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profileChris Sander, Ph.D.

TitleProfessor in Residence of Cell Biology
InstitutionHarvard Medical School
DepartmentCell Biology
AddressHarvard Medical School
Armenise Building 6
200 Longwood Ave
Boston MA 02115
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The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
U24CA220457     (SCHULTZ, NIKOLAUS)Aug 1, 2017 - Jul 31, 2022
NIH/NCI
The cBioPortal for Cancer Genomics
Role: Co-Principal Investigator

R01GM106303     (SANDER, CHRIS)May 3, 2013 - Apr 30, 2017
NIH/NIGMS
Accelerated Determination of 3D Structures of Proteins and Complexes
Role: Principal Investigator

U41HG006623     (SANDER, CHRIS)Sep 22, 2012 - Jun 30, 2018
NIH/NHGRI
Pathway Commons: Research Resource for Biological Pathways
Role: Principal Investigator

R01MH097062     (JU, JINGYUE)Sep 10, 2012 - Jul 31, 2017
NIH/NIMH
Genomic Approaches to Deciphering Memory Circuits
Role: Co-Principal Investigator

U54CA148967     (SANDER, CHRIS)May 1, 2010 - Feb 28, 2015
NIH/NCI
Systems Biology of Diversity in Cancer
Role: Principal Investigator

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 06 27; 19(13):2878-2880. PMID: 28658632.
    View in: PubMed
  2. Sinha R, Winer AG, Chevinsky M, Jakubowski C, Chen YB, Dong Y, Tickoo SK, Reuter VE, Russo P, Coleman JA, Sander C, Hsieh JJ, Hakimi AA. Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection. Nat Commun. 2017 May 10; 8:15165. PMID: 28489074.
    View in: PubMed
  3. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 Mar 14; 18(11):2780-2794. PMID: 28297679.
    View in: PubMed
  4. Senbabaoglu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2017 Mar 01; 18(1):46. PMID: 28249590.
    View in: PubMed
  5. Gao J, Chang MT, Johnsen HC, Gao SP, Sylvester BE, Sumer SO, Zhang H, Solit DB, Taylor BS, Schultz N, Sander C. 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. Genome Med. 2017 Jan 23; 9(1):4. PMID: 28115009.
    View in: PubMed
  6. Reznik E, Wang Q, La K, Schultz N, Sander C. Mitochondrial respiratory gene expression is suppressed in many cancers. Elife. 2017 Jan 18; 6. PMID: 28099114.
    View in: PubMed
  7. Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol. 2017 Feb; 35(2):128-135. PMID: 28092658.
    View in: PubMed
  8. Senbabaoglu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2016 Nov 17; 17(1):231. PMID: 27855702.
    View in: PubMed
  9. Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell. 2016 Sep 22; 167(1):158-170.e12. PMID: 27662088.
    View in: PubMed
  10. Okada T, Lee AY, Qin LX, Agaram N, Mimae T, Shen Y, O'Connor R, López-Lago MA, Craig A, Miller ML, Agius P, Molinelli E, Socci ND, Crago AM, Shima F, Sander C, Singer S. Integrin-a10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma. Cancer Discov. 2016 Oct; 6(10):1148-1165. PMID: 27577794.
    View in: PubMed
  11. Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. 2016 Jul 28; 166(3):766-778. PMID: 27453469.
    View in: PubMed
  12. Spada J, Scholz M, Kirsten H, Hensch T, Horn K, Jawinski P, Ulke C, Burkhardt R, Wirkner K, Loeffler M, Hegerl U, Sander C. Genome-wide association analysis of actigraphic sleep phenotypes in the LIFE Adult Study. J Sleep Res. 2016 Dec; 25(6):690-701. PMID: 27126917.
    View in: PubMed
  13. Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell. 2016 May 05; 165(4):963-75. PMID: 27087444; PMCID: PMC5024353 [Available on 05/05/17].
  14. Chen F, Zhang Y, Senbabaoglu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 Mar 15; 14(10):2476-89. PMID: 26947078; PMCID: PMC4794376.
  15. Senbabaoglu Y, Sümer SO, Sánchez-Vega F, Bemis D, Ciriello G, Schultz N, Sander C. A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PLoS Comput Biol. 2016 Feb; 12(2):e1004765. PMID: 26928298; PMCID: PMC4771175.
  16. Reznik E, Miller ML, Senbabaoglu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C. Mitochondrial DNA copy number variation across human cancers. Elife. 2016 Feb 22; 5. PMID: 26901439; PMCID: PMC4775221.
  17. Landa I, Ibrahimpasic T, Boucai L, Sinha R, Knauf JA, Shah RH, Dogan S, Ricarte-Filho JC, Krishnamoorthy GP, Xu B, Schultz N, Berger MF, Sander C, Taylor BS, Ghossein R, Ganly I, Fagin JA. Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. J Clin Invest. 2016 Mar 01; 126(3):1052-66. PMID: 26878173; PMCID: PMC4767360.
