Network Biology

* corresponding author; † equal contribution

Garcia-Molina A, Altmann M, Alkofer A, Epple PM, Dangl JL, Falter-Braun P. LSU network hubs integrate abiotic and biotic stress responses via interaction with the superoxide dismutase FSD2; J Exp Bot 2017 Feb 15;68(5):1185–97.

Steiner A, Rybak K, Altmann M, McFarlane HE, Klaeger S, Nguyen N, Facher E, Ivakov A, Wanner G, Kuster B, Persson S, Braun P, Hauser MT, Assaad F; Cell cycle-regulated PLEIADE/AtMAP65-3 links membrane and microtubule dynamics during plant cytokinesis; Plant J. 2016 Jul 15.

Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P*, Ecker JR*; Mapping transcription factor interactome networks using HaloTag protein arrays; Proc Natl Acad Sci U S A; 2016 Jul 19;113(29):E4238-47

Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP; Pooled-matrix protein interaction screens using Barcode Fusion Genetics; Mol Syst Biol. 2016 Apr 22;12(4):863

Kalinowska K, Nagel MK, Goodman K, Cuyas L, Anzenberger F, Alkofer A, Pax-Ares J, Braun P, Rubio V, Otegui MS, Isono E; Arabidopsis ALIX is required for the endosomal localization of the deubiquitinating enzyme AMSH3; Proc Natl Acad Sci U S A, 2015 Oct 6; 112(40)

Marín-de la Rosa N and Braun P; Primer on Protein–Protein Interaction Maps. eLS, 2015; John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0006205.pub

Hao Y, Colak R, Teyra J, Ignatchenko A, Kislinger T, Braun P, Kaida D, Kim PM; Semi-supervised learning predicts 30-40% of alternative splicing isoforms as novel functional proteins; Cell Reports, 2015, 12, 183–189

Kolb C, Nagel MK, Kalinowska K, Hagmann J, Ichikawa M, Anzensberger F, Alkofer A, Sato MH, Braun P and Isono E; FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis thaliana; Plant Phys., Apr. 2015, pp214

Rolland T†, Taşan M†, Charloteaux B†, Pevzner SJ†, Zhong Q†, Sahni N†, Yi S†, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP*, Vidal M*; A proteome-scale map of the human interactome network; Cell, 2014 Nov 20;159(5):1212-26

Wessling R†, Epple P†, Altmann S†, He Y†, Yang L†, Henz SR, McDonald N, Wiley K, Bader KC, Glasser C, Mukhtar MS, Haigis S, Ghamsari L, Stephens AE, Ecker JR, Vidal M, Jones JD, Mayer KF, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL*, Panstruga R*, and Braun P*; Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life; Cell Host & Microbe. (2014): 16(3), 364-375

Jarsch IK, Konrad SSA, Stratil TF, Urbanus SL, Szymanski W, Braun P, Braun KH, Ott T*; Plasma membranes are subcompartmentalized into a plethora of coexisting and diverse microdomains in Arabidopsis and Nicotiana benthamiana; Plant Cell,  2014; 26(4); 1698-1711

Braun P; Reproducibility restored – on towards the human interactome; Nat. Methods, 2013 6(10); 303-5

Braun P, Aubourg S, van Leene J, de Jaeger G, Lurin C; Plant protein interactomes; Annual Review of Plant Biology, 2013, Vol: 64, 161-187; 2013

Gulbahce N,Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rosen O,  Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, DeCaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL; Viral perturbations of host networks reflect disease etiology; PLoS Computational Biology, 2012; 8(6):e1002531

Braun P*, Gingras AC; History of protein-protein interactions: from egg-white to complex networks;  Proteomics, 2012;12(10):1478-98

Braun P; Benchmarking binary interaction assays: implications for interactome mapping and quality control; Proteomics, 2012;12(10):1499-518

McDermott JE, Braun P, Bonneau R, Hyduke DR; Modeling host-pathogen interactions: computational biology and bioinformatics for infectious disease research, Pac Symp Biocomput. 2012;17:283-286: PMID: 22174283

Anders L*, Ke N, Hydbring P, Zhai H, Choi Y, Vidal M, Braun P, Sicinski P*; A Systematic Substrate Screen Links CDK4/6 to Senescence Suppression in Cancer Cells through FOXM1; Cancer Cell, 2011 Nov 15; 20(5):620-34.

