publications

Lab members are shown in boldface letters. Asterisks*  indicate shared first or senior authorships.

2018

  1. Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE. Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Proteome Sci 2018 Aug 18th, https://doi.org/10.1186/s12953-018-0143-7
  2. Reyna M, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Tamayo SP, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JSS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, Mering CV, Sahinalp SC, Valencia A, Reimand J, Stuart JM, Raphael BJ, PCAWG Drivers and Functional Annotation Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes. Pathway and network analysis of more than 2,500 whole cancer genomes. bioRxiv 2018 Aug 7th 385294, doi: https://doi.org/10.1101/385294
  3. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.
  4. Goel RK, Paczkowska M, Reimand J, Napper S, Erique L. Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS . Mol. Cell. Proteomics 2018 March 1st, doi:10.1074/mcp.ra118.000643
  5. Dzneladze I, Woolley JF, Rossell C, Han Y, Rashid A, Jain M, Reimand J, Minden M, Salmena L. SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML. PLOS One 2018 Feb 7th, 13(2):e0191510, doi:https://doi.org/10.1371/journal.pone.0191510
  6. Krassowski M, Paczkowska M, Cullion K, Huang T, Dzneladze I, Ouellette BFF, Yamada JT, Fradet-Turcotte A, Reimand J. ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. Nucleic Acids Research 2018 Jan 4th, 46(D1):D901-D910, doi: https://doi.org/10.1093/nar/gkx973
  7. Mack SC, Pajtler KW, Chavez L, Okonechnikov K, Bertrand KC, Wang X, Erkek S, Federation A, Song A, Lee C, Wang X, McDonald L, Morrow JJ, Saiakhova A, Sin-Chan P, Wu Q, Michaelraj KA, Miller TE, Hubert CG, Ryzhova M, Garzia L, Donovan L, Dombrowski S, Factor DC, Luu B, Valentim CLL, Gimple RC, Morton A, Kim L, Prager BC, Lee JJY, Wu X, Zuccaro J, Thompson Y, Holgado BL, Reimand J, Ke SQ, Tropper A, Lai S, Vijayarajah S, Doan S, Mahadev V, Miñan AF, Gröbner SN, Lienhard M, Zapatka M, Huang Z, Aldape KD, Carcaboso AM, Houghton PJ, Keir ST, Milde T, Witt H, Li Y, Li CJ, Bian XW, Jones DTW, Scott I, Singh SK, Huang A, Dirks PB, Bouffet E, Bradner JE, Ramaswamy V, Jabado N, Rutka JT, Northcott PA, Lupien M, Lichter P, Korshunov A, Scacheri PC, Pfister SM, Kool M, Taylor MD, Rich JN. Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. Nature. 2018 Jan 4;553(7686):101-105. doi: https://doi.org/10.1038/nature25169

2017

  1. Reimand J*, Isserlin R*, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD. Pathway enrichment analysis of -omics data. bioRxiv 2017 Dec 12th, 232835, doi: https://doi.org/10.1101/232835
  2. Wadi L*, Uuskula-Reimand L*, Isaev K*, Shuai S, Huang V, Liang M, Thompson D, Li Y, Ruan L, Paczkowska M, Krassowski M, Dzneladze I, Kron K, Murison A, Mazrooei P, Bristow RG, Simpson JT, Lupien M, Wilson MD, Stein LD, Boutros PC, Reimand J. Candidate cancer driver mutations in super-enhancers and long-range chromatin interaction networks. bioRxiv 2017 Dec 19th 236802, doi: https://doi.org/10.1101/236802
  3. Rheinbay E, Nielsen MM, Abascal F, Tiao G, Hornshoj H, Hess JM, Pedersen RI, Feuerbach L, Sabarinathan R, Madsen HT, Kim J, Mularoni L, Shuai S, Camaioni AAL, Herrmann C, Maruvka YE, Shen C, Amin SB, Bertl J, Dhingra P, Diamanti K, Gonzalez-Perez A, Guo Q, Haradhvala NJ, Isaev K, Juul M, Komorowski J, Lee D, Lochovsky L, Liu EM, Pich O, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Zhang J, Boroevich KA, Carlevaro-Fita J, Chakravarty D, Chan CWY, Fonseca NA, Hamilton MP, Hong C, Kahles A, Kim Y, Lehmann K, Johnson TA, Kahraman A, Park K, Saksena G, Sieverling L, Sinnott-Armstrong NA, Campbell PJ, Hobolth A, Kellis M, Lawrence MS, Raphael B, Rubin MA, Sander C, Stein L, Stuart J, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein MB, Khurana E, Lopez-Bigas N, Martincorena I, Pedersen JS, Getz G. Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes. bioRxiv 237313, 2017 Dec 23rd, doi: https://doi.org/10.1101/237313
  4. Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L, Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2017 Jun 12;31(6):737-754.e6. doi: 10.1016/j.ccell.2017.05.005.
  5. Morrissy AS, Cavalli FMG, Remke M, Ramaswamy V, Shih DJH, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DTW, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka J, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJM, Das S, Malkin D, Jabado N, Marra MA, Taylor MD. Spatial heterogeneity in medulloblastoma. Nat Genet. 2017 May;49(5):780-788. doi: 10.1038/ng.3838. Epub 2017 Apr 10.

