Publications

Author ID

2021 Publications

Lopez-Bujanda ZA, Haffner MC, Chaimowitz MG, Chowdhury N, Venturini NJ, Patel RA, Obradovic A, Hansen CS, Jacków J, Maynard JP, Sfanos KS, Abate-Shen C, Bieberich CJ, Hurley PJ, Selby MJ, Korman AJ, Christiano AM, De Marzo AM, Drake CG. 2021. Castration-mediated IL-8 promotes myeloid infiltration and prostate cancer progression.. Nat Cancer. 2(8):803-818.▶ Go to Pubmed

Arrieta VA, Chen AX, J Kane R, Kang SJae, Kassab C, Dmello C, Zhao J, Burdett KB, Upadhyayula PS, Lee-Chang C, Shilati J, Jaishankar D, Chen L, Gould A, Zhang D, Yuan J, Zhao W, Ling X, Burks JK, Laffleur B, Amidei C, Bruce JN, Lukas RV, Yamaguchi JT, Cieremans D, Rothschild G, Basu U, McCord M, Brat DJ, Zhang H, Cooper LAD, Zhang B, Sims P, Cloughesy TF, Prins R, Canoll P, Stupp R, Heimberger AB, Horbinski C, Iwamoto FM, Rabadan R, Sonabend AM. 2021. ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.. Nat Cancer. 2(12):1372-1386.▶ Go to Pubmed

Son J, Ding H, Farb TB, Efanov AM, Sun J, Gore JL, Syed SK, Lei Z, Wang Q, Accili D, Califano A. 2021. BACH2 inhibition reverses β cell failure in type 2 diabetes models.. J Clin Invest. 131(24)▶ Go to Pubmed

Blockus H, Rolotti SV, Szoboszlay M, Peze-Heidsieck E, Ming T, Schroeder A, Apostolo N, Vennekens KM, Katsamba PS, Bahna F, Mannepalli S, Ahlsen G, Honig B, Shapiro L, de Wit J, Losonczy A, Polleux F. 2021. Synaptogenic activity of the axon guidance molecule Robo2 underlies hippocampal circuit function.. Cell Rep. 37(3):109828.▶ Go to Pubmed

AlQuraishi M, Sorger PK. 2021. Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.. Nat Methods. 18(10):1169-1180.▶ Go to Pubmed

Park S, Rong L, Owczarek TB, Di Bernardo M, Shoulson RL, Chua C-W, Kim JY, Lankarani A, Chakrapani P, Syed T, McKiernan JM, Solit DB, Shen MM, Al-Ahmadie HA, Abate-Shen C. 2021. Novel mouse models of bladder cancer identify a prognostic signature associated with risk of disease progression.. Cancer Res. ▶ Go to Pubmed

Prieto C, Nguyen DTT, Liu Z, Wheat J, Perez A, Gourkanti S, Chou T, Barin E, Velleca A, Rohwetter T, Chow A, Taggart J, Savino AM, Hoskova K, Dhodapkar M, Schurer A, Barlowe TS, Vu LP, Leslie C, Steidl U, Rabadan R, Kharas MG. 2021. Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia.. Nat Cancer. 2:741-757.▶ Go to Pubmed

González-Buendia E, Zhao J, Wang L, Mukherjee S, Zhang D, Arrieta VA, Feldstein E, J Kane R, Kang SJae, Lee-Chang C, Mahajan A, Chen L, Realubit R, Karan C, Magnuson L, Horbinski C, Marshall SA, Sarkaria JN, Mohyeldin A, Nakano I, Bansal M, James CD, Brat DJ, Ahmed A, Canoll P, Rabadan R, Shilatifard A, Sonabend AM. 2021. TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas.. Clin Cancer Res. ▶ Go to Pubmed

AlQuraishi M. 2021. Protein-structure prediction revolutionized.. Nature. 596(7873):487-488.▶ Go to Pubmed

Gomez K, Rabadan R. 2021. A persistent look at how tumours evade therapy.. Nature. 596(7873):491-493.▶ Go to Pubmed

Patiño-Galindo JAngel, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R. 2021. Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.. Genome Med. 13(1):124.▶ Go to Pubmed

Bouatta N, Sorger P, AlQuraishi M. 2021. Protein structure prediction by AlphaFold2: are attention and symmetries all you need? Acta Crystallogr D Struct Biol. 77(Pt 8):982-991.▶ Go to Pubmed

Landsburg DJ, Barta SK, Ramchandren R, Batlevi C, Iyer S, Kelly K, Micallef IN, Smith SM, Stevens DA, Alvarez M, Califano A, Shen Y, Bosker G, Parker J, Soikes R, Martinez E, von Roemeling R, Martell RE, Oki Y. 2021. Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses.. Br J Haematol. ▶ Go to Pubmed

