol. 152(2), 2009
PMID: 20007449

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.
Toufighi K, Brady SM, Austin R, Ly E, Provart NJ., Plant J. 43(1), 2005
PMID: 15960624

The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W., Plant Physiol. 136(1), 2004
PMID: 15375207

The KEGG database.
Kanehisa M., Novartis Found. Symp. 247(), 2002
PMID: 12539951

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.
Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, Tao Y, Kristiansen K, Zhang X, Li S, Yang H, Wang J, Wang J., Genome Res. 20(5), 2010
PMID: 20305017

Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment.
EPIC Planning Committee, Berger F, Cao XF, Chandler V, Dennis L, Martienssen R, Meyers B, Pikaard C, Peacock J, Richards E, Wagner D, Weigel D, Colot V, Deal R, Dean C, Ecker J, Gehring M, Gregory B, Rodrigo G, Gutierrez-Marcos J, Hasebe M, Hwang ID, Jacobsen S, Kakutani T, Li J, Michaels S, Noh YS, Provart N, Vaughn M., Plant Cell 24(6), 2012
PMID: 22751210

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.
Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE., Am. J. Bot. 99(2), 2012
PMID: 22291167

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21076153

Phytozome: a comparative platform for green plant genomics.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22110026

The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22121220

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE., Bioinformatics 25(20), 2009
PMID: 19654113

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV., Plant Cell 20(6), 2008
PMID: 18591350

PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.
Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T., Plant Cell Physiol. 50(7), 2009
PMID: 19528193

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.
Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE., BMC Genomics 12(), 2011
PMID: 22008187

TableView: portable genomic data visualization.
Johnson JE, Stromvik MV, Silverstein KA, Crow JA, Shoop E, Retzel EF., Bioinformatics 19(10), 2003
PMID: 12835275

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium, Bastow R, Beynon J, Estelle M, Friesner J, Grotewold E, Lavagi I, Lindsey K, Meyers B, Provart N, Benfey P, Birney E, Braun P, Brendel V, Buell R, Caccamo M, Carrington J, Cherry M, Ecker J, Eppig J, Forster M, Gutierrez R, Hilson P, Huala E, Katari M, Kersey P, Kudla J, Ma H, Matsui M, Matthews K, May S, Mayer K, Millar A, Millar H, Mjolsness E, Mockler T, Nikolau B, Nordborg M, Rawlings C, Schofield P, Schoof H, Schroeder JI, Sen TZ, Stanzione D, Town C, Toyoda T, Vision T, Walsh S, Wang X, Ware D, Weckwerth W, Yang W., Plant Cell 22(8), 2010
PMID: 20807877

A predicted interactome for Arabidopsis.
Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M., Plant Physiol. 145(2), 2007
PMID: 17675552

Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kahari A, Kulesha E, Macias JR, Reeves GA, Prlic A., BMC Bioinformatics 9 Suppl 8(), 2008
PMID: 18673527

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D., Front Plant Sci 2(), 2011
PMID: 22645531

Tabix: fast retrieval of sequence features from generic TAB-delimited files.
Li H., Bioinformatics 27(5), 2011
PMID: 21208982

Dissecting plant genomes with the PLAZA comparative genomics platform.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K., Plant Physiol. 158(2), 2011
PMID: 22198273

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21059685

The developmental dynamics of the maize leaf transcriptome.
Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP., Nat. Genet. 42(12), 2010
PMID: 21037569

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651