2015-2016 – with OICR and reimandlab.org

  1. Wadi L, Meyer M, Weiser J, Stein LD, Reimand J. Impact of outdated gene annotations on pathway enrichment analysis. Nat Methods. 2016 Aug 30;13(9):705-6. doi: 10.1038/nmeth.3963. [bioRxiv http://dx.doi.org/10.1101/049288][ePDF: http://rdcu.be/j1Z8]
  2. Uusküla-Reimand L, Hou H, Samavarchi-Tehrani P, Rudan MV, Liang M, Medina-Rivera A, Mohammed H, Schmidt D, Schwalie P, Young EJ, Reimand J, Hadjur S, Gingras AC, Wilson MD. Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders. Genome Biol. 2016 Aug 31;17(1):182. doi: 10.1186/s13059-016-1043-8.
  3. Narayan S, Bader GD*, Reimand J*. Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. Genome Med. 2016 May 12;8(1):55. doi: 10.1186/s13073-016-0311-2.
  4. Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J. g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016 Apr 20. pii: gkw199. [Epub ahead of print] PubMed PMID: 27098042.
  5. Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DT, Capper D, Sill M, Buchhalter I, Northcott PA, Leis I, Ryzhova M, Koelsche C, Pfaff E, Allen SJ, Balasubramanian G, Worst BC, Pajtler KW, Brabetz S, Johann PD, Sahm F, Reimand J, Mackay A, Carvalho DM, Remke M, Phillips JJ, Perry A, Cowdrey C, Drissi R, Fouladi M, Giangaspero F, Łastowska M, Grajkowska W, Scheurlen W, Pietsch T, Hagel C, Gojo J, Lötsch D, Berger W, Slavc I, Haberler C, Jouvet A, Holm S, Hofer S, Prinz M, Keohane C, Fried I, Mawrin C, Scheie D, Mobley BC, Schniederjan MJ, Santi M, Buccoliero AM, Dahiya S, Kramm CM, von Bueren AO, von Hoff K, Rutkowski S, Herold-Mende C, Frühwald MC, Milde T, Hasselblatt M, Wesseling P, Rößler J, Schüller U, Ebinger M, Schittenhelm J, Frank S, Grobholz R, Vajtai I, Hans V, Schneppenheim R, Zitterbart K, Collins VP, Aronica E, Varlet P, Puget S, Dufour C, Grill J, Figarella-Branger D, Wolter M, Schuhmann MU, Shalaby T, Grotzer M, van Meter T, Monoranu CM, Felsberg J, Reifenberger G, Snuderl M, Forrester LA, Koster J, Versteeg R, Volckmann R, van Sluis P, Wolf S, Mikkelsen T, Gajjar A, Aldape K, Moore AS, Taylor MD, Jones C, Jabado N, Karajannis MA, Eils R, Schlesner M, Lichter P, von Deimling A, Pfister SM, Ellison DW, Korshunov A, Kool M. New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell. 2016 Feb 25;164(5):1060-72. doi: 10.1016/j.cell.2016.01.015. PubMed PMID: 26919435.
  6. Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent clonal selection dominates medulloblastoma at recurrence. Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13. PubMed PMID: 26760213.
  7. Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe’er D, Moffat J, Neel BG. Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance. Cell. 2016 Jan 14;164(1-2):293-309. doi: 10.1016/j.cell.2015.11.062. PubMed PMID: 26771497; PubMed Central PMCID: PMC4724865.
  8. Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP. Systematic analysis of somatic mutations impacting gene expression in 12 tumour types. Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554. PubMed PMID: 26436532; PubMed Central PMCID: PMC4600750.
  9. Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA, Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY. EAG2 potassium channel with evolutionarily conserved function as a brain tumor target. Nat Neurosci. 2015 Sep;18(9):1236-46. doi: 10.1038/nn.4088. Epub 2015 Aug 10. PubMed PMID: 26258683; PubMed Central PMCID: PMC4639927.