  18. Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 2016 Jan 11; 29(1):104-116. PMID: 26766592; PMCID: PMC4809063 [Available on 01/11/17].
  19. Luna A, Babur Ö, Aksoy BA, Demir E, Sander C. PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics. 2016 Apr 15; 32(8):1262-4. PMID: 26685306; PMCID: PMC4824129.
  20. Luna A, Rajapakse VN, Sousa FG, Gao J, Schultz N, Varma S, Reinhold W, Sander C, Pommier Y. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. Bioinformatics. 2016 Apr 15; 32(8):1272-4. PMID: 26635141; PMCID: PMC4907377 [Available on 04/15/17].
  21. Gauthier NP, Reznik E, Gao J, Sumer SO, Schultz N, Sander C, Miller ML. MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. Nucleic Acids Res. 2016 Jan 04; 44(D1):D986-91. PMID: 26590264; PMCID: PMC4702822.
  22. Jawinski P, Sander C, Mauche N, Spada J, Huang J, Schmidt A, Häntzsch M, Burkhardt R, Scholz M, Hegerl U, Hensch T. Brain Arousal Regulation in Carriers of Bipolar Disorder Risk Alleles. Neuropsychobiology. 2015; 72(2):65-73. PMID: 26509803.
    View in: PubMed
  23. Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 08; 163(2):506-19. PMID: 26451490; PMCID: PMC4603750 [Available on 10/08/16].
  24. Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. Cell Syst. 2015 Sep 23; 1(3):197-209. PMID: 27135912; PMCID: PMC4982675.
  25. Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C. Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells. Elife. 2015 Aug 18; 4. PMID: 26284497; PMCID: PMC4539601.
  26. Stein RR, Marks DS, Sander C. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PLoS Comput Biol. 2015 Jul; 11(7):e1004182. PMID: 26225866; PMCID: PMC4520494.
  27. Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. 2015 Sep; 15(18):3193-208. PMID: 26097198; PMCID: PMC4758406.
  28. 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. Pathway and network analysis of cancer genomes. Nat Methods. 2015 Jul; 12(7):615-621. PMID: 26125594; PMCID: PMC4717906.
  29. Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nat Methods. 2015 Aug; 12(8):751-4. PMID: 26121406; PMCID: PMC4521990.
  30. Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. PMID: 26061751; PMCID: PMC4530011 [Available on 12/25/15].
  31. Reznik E, Sander C. Extensive decoupling of metabolic genes in cancer. PLoS Comput Biol. 2015 May; 11(5):e1004176. PMID: 25961905; PMCID: PMC4427321.
  32. Hayat S, Sander C, Marks DS, Elofsson A. All-atom 3D structure prediction of transmembrane ß-barrel proteins from sequences. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):5413-8. PMID: 25858953; PMCID: PMC4418893.
  33. Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, Miller ML, Rekhtman N, Moreira AL, Ibrahim F, Bruggeman C, Gasmi B, Zappasodi R, Maeda Y, Sander C, Garon EB, Merghoub T, Wolchok JD, Schumacher TN, Chan TA. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015 Apr 03; 348(6230):124-8. PMID: 25765070; PMCID: PMC4993154.
  34. Erson-Omay EZ, Çaglayan AO, Schultz N, Weinhold N, Omay SB, Özduman K, Köksal Y, Li J, Serin Harmanci A, Clark V, Carrión-Grant G, Baranoski J, Çaglar C, Barak T, Coskun S, Baran B, Köse D, Sun J, Bakircioglu M, Moliterno Günel J, Pamir MN, Mishra-Gorur K, Bilguvar K, Yasuno K, Vortmeyer A, Huttner AJ, Sander C, Günel M. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis. Neuro Oncol. 2015 Oct; 17(10):1356-64. PMID: 25740784; PMCID: PMC4578578 [Available on 10/01/16].
  35. Babur Ö, Gönen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E. Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome Biol. 2015 Feb 26; 16:45. PMID: 25887147; PMCID: PMC4381444.
  36. Hakimi AA, Tickoo SK, Jacobsen A, Sarungbam J, Sfakianos JP, Sato Y, Morikawa T, Kume H, Fukayama M, Homma Y, Chen YB, Sankin A, Mano R, Coleman JA, Russo P, Ogawa S, Sander C, Hsieh JJ, Reuter VE. TCEB1-mutated renal cell carcinoma: a distinct genomic and morphological subtype. Mod Pathol. 2015 Jun; 28(6):845-853. PMID: 25676555; PMCID: PMC4449825.
  37. Sousa FG, Matuo R, Tang SW, Rajapakse VN, Luna A, Sander C, Varma S, Simon PH, Doroshow JH, Reinhold WC, Pommier Y. Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity. DNA Repair (Amst). 2015 Apr; 28:107-15. PMID: 25758781; PMCID: PMC4385398.
