Song Y, Miao Z, Brazma A, Papatheodorou I.
Nature communications,
2023
doi:10.1038/s41467-023-41855-w.
Vathrakokoili Pournara A, Miao Z, Beker OY, Nolte N, Nolte N, Brazma A, Papatheodorou I.
Preprint,
2023
doi:10.1101/2023.01.19.523443.
Vasudev NS, Scelo G, Glennon KI, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Cartledge J, Soomro N, Adeyoju A, Patel PM, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE.
Clinical cancer research : an official journal of the American Association for Cancer Research,
2023
doi:10.1158/1078-0432.ccr-22-1936.
Katkat E, Demirci Y, Heger G, Karagulle D, Papatheodorou I, Brazma A, Ozhan G.
Preprint,
2022
doi:10.1101/2022.03.11.483949.
Li X, Garg M, Jia T, Liao Q, Yuan L, Li M, Wu Z, Wu W, Bi Y, George N, Papatheodorou I, Brazma A, Luo H, Fang S, Miao Z, Shu Y.
Frontiers in immunology,
2022
doi:10.3389/fimmu.2021.781432.
Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, Vizcaíno JA.
Nucleic acids research,
2022
doi:10.1093/nar/gkab1038.
Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.
Nucleic acids research,
2022
doi:10.1093/nar/gkab1030.
Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A.
Journal of molecular biology,
2022
doi:10.1016/j.jmb.2022.167505.
Demirci Y, Heger G, Katkat E, Papatheodorou I, Brazma A, Ozhan G.
Frontiers in cell and developmental biology,
2022
doi:10.3389/fcell.2022.813314.
Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R.
Nature communications,
2022
doi:10.1038/s41467-022-30365-w.
Theiss M, Hériché J, Russell C, Helekal D, Soppitt A, Ries J, Ellenberg J, Brazma A, Uhlmann V.
Preprint,
2022
doi:10.1101/2022.05.17.492295.
Theiss M, Brazma A, Uhlmann V, Hériché J.
Preprint,
2022
doi:10.1101/2022.05.30.493957.
Song Y, Miao Z, Brazma A, Papatheodorou I.
Preprint,
2022
doi:10.1101/2022.09.27.509674.
Lopez PC, Holinski A, Russell C, Uhlmann V, Brazma A, Swedlow J.
2022
doi:10.6019/tol.microscopyimagematerials-t.2022.00001.1.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium.
Nature communications,
2022
doi:10.1038/s41467-022-32333-w.
Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network.
Nature medicine,
2021
doi:10.1038/s41591-020-01227-z.
Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A.
Nucleic acids research,
2021
doi:10.1093/nar/gkaa1062.
Rustici G, Williams E, Barzine M, Brazma A, Bumgarner R, Chierici M, Furlanello C, Greger L, Jurman G, Miller M, Ouellette BF, Quackenbush J, Reich M, Stoeckert CJ, Taylor RC, Trutane SC, Weller J, Wilhelm B, Winegarden N.
Preprint,
2021
doi:10.1101/2020.12.31.425022.
Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z.
Preprint,
2021
doi:10.1101/2021.01.24.427089.
Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R.
Nature communications,
2021
doi:10.1038/s41467-021-21207-2.
Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA.
Scientific data,
2021
doi:10.1038/s41597-021-00890-2.
Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I.
Nature methods,
2021
doi:10.1038/s41592-021-01102-w.
Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A.
Nature methods,
2021
doi:10.1038/s41592-021-01166-8.
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y.
Preprint,
2021
doi:10.1101/2021.05.21.445143.
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y.
Nature communications,
2021
doi:10.1038/s41467-021-26111-3.
Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z.
Scientific reports,
2021
doi:10.1038/s41598-021-00121-z.
Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A.
Preprint,
2021
doi:10.1101/2021.12.17.473169.
Garg M, Couturier D, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop T, Corrie P, Adams DJ, Brazma A, Rabbie R.
Preprint,
2020
doi:10.1101/2020.02.24.961771.
Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.
Nucleic acids research,
2020
doi:10.1093/nar/gkz947.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium.
Nature communications,
2020
doi:10.1038/s41467-019-13885-w.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Consortium.
Nature,
2020
doi:10.1038/s41586-020-1970-0.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.
Nature,
2020
doi:10.1038/s41586-020-1969-6.
Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L.
Microorganisms,
2020
doi:10.3390/microorganisms8081196.
Hornigold N, Dunn KR, Craven RA, Zougman A, Trainor S, Shreeve R, Brown J, Sewell H, Shires M, Knowles M, Fukuwatari T, Maher ER, Burns J, Bhattarai S, Menon M, Brazma A, Scelo G, Feulner L, Riazalhosseini Y, Lathrop M, Harris A, Selby PJ, Banks RE, Vasudev NS.
British journal of cancer,
2020
doi:10.1038/s41416-020-0874-y.
Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA.
Nature methods,
2020
doi:10.1038/s41592-020-0825-9.
Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Vizcaíno JA, Choudhary JS, Brazma A, Viksna J.
Proteomics,
2020
doi:10.1002/pmic.202000009.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL.
Nature,
2020
doi:10.1038/s41586-020-2766-y.
Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I.
Nature biotechnology,
2020
doi:10.1038/s41587-020-00744-z.
Kurbatova N, Garg M, Whiley L, Chekmeneva E, Jiménez B, Gómez-Romero M, Pearce J, Kimhofer T, D'Hondt E, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Aarsland D, Nevado-Holgado A, Liu B, Snowden S, Proitsi P, Ashton NJ, Hye A, Legido-Quigley C, Lewis MR, Nicholson JK, Holmes E, Brazma A, Lovestone S.
Scientific reports,
2020
doi:10.1038/s41598-020-78031-9.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA.
Nucleic acids research,
2019
doi:10.1093/nar/gky1106.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A.
Nucleic acids research,
2019
doi:10.1093/nar/gky964.
Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J.
Cell,
2019
doi:10.1016/j.cell.2019.08.018.
Ruklisa D, Brazma A, Cerans K, Schlitt T, Viksna J.
BMC bioinformatics,
2019
doi:10.1186/s12859-019-2909-z.
Maruyama SR, Carvalho B, González-Porta M, Rung J, Brazma A, Gustavo Gardinassi L, Ferreira BR, Banin TM, Veríssimo CJ, Katiki LM, de Miranda-Santos IKF.
NPJ vaccines,
2019
doi:10.1038/s41541-019-0145-1.
Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA.
Preprint,
2019
doi:10.1101/665968.
Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y.
Cell reports,
2018
doi:10.1016/j.celrep.2018.04.031.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J.
Nucleic acids research,
2018
doi:10.1093/nar/gkx965.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R.
Nucleic acids research,
2018
doi:10.1093/nar/gkx1158.
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.
Genome research,
2018
doi:10.1101/gr.234096.117.
Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y.
Oncotarget,
2018
doi:10.18632/oncotarget.25382.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U.
Scientific reports,
2018
doi:10.1038/s41598-018-31659-0.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR.
Nature methods,
2018
doi:10.1038/s41592-018-0169-x.
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E.
Nature methods,
2018
doi:10.1038/s41592-018-0195-8.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U.
BMC medical informatics and decision making,
2017
doi:10.1186/s12911-017-0424-6.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y.
Scientific reports,
2017
doi:10.1038/srep44876.
Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A.
Bioinformatics (Oxford, England),
2017
doi:10.1093/bioinformatics/btx143.
Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, PCAWG3.
Preprint,
2017
doi:10.1101/148684.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Berna J, Tubio JM, McMurran CE, Young AM, Young MD, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U.
Preprint,
2017
doi:10.1101/146811.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.
Cell reports,
2017
doi:10.1016/j.celrep.2017.07.025.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ, on behalf of the PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/099861.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR.
Nature methods,
2017
doi:10.1038/nmeth.4326.