2015 and earlier – Jüri’s publications

  1. Wagih O, Reimand J*, Bader GD*. MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. Nat Methods. 2015 Jun;12(6):531-3. doi:10.1038/nmeth.3396. Epub 2015 May 4. PubMed PMID: 25938373.
  2. Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N,
    Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM. Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. Cancer Cell. 2015 May 11;27(5):728-43.
    doi: 10.1016/j.ccell.2015.04.002. PubMed PMID: 25965575; PubMed Central PMCID: PMC4712639.
  3. Meyer M*, Reimand J*, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, Bader GD, Dirks PB. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc Natl Acad Sci USA. 2015 Jan 20;112(3):851-6. doi: 10.1073/pnas.1320611111. Epub 2015 Jan 5. PubMed PMID:25561528; PubMed Central PMCID: PMC4311802.
  4. Reimand J, Wagih O, Bader GD. Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PLoS Genet. 2015 Jan 22;11(1):e1004919. doi: 10.1371/journal.pgen.1004919. eCollection 2015 Jan. PubMed PMID: 25611800; PubMed Central PMCID: PMC4303425.
  5. Leung A, Bader GD*, Reimand J*. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172. Epub 2014 Apr 8. PubMed PMID: 24713437; PubMed
    Central PMCID: PMC4103591.
  6. Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R,
    Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM; ICGC PedBrain Tumor Project. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell. 2014 Mar 17;25(3):393-405. doi: 10.1016/j.ccr.2014.02.004. PubMed PMID: 24651015; PubMed Central PMCID:
    PMC4493053.
  7. Reimand J, Wagih O, Bader GD. The mutational landscape of phosphorylation signaling in cancer. Sci Rep. 2013 Oct 2;3:2651. doi: 10.1038/srep02651. PubMed PMID: 24089029; PubMed Central PMCID: PMC3788619.
  8. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013 Oct 2;3:2650. doi: 10.1038/srep02650. PubMed PMID: 24084849; PubMed Central PMCID: PMC3788361.
  9. Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562. PubMed PMID: 23900255; PubMed Central PMCID: PMC3919555.
  10. Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol. 2013;9:637. doi: 10.1038/msb.2012.68. PubMed PMID: 23340843; PubMed Central PMCID: PMC3564258.
  11. Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L. Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice. Oncogenesis. 2012 Sep 3;1:e26. doi: 10.1038/oncsis.2012.28. PubMed PMID: 23552839; PubMed Central PMCID: PMC3503296.
  12. Reimand J, Hui S, Jain S, Law B, Bader GD. Domain-mediated protein interaction prediction: From genome to network. FEBS Lett. 2012 Aug 14;586(17):2751-63. doi: 10.1016/j.febslet.2012.04.027. Epub 2012 May 3. Review. PubMed PMID: 22561014.
  13. Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels
    EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Aug 2;488(7409):49-56. doi: 10.1038/nature11327. PubMed PMID: 22832581; PubMed Central PMCID: PMC3683624.
  14. Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM. m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Genome Biol. 2012 Jun 21;13(6):R55. doi: 10.1186/gb-2012-13-6-r55. PubMed PMID: 22720667; PubMed Central PMCID:
    PMC3446321.
  15. Altmäe S*, Reimand J*, Hovatta O, Zhang P, Kere J, Laisk T, Saare M, Peters M, Vilo J, Stavreus-Evers A, Salumets A. Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks. Mol Endocrinol. 2012 Jan;26(1):203-17. doi: 10.1210/me.2011-1196. Epub 2011 Nov 10. PubMed PMID: 22074951.
  16. Uusküla L, Männik J, Rull K, Minajeva A, Kõks S, Vaas P, Teesalu P, Reimand J*, Laan M*. Mid-gestational gene expression profile in placenta and link to pregnancy complications. PLoS One. 2012;7(11):e49248. doi: 10.1371/journal.pone.0049248. Epub 2012 Nov 7. PubMed PMID: 23145134; PubMed Central PMCID: PMC3492272.
  17. Reimand J, Arak T, Vilo J. g:Profiler–a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 2011 Jul;39(Web Server issue):W307-15. doi: 10.1093/nar/gkr378. Epub 2011 Jun 6. PubMed PMID: 21646343; PubMed Central PMCID: PMC3125778.
  18. Lõoke M, Reimand J, Sedman T, Sedman J, Järvinen L, Värv S, Peil K, Kristjuhan K, Vilo J, Kristjuhan A. Relicensing of transcriptionally inactivated replication origins in budding yeast. J Biol Chem. 2010 Dec 17;285(51):40004-11. doi: 10.1074/jbc.M110.148924. Epub 2010 Oct 20. PubMed PMID: 20962350; PubMed
    Central PMCID: PMC3000982.
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  22. Krushevskaya D, Peterson H, Reimand J, Kull M, Vilo J. VisHiC–hierarchical functional enrichment analysis of microarray data. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W587-92. doi: 10.1093/nar/gkp435. Epub 2009 May 29. PubMed PMID: 19483095; PubMed Central PMCID: PMC2703939.
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  26. Adler P*, Reimand J*, Jänes J, Kolde R, Peterson H, Vilo J. KEGGanim: pathway animations for high-throughput data. Bioinformatics. 2008 Feb 15;24(4):588-90. Epub 2007 Dec 1. PubMed PMID: 18056068.
  27. Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200. Epub 2007 May 3. PubMed PMID: 17478515; PubMed Central PMCID: PMC1933153.