  38. Kaushik P, Molinelli EJ, Miller ML, Wang W, Korkut A, Liu W, Ju Z, Lu Y, Mills G, Sander C. Spatial normalization of reverse phase protein array data. PLoS One. 2014; 9(12):e97213. PMID: 25501559; PMCID: PMC4264691.
  39. Wanjala J, Taylor BS, Chapinski C, Hieronymus H, Wongvipat J, Chen Y, Nanjangud GJ, Schultz N, Xie Y, Liu S, Lu W, Yang Q, Sander C, Chen Z, Sawyers CL, Carver BS. Identifying actionable targets through integrative analyses of GEM model and human prostate cancer genomic profiling. Mol Cancer Ther. 2015 Jan; 14(1):278-88. PMID: 25381262; PMCID: PMC4297258.
  40. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015 Jan 08; 517(7533):205-8. PMID: 25337874; PMCID: PMC4354891.
  41. Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014 Nov; 46(11):1160-5. PMID: 25261935; PMCID: PMC4217527.
  42. Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife. 2014 Sep 25; 3. PMID: 25255213; PMCID: PMC4360534.
  43. Shinbrot E, Henninger EE, Weinhold N, Covington KR, Göksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 2014 Nov; 24(11):1740-50. PMID: 25228659; PMCID: PMC4216916.
  44. Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics. 2014 Sep 01; 30(17):i482-8. PMID: 25161237; PMCID: PMC4147911.
  45. Babur Ö, Dogrusoz U, Çakir M, Aksoy BA, Schultz N, Sander C, Demir E. Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics. 2014 Aug 03; 15:642. PMID: 25086704; PMCID: PMC4131037.
  46. Hieronymus H, Schultz N, Gopalan A, Carver BS, Chang MT, Xiao Y, Heguy A, Huberman K, Bernstein M, Assel M, Murali R, Vickers A, Scardino PT, Sander C, Reuter V, Taylor BS, Sawyers CL. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A. 2014 Jul 29; 111(30):11139-44. PMID: 25024180; PMCID: PMC4121784.
  47. Rendleman J, Antipin Y, Reva B, Adaniel C, Przybylo JA, Dutra-Clarke A, Hansen N, Heguy A, Huberman K, Borsu L, Paltiel O, Ben-Yehuda D, Brown JR, Freedman AS, Sander C, Zelenetz A, Klein RJ, Shao Y, Lacher M, Vijai J, Offit K, Kirchhoff T. Genetic variation in DNA repair pathways and risk of non-Hodgkin's lymphoma. PLoS One. 2014; 9(7):e101685. PMID: 25010664; PMCID: PMC4092067.
  48. Oricchio E, Ciriello G, Jiang M, Boice MH, Schatz JH, Heguy A, Viale A, de Stanchina E, Teruya-Feldstein J, Bouska A, McKeithan T, Sander C, Tam W, Seshan VE, Chan WC, Chaganti RS, Wendel HG. Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. J Exp Med. 2014 Jun 30; 211(7):1379-91. PMID: 24913233; PMCID: PMC4076578.
  49. Spada J, Sander C, Burkhardt R, Häntzsch M, Mergl R, Scholz M, Hegerl U, Hensch T. Genetic association of objective sleep phenotypes with a functional polymorphism in the neuropeptide S receptor gene. PLoS One. 2014; 9(6):e98789. PMID: 24896296; PMCID: PMC4045816.
  50. Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W337-43. PMID: 24799431; PMCID: PMC4086098.
  51. Aksoy BA, Demir E, Babur Ö, Wang W, Jing X, Schultz N, Sander C. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics. 2014 Jul 15; 30(14):2051-9. PMID: 24665131; PMCID: PMC4080742.
  52. Voss MH, Hakimi AA, Pham CG, Brannon AR, Chen YB, Cunha LF, Akin O, Liu H, Takeda S, Scott SN, Socci ND, Viale A, Schultz N, Sander C, Reuter VE, Russo P, Cheng EH, Motzer RJ, Berger MF, Hsieh JJ. Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy. Clin Cancer Res. 2014 Apr 01; 20(7):1955-64. PMID: 24622468; PMCID: PMC4140619.
  53. Gao J, Ciriello G, Sander C, Schultz N. Collection, integration and analysis of cancer genomic profiles: from data to insight. Curr Opin Genet Dev. 2014 Feb; 24:92-8. PMID: 24584084; PMCID: PMC4084973.
  54. Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, Kaushik P, He Q, Mills G, Solit DB, Pratilas CA, Weigt M, Braunstein A, Pagnani A, Zecchina R, Sander C. Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol. 2013; 9(12):e1003290. PMID: 24367245; PMCID: PMC3868523.
  55. Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol. 2013; 9(12):e1003388. PMID: 24348232; PMCID: PMC3861043.
  56. Li L, Shen C, Nakamura E, Ando K, Signoretti S, Beroukhim R, Cowley GS, Lizotte P, Liberzon E, Bair S, Root DE, Tamayo P, Tsherniak A, Cheng SC, Tabak B, Jacobsen A, Hakimi AA, Schultz N, Ciriello G, Sander C, Hsieh JJ, Kaelin WG. SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell. 2013 Dec 09; 24(6):738-50. PMID: 24332042; PMCID: PMC3910168.
