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Items: 41

1.

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities.

Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P, Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R.

J Cell Biol. 2018 Aug 6;217(8):2951-2974. doi: 10.1083/jcb.201804042. Epub 2018 Jun 19.

2.

Exercise-responsive phosphoproteins in the heart.

Guo H, Isserlin R, Emili A, Burniston JG.

J Mol Cell Cardiol. 2017 Oct;111:61-68. doi: 10.1016/j.yjmcc.2017.08.001. Epub 2017 Aug 4.

PMID:
28826663
3.

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

El-Hachem N, Gendoo DMA, Ghoraie LS, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader GD, Goldenberg A, Haibe-Kains B.

Cancer Res. 2017 Jun 1;77(11):3057-3069. doi: 10.1158/0008-5472.CAN-17-0096. Epub 2017 Mar 17.

4.

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations.

Kucera M, Isserlin R, Arkhangorodsky A, Bader GD.

F1000Res. 2016 Jul 15;5:1717. eCollection 2016.

5.

Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy.

Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12592-12597. Epub 2016 Oct 14.

6.

Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors.

Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G.

Cell Stem Cell. 2016 Sep 1;19(3):383-96. doi: 10.1016/j.stem.2016.06.008. Epub 2016 Jul 14.

7.

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.

Lechman ER, Gentner B, Ng SWK, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JCY, Naldini L, Dick JE.

Cancer Cell. 2016 Apr 11;29(4):602-606. doi: 10.1016/j.ccell.2016.03.015. No abstract available.

8.

Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis.

Kamdar SN, Ho LT, Kron KJ, Isserlin R, van der Kwast T, Zlotta AR, Fleshner NE, Bader G, Bapat B.

Clin Epigenetics. 2016 Mar 15;8:32. doi: 10.1186/s13148-016-0195-4. eCollection 2016.

9.

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.

Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE.

Cancer Cell. 2016 Feb 8;29(2):214-28. doi: 10.1016/j.ccell.2015.12.011. Epub 2016 Jan 28. Erratum in: Cancer Cell. 2016 Apr 11;29(4):602-6.

10.

Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages.

Chamberlain MD, Wells LA, Lisovsky A, Guo H, Isserlin R, Talior-Volodarsky I, Mahou R, Emili A, Sefton MV.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10673-8. doi: 10.1073/pnas.1508826112. Epub 2015 Aug 10.

11.

A Call for Systematic Research on Solute Carriers.

C├ęsar-Razquin A, Snijder B, Frappier-Brinton T, Isserlin R, Gyimesi G, Bai X, Reithmeier RA, Hepworth D, Hediger MA, Edwards AM, Superti-Furga G.

Cell. 2015 Jul 30;162(3):478-87. doi: 10.1016/j.cell.2015.07.022. Review.

12.

Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.

Guo H, Garcia-Vedrenne AE, Isserlin R, Lugowski A, Morada A, Sun A, Miao Y, Kuzmanov U, Wan C, Ma H, Foltz K, Emili A.

Proteomics. 2015 Dec;15(23-24):4080-95. doi: 10.1002/pmic.201500159. Epub 2015 Sep 7.

PMID:
26227301
13.

Cardioprotective Signature of Short-Term Caloric Restriction.

Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T, Li RK, Fish JE, Bader GD, Husain M.

PLoS One. 2015 Jun 22;10(6):e0130658. doi: 10.1371/journal.pone.0130658. eCollection 2015.

14.

Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action.

Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G.

Biochem J. 2015 Jul 1;469(1):71-82. doi: 10.1042/BJ20141455. Epub 2015 Apr 27.

15.

Social Network: a Cytoscape app for visualizing co-authorship networks.

Kofia V, Isserlin R, Buchan AM, Bader GD.

Version 3. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:481. doi: 10.12688/f1000research.6804.3. eCollection 2015.

16.

Large-scale label-free phosphoproteomics: from technology to data interpretation.

Guo H, Isserlin R, Lugowski A, Kuzmanov U, Emili A.

Bioanalysis. 2014 Sep;6(18):2403-20. doi: 10.4155/bio.14.188. Review.

PMID:
25384593
17.

Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.

Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A.

Mol Biosyst. 2015 Jan;11(1):239-51. doi: 10.1039/c4mb00265b. Epub 2014 Oct 31.

18.

Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.

Isserlin R, Merico D, Voisin V, Bader GD.

F1000Res. 2014 Jul 1;3:141. doi: 10.12688/f1000research.4536.1. eCollection 2014.

19.

A draft map of the human proteome.

Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A.

Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302.

20.

Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis.

Dagley LF, Croft NP, Isserlin R, Olsen JB, Fong V, Emili A, Purcell AW.

