Photo of Chris Sander, PhD

Chris Sander, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 582-9717


chris@sanderlab.org

Photo of Chris Sander, PhD

Dana-Farber Cancer Institute
Phone: (617) 582-9717


chris@sanderlab.org

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Chris Sander, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Professor, Cell Biology, Harvard Medical School
  • Director, cBio Center, Dana-Farber Cancer Institute

DF/HCC PROGRAM AFFILIATION

Research Abstract

The overall goal of the work in the Sander lab is to solve biological problems using quantitative methods from bioinformatics, statistical physics, data sciences, statistics, computer science, and mathematics. We apply these computational methods to build predictive network models of molecular and cell-cell interactions, to support cancer precision medicine, and to make discoveries in structural and evolutionary biology.

Sander is an internationally recognized expert in computational and systems biology, cancer biology, and structural biology. He has extensive experience in cancer genomics, is a leader in The Cancer Genome Atlas (TCGA) project, and his group created the cBioPortal for Cancer Genomics. Sander’s laboratory has developed quantitative computational network models of cancer cells, which are predictive of drug response. His group has developed algorithms for pathway analysis and the design of combination therapies, with translational collaborations in melanoma, sarcoma, glioblastoma, kidney cancer, and prostate cancer.

His current research includes: (1) deriving quantitatively predictive network models from high-throughput molecular profiling; (2) discovering molecular processes responsible for oncogenesis and response to therapy across different cancer types; (3) rendering human biological knowledge computable and accessible, as an aid to biomedical discovery (cBioPortal, Pathway Commons); and (4) using evolutionary constraints derived from rich sequence information to predict previously unknown 3D structures of proteins and RNAs and to identify functional sites on both known and unknown structures.