  57. Hakimi AA, Furberg H, Zabor EC, Jacobsen A, Schultz N, Ciriello G, Mikklineni N, Fiegoli B, Kim PH, Voss MH, Shen H, Laird PW, Sander C, Reuter VE, Motzer RJ, Hsieh JJ, Russo P. An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. J Natl Cancer Inst. 2013 Dec 18; 105(24):1862-70. PMID: 24285872; PMCID: PMC3866155.
  58. Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One. 2013; 8(11):e80306. PMID: 24265805; PMCID: PMC3827191.
  59. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. PMID: 24120142; PMCID: PMC3910500.
  60. Ciriello G, Sinha R, Hoadley KA, Jacobsen AS, Reva B, Perou CM, Sander C, Schultz N. The molecular diversity of Luminal A breast tumors. Breast Cancer Res Treat. 2013 Oct; 141(3):409-20. PMID: 24096568; PMCID: PMC3824397.
  61. Jacobsen A, Silber J, Harinath G, Huse JT, Schultz N, Sander C. Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol. 2013 Nov; 20(11):1325-32. PMID: 24096364; PMCID: PMC3982325.
  62. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013 Oct; 45(10):1127-33. PMID: 24071851; PMCID: PMC4320046.
  63. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849; PMCID: PMC3919969.
  64. Miller ML, Molinelli EJ, Nair JS, Sheikh T, Samy R, Jing X, He Q, Korkut A, Crago AM, Singer S, Schwartz GK, Sander C. Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. Sci Signal. 2013 Sep 24; 6(294):ra85. PMID: 24065146; PMCID: PMC4000046.
  65. Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Using biological pathway data with paxtools. PLoS Comput Biol. 2013; 9(9):e1003194. PMID: 24068901; PMCID: PMC3777916.
  66. Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E. Pattern search in BioPAX models. Bioinformatics. 2014 Jan 01; 30(1):139-40. PMID: 24045775; PMCID: PMC3866551.
  67. Rodchenkov I, Demir E, Sander C, Bader GD. The BioPAX Validator. Bioinformatics. 2013 Oct 15; 29(20):2659-60. PMID: 23918249; PMCID: PMC3789551.
  68. 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. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug; 10(8):723-9. PMID: 23900255; PMCID: PMC3919555.
  69. Iyer G, Al-Ahmadie H, Schultz N, Hanrahan AJ, Ostrovnaya I, Balar AV, Kim PH, Lin O, Weinhold N, Sander C, Zabor EC, Janakiraman M, Garcia-Grossman IR, Heguy A, Viale A, Bochner BH, Reuter VE, Bajorin DF, Milowsky MI, Taylor BS, Solit DB. Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol. 2013 Sep 01; 31(25):3133-40. PMID: 23897969; PMCID: PMC3753703.
  70. Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C, Miller ML. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods. 2013 Aug; 10(8):768-73. PMID: 23817070; PMCID: PMC4002004.
  71. Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C. PiHelper: an open source framework for drug-target and antibody-target data. Bioinformatics. 2013 Aug 15; 29(16):2071-2. PMID: 23766416; PMCID: PMC3722529.
  72. Ho AS, Kannan K, Roy DM, Morris LG, Ganly I, Katabi N, Ramaswami D, Walsh LA, Eng S, Huse JT, Zhang J, Dolgalev I, Huberman K, Heguy A, Viale A, Drobnjak M, Leversha MA, Rice CE, Singh B, Iyer NG, Leemans CR, Bloemena E, Ferris RL, Seethala RR, Gross BE, Liang Y, Sinha R, Peng L, Raphael BJ, Turcan S, Gong Y, Schultz N, Kim S, Chiosea S, Shah JP, Sander C, Lee W, Chan TA. The mutational landscape of adenoid cystic carcinoma. Nat Genet. 2013 Jul; 45(7):791-8. PMID: 23685749; PMCID: PMC3708595.
  73. Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, Takeda S, Voss MH, Tickoo SK, Reuter VE, Russo P, Cheng EH, Sander C, Motzer RJ, Hsieh JJ. Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res. 2013 Jun 15; 19(12):3259-67. PMID: 23620406; PMCID: PMC3708609.
  74. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013 Apr 02; 6(269):pl1. PMID: 23550210; PMCID: PMC4160307.
  75. Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N. Using MEMo to discover mutual exclusivity modules in cancer. Curr Protoc Bioinformatics. 2013 Mar; Chapter 8:Unit 8.17. PMID: 23504936.
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  76. Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A. 2013 Mar 12; 110(11):4245-50. PMID: 23431203; PMCID: PMC3600490.
  77. Domcke S, Sinha R, Levine DA, Sander C, Schultz N. Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun. 2013; 4:2126. PMID: 23839242; PMCID: PMC3715866.