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J, on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/176487.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.
Cell reports,
2017
doi:10.1016/j.celrep.2017.08.010.
Torrente A, Brazma A.
Bioinformatics (Oxford, England),
2017
doi:10.1093/bioinformatics/btx532.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/183889.
Thybert D, Roller M, Navarro FC, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin A, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Quail MA, Sisu C, Stanke M, Stefflova K, Oosterhout CV, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams D, Brazma A, Gerstein M, Paten B, Pham S, Keane T, Odom DT, Flicek P.
Preprint,
2017
doi:10.1101/158659.
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen H, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Rätsch G, Schwarz R, Stegle O, PCAWG Group 3.
Preprint,
2017
doi:10.1101/225441.
Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodríguez-Martín B, Rabionet R, Yakneen S, Escaramis G, Li Y, Saini N, Roberts SA, Demidov GM, Pitkänen E, Delaneau O, Heredia-Genestar JM, Weischenfeldt J, Shringarpure SS, Chen J, Nakagawa H, Alexandrov LB, Drechsel O, Dursi LJ, Segre AV, Garrison E, Erkek S, Habermann N, Urban L, Khurana E, Cafferkey A, Hayashi S, Imoto S, Aaltonen LA, Alvarez EG, Baez-Ortega A, Bailey M, Bosio M, Bruzos AL, Buchhalter I, Bustamante CD, Calabrese C, DiBiase A, Gerstein M, Holik AZ, Hua X, Huang K, Letunic I, Klimczak LJ, Koster R, Kumar S, McLellan M, Mashl J, Mirabello L, Newhouse S, Prasad A, Rätsch G, Schlesner M, Schwarz R, Sharma P, Shmaya T, Sidiropoulos N, Song L, Susak H, Tanskanen T, Tojo M, Wedge DC, Wright M, Wu Y, Ye K, Yellapantula VD, Zamora J, Butte AJ, Getz G, Simpson J, Ding L, Marques-Bonet T, Navarro A, Brazma A, Campbell P, Chanock SJ, Chatterjee N, Stegle O, Siebert R, Ossowski S, Harismendy O, Gordenin DA, Tubio JM, Vega FMDL, Easton DF, Estivill X, Korbel JO, on behalf of the PCAWG Germline Working group%, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.
Preprint,
2017
doi:10.1101/208330.
Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S.
Bioinformatics (Oxford, England),
2016
doi:10.1093/bioinformatics/btv762.
Zhou Y, Oskolkov N, Shcherbina L, Ratti J, Kock KH, Su J, Martin B, Oskolkova MZ, Göransson O, Bacon J, Li W, Bucciarelli S, Cilio C, Brazma A, Thatcher B, Rung J, Wierup N, Renström E, Groop L, Hansson O.
Molecular and cellular endocrinology,
2016
doi:10.1016/j.mce.2016.01.027.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å.
International journal of cancer,
2016
doi:10.1002/ijc.30142.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.
Nature communications,
2016
doi:10.1038/ncomms11778.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A.
PloS one,
2016
doi:10.1371/journal.pone.0157484.
Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.
Nucleic acids research,
2015
doi:10.1093/nar/gkv1045.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology,
2015
doi:10.15252/msb.20156658.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O.
Skeletal muscle,
2015
doi:10.1186/s13395-015-0059-1.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.
PloS one,
2015
doi:10.1371/journal.pone.0137367.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.
BMC genomics,
2015
doi:10.1186/1471-2164-16-s8-s2.
Kirsanova C, Brazma A, Rustici G, Sarkans U.
Bioinformatics (Oxford, England),
2015
doi:10.1093/bioinformatics/btv199.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.
PloS one,
2014
doi:10.1371/journal.pone.0104567.
Marguerat S, Lawler K, Brazma A, Bähler J.
RNA biology,
2014
doi:10.4161/rna.29196.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.
Nucleic acids research,
2014
doi:10.1093/nar/gku1057.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM.