Arabidopsis Interactome Mapping Consortium; Braun P* (Chair) et al.; Network evolution in a plant interactome map; Science 2011 Jul 29; 333:596-601

Mukhtar SM†, Carvunis AR†, Dreze M†, Epple P†, Steinbrenner J, Tasan M, Moore J, Galli M, Hao T, Ghamsari L, Nishimura MT, Romero V, Poulin M, Gebreab F, Tam S, He Y, Harbort CJ, Donovan S, McDonald N, Cusick M, Hill DE, Roth FP, Ecker JR, Vidal M*, Beynon J*, Braun P*, Dangl JL*; Independently evolved virulence effectors converge onto hubs in a plant immune system network; Science 2011 Jul 29; 333:601-7

Yu H, Tardivo L†, Tam S†, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P*, Vidal M*; Next-generation sequencing to generate interactome datasets; Nat. Methods, 2011 Apr 26; 8(6) 478-80

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, Gutiérrez 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; An international bioinformatics infrastructure to underpin the Arabidopsis community; Plant Cell 2010 Aug; 22(8):2530-6

Dreze M, Monachello D, Lurin C, Cusick ME, Hill DE, Vidal M, Braun P; High-quality binary interactome mapping; Methods Enzymol 2010; 470:281-315

Braun P*, Tasan M, Cusick ME, Hill DE, Vidal M*; Exhaustive benchmarking of the yeast two-hybrid system Reply; Nat Methods 2010 Sep; 7(9): 668-668

Braun P†*, Tasan T†, Dreze M†, Barrios-Rodiles M, Lemmens I, Sahalie JM, Murray R, Venkatesan K, Rual JF, Cusick ME, Pawson T, Hill DE, Tavernier J*, Wrana J*, Roth FP*, Vidal M*; An experimentally derived confidence score for binary protein-protein interactions; Nat Methods 2009 Jan; 6(1):91-7

Simonis N†, Rual JF†, Carvunis AR†, Tasan M†, Lemmens I†, Hirozane-Kishikawa T, Hao T,  Sahalie JM, Gebreab F, Cevik S, Klitgord N, Venkatesan K, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, De Smet AS, Kao HL, Simon C, Smolyar A, Ahn  JS, Tewari M, Boxem M, Milstein S, Haiyuan Yu, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP & Vidal M*; A high-quality high-throughput Caenorhabditis elegans protein-protein interaction map; Nat Methods 2009 Jan; 6(1):47-54

Venkatesan K†, Rual JF†, Vazquez A†, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X7, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, De Smet AS, Goh KI, Yildirim MA, Dann E, Smolyar A, Vinayagam A, Braun P, Simonis N, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lalowski M, Timm J, Rau K, Boone C, Cusick ME, Hill DE, Tavernier J, Wanker EE, Barabási AL & Vidal M*; Empirical Sizing of the Human Interactome; Nat Methods 2009 Jan; 6(1):83-90

Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, Roth FP, Vidal M; Literature-curated protein interaction datasets; Nat Methods 2009 Jan; 6:39-46

Yu H†, Braun P†, Yildirim MA†, Lemmons I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gabreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási A-L, Tavernier J, Hill DE, Vidal M*;  High-quality binary protein interaction map of the yeast interactome network.; Science 2008 Oct; 322:104-10

Braun P*, Rietman E, Vidal M; Networking metabolites and diseases; Proc Natl Acad Sci U S A 2008 Jul;105(29):9849-50

Braun P, LaBaer J.; High throughput purification of proteins from Escherichia Coli; Cell Biology: A Laboratory Handbook, 3rd Edition, Volume 4. Elsevier Academic Press: Burlington, MA (2006): 73-77

Braun P*, Cusick ME, Vidal M; QUICKstep and GS-TAP: new moves for protein-interaction analysis; Nat Methods 2006; 3(12):975-6

Braun P*, LaBaer J; High throughput protein production for functional proteomics; Trends in Biotechnology 2003 Sep; 21(9):383-8

Podgrabinska S, Braun P, Velasco P, Kloos B, Pepper MS, Jackson DG, Skobe M*; Molecular characterization of lymphatic endothelial cells; Proc Natl Acad Sci U S A 2002 Dec; 99(25):16069-74

Braun P, Hu Y, Shen B, Halleck A, Koundinya M, Harlow E, LaBaer J*; Proteome Scale Purification of Human Proteins from Bacteria; Proc Natl Acad Sci U S A 2002 Mar; 99 (5): 2654-9

Brizuela L, Braun P, LaBaer J*; FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics; Mol Biochem Par. 2001 Dec; 118(2):155-165

Eisenhardt D, Fiala A, Braun P, Rosenboom H, Kress H, Ebert PR, Menzel R*; Cloning of a catalytic subunit of cAMP-dependent protein kinase from the honeybee (Apis mellifera) and its localization in the brain; Insect Mol Biol. 2001 Apr; 10(2):173-81

Classon M, Salama S, Gorka C, Mulloy R, Braun P, Harlow E*; Combinatorial roles for pRb, p107, and p130 in E2F-mediated cell cycle control; Proc Natl Acad Sci U S A 2000 Sep 26; 97(20):10820-5

Vidal M, Braun P, Chen E, Boeke JD, Harlow E*; Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system; Proc Natl Acad Sci U S A 1996 Sep; 93(19):10321-6