Sweet K, Bhatnagar B, Döhner H, Donnellan W, Frankfurt O, Heuser M, Kota V, Liu H, Raffoux E, Roboz GJ, Röllig C, Showel MM, Strickland SA, Vives S, Tang S, Unger TJ, Joshi A, Shen Y, Alvarez MJ, Califano A, Crochiere M, Landesman Y, Kauffman M, Shah J, Shacham S, Savona MR, Montesinos P. 2021. A 2:1 randomized, open-label, phase II study of selinexor vs. physician's choice in older patients with relapsed or refractory acute myeloid leukemia.. Leuk Lymphoma. :1-12.▶ Go to Pubmed

Manji GA, Van Tine BA, Lee SM, Raufi AG, Pellicciotta I, Hirbe AC, Pradhan J, Chen A, Rabadan R, Schwartz GK. 2021. A Phase I Study of the Combination of Pexidartinib and Sirolimus to Target Tumor-Associated Macrophages in Unresectable Sarcoma and Malignant Peripheral Nerve Sheath Tumors.. Clin Cancer Res. ▶ Go to Pubmed

Giacobbe A, Abate-Shen C. 2021. Modeling metastasis in mice: a closer look.. Trends Cancer. 7(10):916-929.▶ Go to Pubmed

Zhu K, Cai L, Cui C, Toyos JR de Los, Anastassiou D. 2021. Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts.. PLoS Comput Biol. 17(7):e1009228.▶ Go to Pubmed

Troyanovsky RB, Sergeeva AP, Indra I, Chen C-S, Kato R, Shapiro L, Honig B, Troyanovsky SM. 2021. Sorting of cadherin-catenin-associated proteins into individual clusters.. Proc Natl Acad Sci U S A. 118(29)▶ Go to Pubmed

Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. 2021. Molecular topography of an entire nervous system.. Cell. 184(16):4329-4347.e23.▶ Go to Pubmed

Lopez-Bujanda ZA, Obradovic A, Nirschl TR, Crowley L, Macedo R, Papachristodoulou A, O'Donnell T, Laserson U, Zarif JC, Reshef R, Yuan T, Soni MK, Antonarakis ES, Haffner MC, H Larman B, Shen MM, Muranski P, Drake CG. 2021. TGM4: an immunogenic prostate-restricted antigen.. J Immunother Cancer. 9(6)▶ Go to Pubmed

Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. 2021. Dynamic landscape of protein occupancy across the Escherichia coli chromosome.. PLoS Biol. 19(6):e3001306.▶ Go to Pubmed

Kearney M, Franks L, Lee S, Tiersten A, Makower DF, Cigler T, Mundi P, Chi D-C, Goel A, Klein P, Andreopoulou E, Sparano J, Trivedi M, Accordino M, Califano A, Hershman DL, Silva J, Kalinsky K. 2021. Phase I/II trial of ruxolitinib in combination with trastuzumab in metastatic HER2 positive breast cancer.. Breast Cancer Res Treat. 189(1):177-185.▶ Go to Pubmed

Koss H, Honig B, Shapiro L, Palmer AG. 2021. Dimerization of Cadherin-11 involves multi-site coupled unfolding and strand swapping.. Structure. ▶ Go to Pubmed

Chen D, Chu B, Yang X, Liu Z, Jin Y, Kon N, Rabadan R, Jiang X, Stockwell BR, Gu W. 2021. iPLA2β-mediated lipid detoxification controls p53-driven ferroptosis independent of GPX4.. Nat Commun. 12(1):3644.▶ Go to Pubmed

Affo S, Nair A, Brundu F, Ravichandra A, Bhattacharjee S, Matsuda M, Chin LK, Filliol A, Wen W, Song X, Decker A, Worley J, Caviglia JMatias, Yu L, Yin D, Saito Y, Savage T, Wells RG, Mack M, Zender L, Arpaia N, Remotti HE, Rabadan R, Sims P, Leblond A-L, Weber A, Riener M-O, Stockwell BR, Gaublomme J, Llovet JM, Kalluri R, Michalopoulos GK, Seki E, Sia D, Chen X, Califano A, Schwabe RF. 2021. Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations.. Cancer Cell. 39(6):883.▶ Go to Pubmed

Scotto L, Kinahan C, Douglass E, Deng C, Safari M, Casadei B, Marchi E, Lue JK, Montanari F, Falchi L, Qiao C, Renu N, Bates SE, Califano A, O'Connor OA. 2021. Targeting the T-Cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune-Modulatory Signaling Pathways.. Mol Cancer Ther. 20(8):1422-1430.▶ Go to Pubmed

Fangazio M, Ladewig E, Gomez K, Garcia-Ibanez L, Kumar R, Teruya-Feldstein J, Rossi D, Filip I, Pan-Hammarström Q, Inghirami G, Boldorini R, Ott G, Staiger AM, Chapuy B, Gaidano G, Bhagat G, Basso K, Rabadan R, Pasqualucci L, Dalla-Favera R. 2021. Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma.. Proc Natl Acad Sci U S A. 118(22)▶ Go to Pubmed