Nature communications,
2014
doi:10.1038/ncomms6135.
Fonseca NA, Marioni J, Brazma A.
PloS one,
2014
doi:10.1371/journal.pone.0107026.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research,
2013
doi:10.1093/nar/gkt1270.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research,
2013
doi:10.1093/nar/gkt1081.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome biology,
2013
doi:10.1186/gb-2013-14-7-r70.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM.
BMC systems biology,
2013
doi:10.1186/1752-0509-7-52.
ENCODE Project Consortium.
Nature,
2012
doi:10.1038/nature11247.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome research,
2012
doi:10.1101/gr.142281.112.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics (Oxford, England),
2012
doi:10.1093/bioinformatics/bts605.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic acids research,
2012
doi:10.1093/nar/gks1174.
Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J.
Gene,
2012
doi:10.1016/j.gene.2012.11.084.
Rung J, Brazma A.
Nature reviews. Genetics,
2012
doi:10.1038/nrg3394.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.
Nucleic acids research,
2011
doi:10.1093/nar/gkr937.
Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.
Nucleic acids research,
2011
doi:10.1093/nar/gkr913.
Rung J, Brazma A.
2011
doi:10.1007/978-94-007-1567-7_5.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics (Oxford, England),
2011
doi:10.1093/bioinformatics/btr012.
International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Nature,
2010
doi:10.1038/nature08987.
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.
Bioinformatics (Oxford, England),
2010
doi:10.1093/bioinformatics/btq099.
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.
Nature biotechnology,
2010
doi:10.1038/nbt0410-322.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome biology,
2010
doi:10.1186/gb-2010-11-12-r124.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.
Nucleic acids research,
2010
doi:10.1093/nar/gkq1040.
Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M.
Bioinformatics (Oxford, England),
2010
doi:10.1093/bioinformatics/btq693.
Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A.
Nucleic acids research,
2009
doi:10.1093/nar/gkp936.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.
BMC bioinformatics,
2009
doi:.
Gehlenborg N, Brazma A.
BMC bioinformatics,
2009
doi:.
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.
Bioinformatics (Oxford, England),
2009
doi:10.1093/bioinformatics/btp420.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics (Oxford, England),
2009
doi:10.1093/bioinformatics/btp354.
Brazma A.
TheScientificWorldJournal,
2009
doi:10.1100/tsw.2009.57.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.
Nature biotechnology,
2008
doi:10.1038/nbt.1411.
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S, Members of the RSBI Working Group.
Omics : a journal of integrative biology,
2008
doi:10.1089/omi.2008.0019.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.
Nucleic acids research,
2008
doi:10.1093/nar/gkn889.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Current protocols in bioinformatics,
2008
doi:10.1002/0471250953.bi0713s23.
Brazma A, Miyano S, Akutsu T.
2008
doi:10.1142/p544.
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.
Molecular oncology,
2008
doi:10.1016/j.molonc.2008.11.003.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.
Nucleic acids research,
2007
doi:10.1093/nar/gkm797.
Samsonova AA, Niranjan M, Russell S, Brazma A.
PLoS computational biology,
2007
doi:10.1371/journal.pcbi.0030144.
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A.
Genome biology,
2007
doi:10.1186/gb-2007-8-5-r73.
Schlitt T, Brazma A.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences,
2006
doi:10.1098/rstb.2005.1806.
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.
Nature biotechnology,
2006
doi:10.1038/nbt0106-21a.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.
Nature,
2006
doi:10.1038/440024a.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.
Nature biotechnology,
2006
doi:10.1038/nbt1106-1321.
Brazma A, Krestyaninova M, Sarkans U.
Nature reviews. Genetics,
2006
doi:10.1038/nrg1922.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.
BMC bioinformatics,
2006
doi:10.1186/1471-2105-7-489.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.
Nucleic acids research,
2006
doi:10.1093/nar/gkl995.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods in enzymology,
2006
doi:10.1016/s0076-6879(06)11020-4.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England),
2005
doi:10.1093/bioinformatics/btk022.
Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.
Plant physiology,
2005
doi:10.1104/pp.105.063156.
Torrente A, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England),
2005
doi:10.1093/bioinformatics/bti644.
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.
Nucleic acids research,
2005
doi:10.1093/nar/gki056.
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.
Bioinformatics (Oxford, England),
2004
doi:10.1093/bioinformatics/bti157.
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, MGED Society.
Environmental health perspectives,
2004
doi:10.1289/ehp.112-1277123.
Brazma A, Freeman T, Gardiner K, Weissman S, Werner T, Korn B.
Cytogenetic and genome research,
2004
doi:10.1159/000078003.
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.
Nucleic acids research,
2004
doi:10.1093/nar/gkh470.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nature biotechnology,
2004
doi:10.1038/nbt926.
Soinov LA, Krestyaninova MA, Brazma A.
Genome biology,
2003
doi:10.1186/gb-2003-4-1-r6.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic acids research,
2003
doi:10.1093/nar/gkg066.
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.
Nucleic acids research,
2003
doi:10.1093/nar/gkg091.
Brazma A, Ikeo K, Tateno Y.
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme,
2003
doi:.
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.
Comptes rendus biologies,
2003
doi:10.1016/j.crvi.2003.09.026.
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A.
Genome research,
2003
doi:10.1101/gr.1111403.
Hoheisel J, Brazma A, Büssow K, Cantor CR, Christians FC, Chui G, Diaz R, Drmanac R, Drmanac S, Eickhoff H, Fellenberg K, Hannenhalli S, Hoheisel J, Hou A, Hubbell E, Jin H, Jin P, Jurinke C, Konthur Z, Köster H, Kwon S, Lacy S, Lehrach H, Lipshutz R, Little D, Lueking A, McGall GH, Moeur B, Nordhoff E, Nyarsik L, Pevzner PA, Robinson A, Sarkans U, Shafto J, Sohail M, Southern EM, Swanson D, Ukrainczyk T, van den Boom D, Vilo J, Vingron M, Walter G, Xu C.
2002
doi:10.1007/3-540-45713-5.
Schlitt T, Brazma A.
Comparative and functional genomics,
2002
doi:10.1002/cfg.220.
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J.
Bioinformatics (Oxford, England),
2002
doi:10.1093/bioinformatics/18.suppl_2.s202.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data.
Bioinformatics (Oxford, England),
2002
doi:10.1093/bioinformatics/18.11.1409.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data (MGED) Society.
Science (New York, N.Y.),
2002
doi:10.1126/science.298.5593.539b.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K.
Advances in biochemical engineering/biotechnology,
2002
doi:10.1007/3-540-45713-5_7.
Brazma A.
Bioinformatics (Oxford, England),
2001
doi:10.1093/bioinformatics/17.2.113.
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.
Nature genetics,
2001
doi:10.1038/ng1201-365.
Brazma A, Vilo J.
Microbes and infection,
2001
doi:10.1016/s1286-4579(01)01440-x.
Brazma A, Vilo J.
FEBS letters,
2000
doi:10.1016/s0014-5793(00)01772-5.
Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E.
Proceedings. International Conference on Intelligent Systems for Molecular Biology,
2000
doi:.
Brazma A, Robinson A, Cameron G, Ashburner M.
Nature,
2000
doi:10.1038/35001676.
Brāzma A, Jonassen I, Vilo J, Ukkonen E.
Lecture notes in computer science,
1998
doi:10.1007/bfb0054081.
Brazma A, Jonassen I, Vilo J, Ukkonen E.
Genome research,
1998
doi:10.1101/gr.8.11.1202.
Brazma A, Jonassen I, Eidhammer I, Gilbert D.
Journal of computational biology : a journal of computational molecular cell biology,
1998
doi:10.1089/cmb.1998.5.279.
Brāzma A.
Lecture notes in computer science,
1991
doi:10.1007/bfb0019359.