Mol Cell Proteomics. 2014 Mar;13(3):679-700. doi: 10.1074/mcp.M113.033340. Epub 2013 Dec 20.

21.

Global proteomic profiling and enrichment maps of dilated cardiomyopathy.

Isserlin R, Merico D, Emili A.

Methods Mol Biol. 2013;1005:53-66. doi: 10.1007/978-1-62703-386-2_5.

PMID:
23606248
22.

Integrative network analysis of signaling in human CD34(+) hematopoietic progenitor cells by global phosphoproteomic profiling using TiO2 enrichment combined with 2D LC-MS/MS and pathway mapping.

Guo H, Isserlin R, Chen X, Wang W, Phanse S, Zandstra PW, Paddison PJ, Emili A.

Proteomics. 2013 Apr;13(8):1325-33. doi: 10.1002/pmic.201200369. Epub 2013 Mar 6.

23.

Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map.

Merico D, Isserlin R, Bader GD.

Methods Mol Biol. 2011;781:257-77. doi: 10.1007/978-1-61779-276-2_12.

PMID:
21877285
24.

Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma.

Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DT, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM.

Cancer Cell. 2011 Aug 16;20(2):143-57. doi: 10.1016/j.ccr.2011.07.007.

25.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

26.

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.

Oesper L, Merico D, Isserlin R, Bader GD.

Source Code Biol Med. 2011 Apr 7;6:7. doi: 10.1186/1751-0473-6-7.

27.

Too many roads not taken.

Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH.

Nature. 2011 Feb 10;470(7333):163-5. doi: 10.1038/470163a. No abstract available.

PMID:
21307913
28.

The Biomolecular Interaction Network Database in PSI-MI 2.5.

Isserlin R, El-Badrawi RA, Bader GD.

Database (Oxford). 2011 Jan 12;2011:baq037. doi: 10.1093/database/baq037. Print 2011.

29.

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

Merico D, Isserlin R, Stueker O, Emili A, Bader GD.

PLoS One. 2010 Nov 15;5(11):e13984. doi: 10.1371/journal.pone.0013984.

30.

Constitutively active calcineurin induces cardiac endoplasmic reticulum stress and protects against apoptosis that is mediated by alpha-crystallin-B.

Bousette N, Chugh S, Fong V, Isserlin R, Kim KH, Volchuk A, Backx PH, Liu P, Kislinger T, MacLennan DH, Emili A, Gramolini AO.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18481-6. doi: 10.1073/pnas.1013555107. Epub 2010 Oct 11.

31.

A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.

Mak AB, Ni Z, Hewel JA, Chen GI, Zhong G, Karamboulas K, Blakely K, Smiley S, Marcon E, Roudeva D, Li J, Olsen JB, Wan C, Punna T, Isserlin R, Chetyrkin S, Gingras AC, Emili A, Greenblatt J, Moffat J.

Mol Cell Proteomics. 2010 May;9(5):811-23. doi: 10.1074/mcp.M000002-MCP201. Epub 2010 Mar 19.

32.

Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.

Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A.

Proteomics. 2010 Mar;10(6):1316-27. doi: 10.1002/pmic.200900412.

33.

Large-scale characterization and analysis of the murine cardiac proteome.

Bousette N, Kislinger T, Fong V, Isserlin R, Hewel JA, Emil A, Gramolini AO.

J Proteome Res. 2009 Apr;8(4):1887-901.

PMID:
19714876
34.

Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery.

Isserlin R, Emili A.

Curr Opin Mol Ther. 2008 Jun;10(3):231-42. Review.

PMID:
18535930
35.

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses.

Gramolini AO, Kislinger T, Alikhani-Koopaei R, Fong V, Thompson NJ, Isserlin R, Sharma P, Oudit GY, Trivieri MG, Fagan A, Kannan A, Higgins DG, Huedig H, Hess G, Arab S, Seidman JG, Seidman CE, Frey B, Perry M, Backx PH, Liu PP, MacLennan DH, Emili A.

Mol Cell Proteomics. 2008 Mar;7(3):519-33. Epub 2007 Nov 30.

36.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

37.

Structure-templated predictions of novel protein interactions from sequence information.

Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, Hogue CW.

PLoS Comput Biol. 2007 Sep;3(9):1783-9.

38.
39.

The Biomolecular Interaction Network Database and related tools 2005 update.

Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, Hogue CW.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24.

40.

Analysis of domain correlations in yeast protein complexes.

Betel D, Isserlin R, Hogue CW.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i55-62.

PMID:
15262781
41.

SeqHound: biological sequence and structure database as a platform for bioinformatics research.

Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.

BMC Bioinformatics. 2002 Oct 25;3:32. Epub 2002 Oct 25.

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