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Items: 50

1.

ID1 Is Critical for Tumorigenesis and Regulates Chemoresistance in Glioblastoma.

Sachdeva R, Wu M, Smiljanic S, Kaskun O, Ghannad-Zadeh K, Celebre A, Isaev K, Morrissy AS, Guan J, Tong J, Chan J, Wilson TM, Al-Omaishi S, Munoz DG, Dirks PB, Moran MF, Taylor MD, Reimand J, Das S.

Cancer Res. 2019 Aug 15;79(16):4057-4071. doi: 10.1158/0008-5472.CAN-18-1357. Epub 2019 Jul 10.

PMID:
31292163
2.

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.

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.

Nat Protoc. 2019 Feb;14(2):482-517. doi: 10.1038/s41596-018-0103-9.

3.

Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma.

Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH.

Nat Commun. 2018 Nov 2;9(1):4651. doi: 10.1038/s41467-018-07182-1.

4.

Assessing Amyloid Pathology in Cognitively Normal Subjects Using 18F-Flutemetamol PET: Comparing Visual Reads and Quantitative Methods.

Collij LE, Konijnenberg E, Reimand J, Kate MT, Braber AD, Alves IL, Zwan M, Yaqub M, van Assema DME, Wink AM, Lammertsma AA, Scheltens P, Visser PJ, Barkhof F, van Berckel BNM.

J Nucl Med. 2019 Apr;60(4):541-547. doi: 10.2967/jnumed.118.211532. Epub 2018 Oct 12.

5.

Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma.

Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH.

Nat Commun. 2018 Oct 8;9(1):4121. doi: 10.1038/s41467-018-06564-9. Erratum in: Nat Commun. 2018 Nov 2;9(1):4651.

6.

Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates.

Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar F, Vizeacoumar F, Lam TT, Lukong KE.

Proteome Sci. 2018 Aug 18;16:16. doi: 10.1186/s12953-018-0143-7. eCollection 2018.

7.

Pathogenic Germline Variants in 10,389 Adult Cancers.

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.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

8.

Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src-related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS).

Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE.

Mol Cell Proteomics. 2018 May;17(5):925-947. doi: 10.1074/mcp.RA118.000643. Epub 2018 Mar 1.

9.

SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML.

Dzneladze I, Woolley JF, Rossell C, Han Y, Rashid A, Jain M, Reimand J, Minden MD, Salmena L.

PLoS One. 2018 Feb 7;13(2):e0191510. doi: 10.1371/journal.pone.0191510. eCollection 2018. Erratum in: PLoS One. 2018 Mar 29;13(3):e0195417.

10.

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.

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.

Nature. 2018 Jan 4;553(7686):101-105. doi: 10.1038/nature25169. Epub 2017 Dec 20.

11.

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins.

Krassowski M, Paczkowska M, Cullion K, Huang T, Dzneladze I, Ouellette BFF, Yamada JT, Fradet-Turcotte A, Reimand J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D901-D910. doi: 10.1093/nar/gkx973.

12.

Intertumoral Heterogeneity within Medulloblastoma Subgroups.

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.

Cancer Cell. 2017 Jun 12;31(6):737-754.e6. doi: 10.1016/j.ccell.2017.05.005.

13.

Spatial heterogeneity in medulloblastoma.

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 JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJM, Das S, Malkin D, Jabado N, Marra MA, Taylor MD.

Nat Genet. 2017 May;49(5):780-788. doi: 10.1038/ng.3838. Epub 2017 Apr 10.

14.

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders.

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.

Genome Biol. 2016 Aug 31;17(1):182. doi: 10.1186/s13059-016-1043-8.

15.

Impact of outdated gene annotations on pathway enrichment analysis.

Wadi L, Meyer M, Weiser J, Stein LD, Reimand J.

Nat Methods. 2016 Aug 30;13(9):705-6. doi: 10.1038/nmeth.3963. No abstract available.

PMID:
27575621
16.

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.

Narayan S, Bader GD, Reimand J.

Genome Med. 2016 May 12;8(1):55. doi: 10.1186/s13073-016-0311-2.

17.

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9. doi: 10.1093/nar/gkw199. Epub 2016 Apr 20.

18.

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs.

Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DTW, 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.

Cell. 2016 Feb 25;164(5):1060-1072. doi: 10.1016/j.cell.2016.01.015.

19.

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance.

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.

Cell. 2016 Jan 14;164(1-2):293-309. doi: 10.1016/j.cell.2015.11.062.

20.

Divergent clonal selection dominates medulloblastoma at recurrence.

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.

Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13.

21.

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

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.

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.

22.

EAG2 potassium channel with evolutionarily conserved function as a brain tumor target.

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.

Nat Neurosci. 2015 Sep;18(9):1236-46. doi: 10.1038/nn.4088. Epub 2015 Aug 10.

23.

Pathway and network analysis of cancer genomes.

Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium.

Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440.

24.

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups.

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.

Cancer Cell. 2015 May 11;27(5):728-43. doi: 10.1016/j.ccell.2015.04.002.

25.

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Wagih O, Reimand J, Bader GD.

Nat Methods. 2015 Jun;12(6):531-3. doi: 10.1038/nmeth.3396. Epub 2015 May 4.

PMID:
25938373
26.

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.

Reimand J, Wagih O, Bader GD.

PLoS Genet. 2015 Jan 22;11(1):e1004919. doi: 10.1371/journal.pgen.1004919. eCollection 2015 Jan.

27.

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity.