Publications from Harvard Catalyst Profiles

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  • Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE, , Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol 2022. PubMed
  • Li X, Dowling EK, Yan G, Dereli Z, Bozorgui B, Imanirad P, Elnaggar JH, Luna A, Menter DG, Pilie PG, Yap TA, Kopetz S, Sander C, Korkut A. Precision combination therapies based on recurrent oncogenic co-alterations. 2022. PubMed
  • Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase 2022. Nucleic Acids Res 2021. PubMed
  • Franz A, Coscia F, Shen C, Charaoui L, Mann M, Sander C. Molecular response to PARP1 inhibition in ovarian cancer cells as determined by mass spectrometry based proteomics. 2021; 14:140. PubMed
  • Sinha R, Luna A, Schultz N, Sander C. A pan-cancer survey of cell line tumor similarity by feature-weighted molecular profiles. Cell Rep Methods 2021; 1:100039. PubMed
  • Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, Vaca Jacome AS, Peckner R, Christianson KE, Jaffe JD, Spellman PT, Aslan JE, Sander C, Demir E. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. 2021; 2:100257. PubMed
  • Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, Ashkenazy H, Ben-Tal N, Bromberg Y, Goldberg T, Kajan L, O'Donoghue S, Sander C, Schafferhans A, Schlessinger A, Vriend G, Mirdita M, Gawron P, Gu W, Jarosz Y, Trefois C, Steinegger M, Schneider R, Rost B. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res 2021. PubMed
  • Kenner B, Chari ST, Kelsen D, Klimstra DS, Pandol SJ, Rosenthal M, Rustgi AK, Taylor JA, Yala A, Abul-Husn N, Andersen DK, Bernstein D, Brunak S, Canto MI, Eldar YC, Fishman EK, Fleshman J, Go VLW, Holt JM, Field B, Goldberg A, Hoos W, Iacobuzio-Donahue C, Li D, Lidgard G, Maitra A, Matrisian LM, Poblete S, Rothschild L, Sander C, Schwartz LH, Shalit U, Srivastava S, Wolpin B. Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. Pancreas 2021; 50:251-279. PubMed
  • Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Syst 2021; 12:128-140.e4. PubMed
  • Joshi S, Gomes ED, Wang T, Corben A, Taldone T, Gandu S, Xu C, Sharma S, Buddaseth S, Yan P, Chan LYL, Gokce A, Rajasekhar VK, Shrestha L, Panchal P, Almodovar J, Digwal CS, Rodina A, Merugu S, Pillarsetty N, Miclea V, Peter RI, Wang W, Ginsberg SD, Tang L, Mattar M, de Stanchina E, Yu KH, Lowery M, Grbovic-Huezo O, O'Reilly EM, Janjigian Y, Healey JH, Jarnagin WR, Allen PJ, Sander C, Erdjument-Bromage H, Neubert TA, Leach SD, Chiosis G. Pharmacologically controlling protein-protein interactions through epichaperomes for therapeutic vulnerability in cancer. Commun Biol 2021; 4:1333. PubMed
  • Luna A, Elloumi F, Varma S, Wang Y, Rajapakse VN, Aladjem MI, Robert J, Sander C, Pommier Y, Reinhold WC. CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. Nucleic Acids Res 2021; 49:D1083-D1093. PubMed
  • Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C. Author-sourced capture of pathway knowledge in computable form using Biofactoid. Elife 2021. PubMed
  • Shin JE, Riesselman AJ, Kollasch AW, McMahon C, Simon E, Sander C, Manglik A, Kruse AC, Marks DS. Protein design and variant prediction using autoregressive generative models. Nat Commun 2021; 12:2403. PubMed
  • Luna A, Siper MC, Korkut A, Durupinar F, Dogrusoz U, Aslan JE, Sander C, Demir E, Babur O. Analyzing causal relationships in proteomic profiles using CausalPath. STAR Protoc 2021; 2:100955. PubMed
  • Yuan C, Babic A, Khalaf N, Nowak JA, Brais LK, Rubinson DA, Ng K, Aguirre AJ, Pandharipande PV, Fuchs CS, Giovannucci EL, Stampfer MJ, Rosenthal MH, Sander C, Kraft P, Wolpin BM. Diabetes, Weight Change, and Pancreatic Cancer Risk. JAMA Oncol 2020. PubMed
  • Nyman E, Stein RR, Jing X, Wang W, Marks B, Zervantonakis IK, Korkut A, Gauthier NP, Sander C. Perturbation biology links temporal protein changes to drug responses in a melanoma cell line. PLoS Comput. Biol. 2020; 16:e1007909. PubMed
  • Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC, . Systematic Assessment of Tumor Purity and Its Clinical Implications. JCO Precis Oncol 2020. PubMed
  • Liu EM, Luna A, Dong G, Sander C. netboxr: Automated discovery of biological process modules by network analysis in R. PLoS ONE 2020; 15:e0234669. PubMed
  • Reguant R, Antipin Y, Sheridan R, Dallago C, Diamantoukos D, Luna A, Sander C, Gauthier NP. AlignmentViewer: Sequence Analysis of Large Protein Families. F1000Res 2020. PubMed
  • Stiffler MA, Poelwijk FJ, Brock KP, Stein RR, Riesselman A, Teyra J, Sidhu SS, Marks DS, Gauthier NP, Sander C. Protein Structure from Experimental Evolution. Cell Syst 2019. PubMed
  • Sala D, Huang YJ, Cole CA, Snyder DA, Liu G, Ishida Y, Swapna GVT, Brock KP, Sander C, Fidelis K, Kryshtafovych A, Inouye M, Tejero R, Valafar H, Rosato A, Montelione GT. Protein structure prediction assisted with sparse NMR data in CASP13. Proteins 2019; 87:1315-1332. PubMed
  • Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience 2019; 21:664-680. PubMed
  • Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res 2019. PubMed
  • Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nat Commun 2019; 10:3682. PubMed
  • Rollins NJ, Brock KP, Poelwijk FJ, Stiffler MA, Gauthier NP, Sander C, Marks DS. Inferring protein 3D structure from deep mutation scans. Nat Genet 2019; 51:1170-1176. PubMed
  • Saito Y, Li L, Coyaud E, Luna A, Sander C, Raught B, Asara JM, Brown M, Muthuswamy SK. LLGL2 rescues nutrient stress by promoting leucine uptake in ER breast cancer. Nature 2019; 569:275-279. PubMed
  • Xu J, Reznik E, Lee HJ, Gundem G, Jonsson P, Sarungbam J, Bialik A, Sanchez-Vega F, Creighton CJ, Hoekstra J, Zhang L, Sajjakulnukit P, Kremer D, Tolstyka Z, Casuscelli J, Stirdivant S, Tang J, Schultz N, Jeng P, Dong Y, Su W, Cheng EH, Russo P, Coleman JA, Papaemmanuil E, Chen YB, Reuter VE, Sander C, Kennedy SR, Hsieh JJ, Lyssiotis CA, Tickoo SK, Hakimi AA. Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma. Elife 2019. PubMed
  • Huang YJ, Brock KP, Ishida Y, Swapna GVT, Inouye M, Marks DS, Sander C, Montelione GT. Combining Evolutionary Covariance and NMR Data for Protein Structure Determination. Methods Enzymol 2019; 614:363-392. PubMed
  • Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience 2018; 10:247-264. PubMed
  • Hopf TA, Green AG, Schubert B, Mersmann S, Schärfe CPI, Ingraham JB, Toth-Petroczy A, Brock K, Riesselman AJ, Palmedo P, Kang C, Sheridan R, Draizen EJ, Dallago C, Sander C, Marks DS. The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics 2018. PubMed
  • Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, , Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 2018; 34:211-224.e6. PubMed
  • Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, , de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, , Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. PubMed
  • Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, , Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 2018; 173:321-337.e10. PubMed
  • Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, , Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep 2018; 23:172-180.e3. PubMed
  • Reznik E, Luna A, Aksoy BA, Liu EM, La K, Ostrovnaya I, Creighton CJ, Hakimi AA, Sander C. A Landscape of Metabolic Variation across Tumor Types. Cell Syst 2018; 6:301-313.e3. PubMed
  • Ebhardt HA, Root A, Liu Y, Gauthier NP, Sander C, Aebersold R. Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. NPJ Syst Biol Appl 2018; 4:26. PubMed
  • 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; 8:15165. PubMed
  • Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol 2017; 35:128-135. PubMed
  • 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; 9:4. PubMed
  • Reznik E, Wang Q, La K, Schultz N, Sander C. Mitochondrial respiratory gene expression is suppressed in many cancers. Elife 2017. PubMed
  • Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, Clemons PA. CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. Database (Oxford) 2017. PubMed
  • Şenbabaoğlu 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; 17:231. PubMed
  • Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell 2016; 165:963-75. PubMed
  • Luna A, Babur Ö, Aksoy BA, Demir E, Sander C. PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics 2016; 32:1262-4. PubMed
  • 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; 32:1272-4. PubMed
  • Reznik E, Miller ML, Şenbabaoğlu 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. PubMed
  • Şenbabaoğlu 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; 12:e1004765. PubMed
  • 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; 44:D986-91. PubMed
  • 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; 1:197-209. PubMed
  • 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. PubMed
  • 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; 16:45. PubMed
  • 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:e97213. PubMed
  • Huang YJ, Brock KP, Sander C, Marks DS, Montelione GT. A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data. Adv Exp Med Biol ; 1105:153-169. PubMed
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DF/HCC members that share similar concepts* with Chris Sander, PhD but have yet to coauthor a publication with this researcher.

* Concepts are MeSH terms, automatically derived from member publications

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