  78. Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne PH, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. J Pathol. 2013 Jan; 229(1):99-110. PMID: 22899370; PMCID: PMC3926301.
  79. Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Biotechnol. 2012 Nov; 30(11):1072-80. PMID: 23138306; PMCID: PMC4319528.
  80. Mitsiades N, Sung CC, Schultz N, Danila DC, He B, Eedunuri VK, Fleisher M, Sander C, Sawyers CL, Scher HI. Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors. Cancer Res. 2012 Dec 01; 72(23):6142-52. PMID: 22971343; PMCID: PMC3685485.
  81. Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M, Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, Bajorin DF, Berger MF, Taylor BS, Solit DB. Genome sequencing identifies a basis for everolimus sensitivity. Science. 2012 Oct 12; 338(6104):221. PMID: 22923433; PMCID: PMC3633467.
  82. Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012 Jun 22; 149(7):1607-21. PMID: 22579045; PMCID: PMC3641781.
  83. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012 May; 2(5):401-4. PMID: 22588877; PMCID: PMC3956037.
  84. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell. 2012 Apr 27; 149(3):693-707. PMID: 22541438; PMCID: PMC3442366.
  85. Shen R, Mo Q, Schultz N, Seshan VE, Olshen AB, Huse J, Ladanyi M, Sander C. Integrative subtype discovery in glioblastoma using iCluster. PLoS One. 2012; 7(4):e35236. PMID: 22539962; PMCID: PMC3335101.
  86. Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012; 7(3):e34546. PMID: 22479643; PMCID: PMC3315571.
  87. Silber J, Jacobsen A, Ozawa T, Harinath G, Pedraza A, Sander C, Holland EC, Huse JT. miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis. PLoS One. 2012; 7(3):e33844. PMID: 22479456; PMCID: PMC3313940.
  88. Hanrahan AJ, Schultz N, Westfal ML, Sakr RA, Giri DD, Scarperi S, Janakiraman M, Janikariman M, Olvera N, Stevens EV, She QB, Aghajanian C, King TA, Stanchina Ed, Spriggs DR, Heguy A, Taylor BS, Sander C, Rosen N, Levine DA, Solit DB. Genomic complexity and AKT dependence in serous ovarian cancer. Cancer Discov. 2012 Jan; 2(1):56-67. PMID: 22328975; PMCID: PMC3274821.
  89. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. PLoS One. 2011; 6(12):e28766. PMID: 22163331; PMCID: PMC3233603.
  90. Taylor BS, DeCarolis PL, Angeles CV, Brenet F, Schultz N, Antonescu CR, Scandura JM, Sander C, Viale AJ, Socci ND, Singer S. Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov. 2011 Dec; 1(7):587-97. PMID: 22328974; PMCID: PMC3274776.
  91. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011 Dec 06; 108(49):E1293-301. PMID: 22106262; PMCID: PMC3241805.
  92. Hoell JI, Larsson E, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T. RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol. 2011 Nov 13; 18(12):1428-31. PMID: 22081015; PMCID: PMC3230689.
  93. Mankoo PK, Shen R, Schultz N, Levine DA, Sander C. Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. PLoS One. 2011; 6(11):e24709. PMID: 22073136; PMCID: PMC3207809.
  94. Lipchina I, Elkabetz Y, Hafner M, Sheridan R, Mihailovic A, Tuschl T, Sander C, Studer L, Betel D. Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev. 2011 Oct 15; 25(20):2173-86. PMID: 22012620; PMCID: PMC3205587.
  95. Somwar R, Erdjument-Bromage H, Larsson E, Shum D, Lockwood WW, Yang G, Sander C, Ouerfelli O, Tempst PJ, Djaballah H, Varmus HE. Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proc Natl Acad Sci U S A. 2011 Sep 27; 108(39):16375-80. PMID: 21930909; PMCID: PMC3182729.
  96. Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2012 Feb; 22(2):398-406. PMID: 21908773; PMCID: PMC3266046.
  97. Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC. Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell. 2011 Aug 16; 20(2):173-86. PMID: 21840483; PMCID: PMC3176728.
  98. Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011 Sep 01; 39(17):e118. PMID: 21727090; PMCID: PMC3177186.
  99. Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, Decarolis PL, Khanin R, O'Connor R, Mihailovic A, Taylor BS, Sheridan R, Gimble JM, Viale A, Crago A, Antonescu CR, Sander C, Tuschl T, Singer S. Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res. 2011 Sep 01; 71(17):5659-69. PMID: 21693658; PMCID: PMC3165140.
  100. Palaskas N, Larson SM, Schultz N, Komisopoulou E, Wong J, Rohle D, Campos C, Yannuzzi N, Osborne JR, Linkov I, Kastenhuber ER, Taschereau R, Plaisier SB, Tran C, Heguy A, Wu H, Sander C, Phelps ME, Brennan C, Port E, Huse JT, Graeber TG, Mellinghoff IK. 18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Res. 2011 Aug 01; 71(15):5164-74. PMID: 21646475; PMCID: PMC3148325.