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.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):851-6. doi: 10.1073/pnas.1320611111. Epub 2015 Jan 5.

28.

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.

Leung A, Bader GD, Reimand J.

Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172. Epub 2014 Apr 8.

29.

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

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.

Cancer Cell. 2014 Mar 17;25(3):393-405. doi: 10.1016/j.ccr.2014.02.004.

30.

The mutational landscape of phosphorylation signaling in cancer.

Reimand J, Wagih O, Bader GD.

Sci Rep. 2013 Oct 2;3:2651. doi: 10.1038/srep02651.

31.

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

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.

Sci Rep. 2013 Oct 2;3:2650. doi: 10.1038/srep02650.

32.

Computational approaches to identify functional genetic variants in cancer genomes.

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.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

33.

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers.

Reimand J, Bader GD.

Mol Syst Biol. 2013;9:637. doi: 10.1038/msb.2012.68.

34.

Mid-gestational gene expression profile in placenta and link to pregnancy complications.

Uusküla L, Männik J, Rull K, Minajeva A, Kõks S, Vaas P, Teesalu P, Reimand J, Laan M.

PLoS One. 2012;7(11):e49248. doi: 10.1371/journal.pone.0049248. Epub 2012 Nov 7.

35.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

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.

Nature. 2012 Aug 2;488(7409):49-56. doi: 10.1038/nature11327.

36.

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.

Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM.

Genome Biol. 2012 Jun 21;13(6):R55. doi: 10.1186/gb-2012-13-6-r55.

37.

Domain-mediated protein interaction prediction: From genome to network.

Reimand J, Hui S, Jain S, Law B, Bader GD.

FEBS Lett. 2012 Aug 14;586(17):2751-63. doi: 10.1016/j.febslet.2012.04.027. Epub 2012 May 3. Review.

38.

Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice.

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.

Oncogenesis. 2012 Sep 3;1:e26. doi: 10.1038/oncsis.2012.28.

39.

Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks.

Altmäe S, Reimand J, Hovatta O, Zhang P, Kere J, Laisk T, Saare M, Peters M, Vilo J, Stavreus-Evers A, Salumets A.

Mol Endocrinol. 2012 Jan;26(1):203-17. doi: 10.1210/me.2011-1196. Epub 2011 Nov 10.

40.

g:Profiler--a web server for functional interpretation of gene lists (2011 update).

Reimand J, Arak T, Vilo J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W307-15. doi: 10.1093/nar/gkr378. Epub 2011 Jun 6.

41.

Relicensing of transcriptionally inactivated replication origins in budding yeast.

Lõoke M, Reimand J, Sedman T, Sedman J, Järvinen L, Värv S, Peil K, Kristjuhan K, Vilo J, Kristjuhan A.

J Biol Chem. 2010 Dec 17;285(51):40004-11. doi: 10.1074/jbc.M110.148924. Epub 2010 Oct 20.

42.

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development.

Billon N, Kolde R, Reimand J, Monteiro MC, Kull M, Peterson H, Tretyakov K, Adler P, Wdziekonski B, Vilo J, Dani C.

Genome Biol. 2010;11(8):R80. doi: 10.1186/gb-2010-11-8-r80. Epub 2010 Aug 3.

43.

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.

Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM.

Nucleic Acids Res. 2010 Aug;38(14):4768-77. doi: 10.1093/nar/gkq232. Epub 2010 Apr 12.

44.

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods.

Adler P, Kolde R, Kull M, Tkachenko A, Peterson H, Reimand J, Vilo J.

Genome Biol. 2009;10(12):R139. doi: 10.1186/gb-2009-10-12-r139. Epub 2009 Dec 4.

45.

The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.

Schulz H, Kolde R, Adler P, Aksoy I, Anastassiadis K, Bader M, Billon N, Boeuf H, Bourillot PY, Buchholz F, Dani C, Doss MX, Forrester L, Gitton M, Henrique D, Hescheler J, Himmelbauer H, Hübner N, Karantzali E, Kretsovali A, Lubitz S, Pradier L, Rai M, Reimand J, Rolletschek A, Sachinidis A, Savatier P, Stewart F, Storm MP, Trouillas M, Vilo J, Welham MJ, Winkler J, Wobus AM, Hatzopoulos AK; Functional Genomics in Embryonic Stem Cells Consortium.

PLoS One. 2009 Sep 3;4(9):e6804. doi: 10.1371/journal.pone.0006804.

46.

VisHiC--hierarchical functional enrichment analysis of microarray data.

Krushevskaya D, Peterson H, Reimand J, Kull M, Vilo J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W587-92. doi: 10.1093/nar/gkp435. Epub 2009 May 29.

47.

Ranking genes by their co-expression to subsets of pathway members.

Adler P, Peterson H, Agius P, Reimand J, Vilo J.

Ann N Y Acad Sci. 2009 Mar;1158:1-13. doi: 10.1111/j.1749-6632.2008.03747.x.

PMID:
19348627
48.

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance.

Reimand J, Tooming L, Peterson H, Adler P, Vilo J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W452-9. doi: 10.1093/nar/gkn230. Epub 2008 May 6.

49.

KEGGanim: pathway animations for high-throughput data.

Adler P, Reimand J, Jänes J, Kolde R, Peterson H, Vilo J.

Bioinformatics. 2008 Feb 15;24(4):588-90. Epub 2007 Dec 1.

PMID:
18056068
50.

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

Reimand J, Kull M, Peterson H, Hansen J, Vilo J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200. Epub 2007 May 3.

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