  101. Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, Olshen A, Rusch V, Ladanyi M. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet. 2011 Jun 05; 43(7):668-72. PMID: 21642991; PMCID: PMC4643098.
  102. Jörnsten R, Abenius T, Kling T, Schmidt L, Johansson E, Nordling TE, Nordlander B, Sander C, Gennemark P, Funa K, Nilsson B, Lindahl L, Nelander S. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol. 2011 Apr 26; 7:486. PMID: 21525872; PMCID: PMC3101951.
  103. Schultz N, Marenstein DR, De Angelis DA, Wang WQ, Nelander S, Jacobsen A, Marks DS, Massagué J, Sander C. Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-ß pathway and reveal microRNA regulation of TGFBR2. Silence. 2011 Mar 14; 2:3. PMID: 21401928; PMCID: PMC3068080.
  104. Clegg NJ, Couto SS, Wongvipat J, Hieronymus H, Carver BS, Taylor BS, Ellwood-Yen K, Gerald WL, Sander C, Sawyers CL. MYC cooperates with AKT in prostate tumorigenesis and alters sensitivity to mTOR inhibitors. PLoS One. 2011 Mar 04; 6(3):e17449. PMID: 21394210; PMCID: PMC3048873.
  105. Guenther T, Schönknecht P, Becker G, Olbrich S, Sander C, Hesse S, Meyer PM, Luthardt J, Hegerl U, Sabri O. Impact of EEG-vigilance on brain glucose uptake measured with [(18)F]FDG and PET in patients with depressive episode or mild cognitive impairment. Neuroimage. 2011 May 01; 56(1):93-101. PMID: 21276863.
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  106. Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Mol Syst Biol. 2010 Nov 16; 6:433. PMID: 21081925; PMCID: PMC3010119.
  107. Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucleic Acids Res. 2011 Jan; 39(Database issue):D411-9. PMID: 21071423; PMCID: PMC3013697.
  108. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D685-90. PMID: 21071392; PMCID: PMC3013659.
  109. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. PMID: 20829833; PMCID: PMC3001121.
  110. Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010; 11(8):R90. PMID: 20799968; PMCID: PMC2945792.
  111. Brill E, Gobble R, Angeles C, Lagos-Quintana M, Crago A, Laxa B, Decarolis P, Zhang L, Antonescu C, Socci ND, Taylor BS, Sander C, Koff A, Singer S. ZIC1 overexpression is oncogenic in liposarcoma. Cancer Res. 2010 Sep 01; 70(17):6891-901. PMID: 20713527; PMCID: PMC3266950.
  112. Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, Decarolis PL, Shah K, Socci ND, Weir BA, Ho A, Chiang DY, Reva B, Mermel CH, Getz G, Antipin Y, Beroukhim R, Major JE, Hatton C, Nicoletti R, Hanna M, Sharpe T, Fennell TJ, Cibulskis K, Onofrio RC, Saito T, Shukla N, Lau C, Nelander S, Silver SJ, Sougnez C, Viale A, Winckler W, Maki RG, Garraway LA, Lash A, Greulich H, Root DE, Sellers WR, Schwartz GK, Antonescu CR, Lander ES, Varmus HE, Ladanyi M, Sander C, Meyerson M, Singer S. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet. 2010 Aug; 42(8):715-21. PMID: 20601955; PMCID: PMC2911503.
  113. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13; 18(1):11-22. PMID: 20579941; PMCID: PMC3198787.
  114. Babur O, Demir E, Gönen M, Sander C, Dogrusoz U. Discovering modulators of gene expression. Nucleic Acids Res. 2010 Sep; 38(17):5648-56. PMID: 20466809; PMCID: PMC2943625.
  115. Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol. 2010 Apr 20; 6:363. PMID: 20404830; PMCID: PMC2872614.
  116. 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, Cross 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, Gardiner BA, 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, Himmelbaue 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, et al. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. PMID: 20393554; PMCID: PMC2902243.
  117. Xavier JB, Sander C. Principle of system balance for drug interactions. N Engl J Med. 2010 Apr 08; 362(14):1339-40. PMID: 20375413.
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  118. Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS One. 2010 Feb 12; 5(2):e8918. PMID: 20169195; PMCID: PMC2820542.
  119. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010 Jan 12; 11(1):R3. PMID: 20067622; PMCID: PMC2847715.
  120. Mu P, Han YC, Betel D, Yao E, Squatrito M, Ogrodowski P, de Stanchina E, D'Andrea A, Sander C, Ventura A. Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev. 2009 Dec 15; 23(24):2806-11. PMID: 20008931; PMCID: PMC2800095.
  121. Babur O, Dogrusoz U, Demir E, Sander C. ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics. 2010 Feb 01; 26(3):429-31. PMID: 20007251; PMCID: PMC2815657.
  122. Veeriah S, Taylor BS, Meng S, Fang F, Yilmaz E, Vivanco I, Janakiraman M, Schultz N, Hanrahan AJ, Pao W, Ladanyi M, Sander C, Heguy A, Holland EC, Paty PB, Mischel PS, Liau L, Cloughesy TF, Mellinghoff IK, Solit DB, Chan TA. Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet. 2010 Jan; 42(1):77-82. PMID: 19946270; PMCID: PMC4002225.
  123. Andres C, Belloni B, Puchta U, Sander CA, Flaig MJ. Re: Clinical factors associated with Merkel cell polyomavirus infection in Merkel cell carcinoma. J Natl Cancer Inst. 2009 Dec 02; 101(23):1655-6; author reply 1656-7. PMID: 19864638.
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  124. Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E. Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron. 2009 Sep 24; 63(6):803-17. PMID: 19778509; PMCID: PMC2875683.
  125. Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug; 27(8):735-41. PMID: 19668183.
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  126. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 2009 Jun; 27(6):549-55. PMID: 19465925; PMCID: PMC2782465.
  127. Veeriah S, Brennan C, Meng S, Singh B, Fagin JA, Solit DB, Paty PB, Rohle D, Vivanco I, Chmielecki J, Pao W, Ladanyi M, Gerald WL, Liau L, Cloughesy TC, Mischel PS, Sander C, Taylor B, Schultz N, Major J, Heguy A, Fang F, Mellinghoff IK, Chan TA. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A. 2009 Jun 09; 106(23):9435-40. PMID: 19478061; PMCID: PMC2687998.
  128. King JC, Xu J, Wongvipat J, Hieronymus H, Carver BS, Leung DH, Taylor BS, Sander C, Cardiff RD, Couto SS, Gerald WL, Sawyers CL. Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet. 2009 May; 41(5):524-6. PMID: 19396167; PMCID: PMC2898503.
  129. Pratilas CA, Taylor BS, Ye Q, Viale A, Sander C, Solit DB, Rosen N. (V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4519-24. PMID: 19251651; PMCID: PMC2649208.
  130. Yi R, Pasolli HA, Landthaler M, Hafner M, Ojo T, Sheridan R, Sander C, O'Carroll D, Stoffel M, Tuschl T, Fuchs E. DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A. 2009 Jan 13; 106(2):498-502. PMID: 19114655; PMCID: PMC2626731.
  131. 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. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb; 3(1):9-17. PMID: 19383362; PMCID: PMC2930781.
  132. Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS. A specificity map for the PDZ domain family. PLoS Biol. 2008 Sep 30; 6(9):e239. PMID: 18828675; PMCID: PMC2553845.
  133. Taylor BS, Barretina J, Socci ND, Decarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. Functional copy-number alterations in cancer. PLoS One. 2008 Sep 11; 3(9):e3179. PMID: 18784837; PMCID: PMC2527508.
  134. Nelander S, Wang W, Nilsson B, She QB, Pratilas C, Rosen N, Gennemark P, Sander C. Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol. 2008; 4:216. PMID: 18766176; PMCID: PMC2564730.
  135. Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing meta-services for biomedical information extraction. Genome Biol. 2008; 9 Suppl 2:S6. PMID: 18834497; PMCID: PMC2559990.
  136. Müller-Hermelink N, Braumüller H, Pichler B, Wieder T, Mailhammer R, Schaak K, Ghoreschi K, Yazdi A, Haubner R, Sander CA, Mocikat R, Schwaiger M, Förster I, Huss R, Weber WA, Kneilling M, Röcken M. TNFR1 signaling and IFN-gamma signaling determine whether T cells induce tumor dormancy or promote multistage carcinogenesis. Cancer Cell. 2008 Jun; 13(6):507-18. PMID: 18538734.
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  137. Aragues R, Sander C, Oliva B. Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics. 2008 Mar 27; 9:172. PMID: 18371197; PMCID: PMC2330045.
  138. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 2008 Jan; 36(Database issue):D149-53. PMID: 18158296; PMCID: PMC2238905.
  139. Betel D, Sheridan R, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol. 2007 Nov; 3(11):e222. PMID: 17997596; PMCID: PMC2065894.
  140. Singer S, Socci ND, Ambrosini G, Sambol E, Decarolis P, Wu Y, O'Connor R, Maki R, Viale A, Sander C, Schwartz GK, Antonescu CR. Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res. 2007 Jul 15; 67(14):6626-36. PMID: 17638873.
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  141. Randall G, Panis M, Cooper JD, Tellinghuisen TL, Sukhodolets KE, Pfeffer S, Landthaler M, Landgraf P, Kan S, Lindenbach BD, Chien M, Weir DB, Russo JJ, Ju J, Brownstein MJ, Sheridan R, Sander C, Zavolan M, Tuschl T, Rice CM. Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A. 2007 Jul 31; 104(31):12884-9. PMID: 17616579; PMCID: PMC1937561.
  142. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007 Jun 29; 129(7):1401-14. PMID: 17604727; PMCID: PMC2681231.
  143. Cotignola J, Reva B, Mitra N, Ishill N, Chuai S, Patel A, Shah S, Vanderbeek G, Coit D, Busam K, Halpern A, Houghton A, Sander C, Berwick M, Orlow I. Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma. BMC Med Genet. 2007 Mar 08; 8:10. PMID: 17346338; PMCID: PMC1831467.
  144. Fulci V, Chiaretti S, Goldoni M, Azzalin G, Carucci N, Tavolaro S, Castellano L, Magrelli A, Citarella F, Messina M, Maggio R, Peragine N, Santangelo S, Mauro FR, Landgraf P, Tuschl T, Weir DB, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Guarini A, Foà R, Macino G. Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood. 2007 Jun 01; 109(11):4944-51. PMID: 17327404.
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  145. Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B. From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol. 2007 Feb 23; 3(2):e12. PMID: 17319736; PMCID: PMC1808026.
  146. 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. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMID: 17947979; PMCID: PMC3685583.
  147. Reva B, Antipin Y, Sander C. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol. 2007; 8(11):R232. PMID: 17976239; PMCID: PMC2258190.
  148. Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics. 2006 Nov 13; 7:497. PMID: 17101041; PMCID: PMC1660554.
  149. Higgins ME, Claremont M, Major JE, Sander C, Lash AE. CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res. 2007 Jan; 35(Database issue):D721-6. PMID: 17088289; PMCID: PMC1781153.
  150. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T. A novel class of small RNAs bind to MILI protein in mouse testes. Nature. 2006 Jul 13; 442(7099):203-7. PMID: 16751777.
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  151. Vilar JM, Jansen R, Sander C. Signal processing in the TGF-beta superfamily ligand-receptor network. PLoS Comput Biol. 2006 Jan; 2(1):e3. PMID: 16446785; PMCID: PMC1356091.
  152. Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D504-6. PMID: 16381921; PMCID: PMC1347488.
  153. John B, Sander C, Marks DS. Prediction of human microRNA targets. Methods Mol Biol. 2006; 342:101-13. PMID: 16957370.
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  154. Monticelli S, Ansel KM, Xiao C, Socci ND, Krichevsky AM, Thai TH, Rajewsky N, Marks DS, Sander C, Rajewsky K, Rao A, Kosik KS. MicroRNA profiling of the murine hematopoietic system. Genome Biol. 2005; 6(8):R71. PMID: 16086853; PMCID: PMC1273638.
  155. Leaman D, Chen PY, Fak J, Yalcin A, Pearce M, Unnerstall U, Marks DS, Sander C, Tuschl T, Gaul U. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell. 2005 Jul 01; 121(7):1097-108. PMID: 15989958.
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  156. Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev. 2005 Jun 01; 19(11):1288-93. PMID: 15937218; PMCID: PMC1142552.
  157. Cary MP, Bader GD, Sander C. Pathway information for systems biology. FEBS Lett. 2005 Mar 21; 579(8):1815-20. PMID: 15763557.
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  158. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods. 2005 Apr; 2(4):269-76. PMID: 15782219.
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  159. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004 Nov; 2(11):e363. PMID: 15502875; PMCID: PMC521178.
  160. Chang J, Nicolas E, Marks D, Sander C, Lerro A, Buendia MA, Xu C, Mason WS, Moloshok T, Bort R, Zaret KS, Taylor JM. miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol. 2004 Jul; 1(2):106-13. PMID: 17179747.
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  161. Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T. Identification of virus-encoded microRNAs. Science. 2004 Apr 30; 304(5671):734-6. PMID: 15118162.
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  162. Palmedo G, Hantschke M, Rütten A, Mentzel T, Hügel H, Flaig MJ, Yazdi AS, Sander CA, Kutzner H. The T1796A mutation of the BRAF gene is absent in Spitz nevi. J Cutan Pathol. 2004 Mar; 31(3):266-70. PMID: 14984580.
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  163. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 06; 303(5659):808-13. PMID: 14764870.
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  164. 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. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb; 22(2):177-83. PMID: 14755292.
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  165. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003; 5(1):R1. PMID: 14709173; PMCID: PMC395733.
  166. Berriz GF, King OD, Bryant B, Sander C, Roth FP. Characterizing gene sets with FuncAssociate. Bioinformatics. 2003 Dec 12; 19(18):2502-4. PMID: 14668247.
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  167. Vitkup D, Sander C, Church GM. The amino-acid mutational spectrum of human genetic disease. Genome Biol. 2003; 4(11):R72. PMID: 14611658; PMCID: PMC329120.
  168. Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 2003 Apr 12; 19(6):717-26. PMID: 12691983.
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  169. Schmid-Wendtner MH, Berking C, Baumert J, Schmidt M, Sander CA, Plewig G, Volkenandt M. Cutaneous melanoma in childhood and adolescence: an analysis of 36 patients. J Am Acad Dermatol. 2002 Jun; 46(6):874-9. PMID: 12063484.
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