Obradovic A, Chowdhury N, Haake SM, Ager C, Wang V, Vlahos L, Guo XV, Aggen DH, W Rathmell K, Jonasch E, Johnson JE, Roth M, Beckermann KE, Rini BI, McKiernan J, Califano A, Drake CG. 2021. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages.. Cell. 184(11):2988-3005.e16.▶ Go to Pubmed

AlQuraishi M. 2021. Machine learning in protein structure prediction.. Curr Opin Chem Biol. 65:1-8.▶ Go to Pubmed

Chen AX, Gartrell RD, Zhao J, Upadhyayula PS, Zhao W, Yuan J, Minns HE, Dovas A, Bruce JN, Lasorella A, Iavarone A, Canoll P, Sims PA, Rabadan R. 2021. Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker.. Genome Med. 13(1):88.▶ Go to Pubmed

Moon CS, Reglero C, Cortes JR, S Quinn A, Alvarez S, Zhao J, Lin W-HW, Cooke AJ, Abate F, Soderquist CR, Fiñana C, Inghirami G, Campo E, Bhagat G, Rabadan R, Palomero T, Ferrando AA. 2021. induces NF-κB signaling-driven peripheral T cell lymphoma.. Nat Cancer. 2(1):98-113.▶ Go to Pubmed

Oh H, Zhao J, Grinberg-Bleyer Y, Postler TS, Wang P, Park S-G, Rabadan R, Hayden MS, Ghosh S. 2021. PDK1 Is Required for Maintenance of CD4 Foxp3 Regulatory T Cell Function.. J Immunol. 206(8):1776-1783.▶ Go to Pubmed

Lencz T, Yu J, Khan RRashid, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. 2021. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.. Neuron. 109(9):1465-1478.e4.▶ Go to Pubmed

Murray D, Petrey D, Honig B. 2021. Integrating 3D structural information into systems biology.. J Biol Chem. 296:100562.▶ Go to Pubmed

Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, Mills GB, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS. 2021. An expanded universe of cancer targets.. Cell. 184(5):1142-1155.▶ Go to Pubmed

Ager CR, Obradovic AZ, Arriaga JM, Chaimowitz MG, Califano A, Abate-Shen C, Drake CG. 2021. Longitudinal Immune Profiling Reveals Unique Myeloid and T-cell Phenotypes Associated with Spontaneous Immunoediting in a Prostate Tumor Model.. Cancer Immunol Res. 9(5):529-541.▶ Go to Pubmed

Cuella-Martin R, Hayward SB, Fan X, Chen X, Huang J-W, Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A. 2021. Functional interrogation of DNA damage response variants with base editing screens.. Cell. 184(4):1081-1097.e19.▶ Go to Pubmed

Joseph TA, Pe'er I. 2021. An Introduction to Whole-Metagenome Shotgun Sequencing Studies.. Methods Mol Biol. 2243:107-122.▶ Go to Pubmed

Patiño-Galindo JAngel, Filip I, Rabadan R. 2021. Global Patterns of Recombination across Human Viruses.. Mol Biol Evol. 38(6):2520-2531.▶ Go to Pubmed

Cheng F, Zhao J, Wang Y, Lu W, Liu Z, Zhou Y, Martin WR, Wang R, Huang J, Hao T, Yue H, Ma J, Hou Y, Castrillon JA, Fang J, Lathia JD, Keri RA, Lightstone FC, Antman EMarshall, Rabadan R, Hill DE, Eng C, Vidal M, Loscalzo J. 2021. Comprehensive characterization of protein-protein interactions perturbed by disease mutations.. Nat Genet. 53(3):342-353.▶ Go to Pubmed

Liu Z, Rabadan R. 2021. Computing the Role of Alternative Splicing in Cancer.. Trends Cancer. 7(4):347-358.▶ Go to Pubmed

Ding H, Yang Y, Xue Y, Seninge L, Gong H, Safavi R, Califano A, Stuart JM. 2021. Prioritizing transcriptional factors in gene regulatory networks with PageRank.. iScience. 24(1):102017.▶ Go to Pubmed

Lo Y-H, Kolahi KS, Du Y, Chang C-Y, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. 2021. A CRISPR/Cas9-Engineered -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation.. Cancer Discov. 11(6):1562-1581.▶ Go to Pubmed

Paull EO, Aytes A, Jones SJ, Subramaniam PS, Giorgi FM, Douglass EF, Tagore S, Chu B, Vasciaveo A, Zheng S, Verhaak R, Abate-Shen C, Alvarez MJ, Califano A. 2021. A modular master regulator landscape controls cancer transcriptional identity.. Cell. 184(2):334-351.e20.▶ Go to Pubmed

Usmanova DR, Plata G, Vitkup D. 2021. The Relationship between the Misfolding Avoidance Hypothesis and Protein Evolutionary Rates in the Light of Empirical Evidence.. Genome Biol Evol. 13(2)▶ Go to Pubmed

Tansey W, Li K, Zhang H, Linderman SW, Rabadan R, Blei DM, Wiggins CH. 2021. Dose-response modeling in high-throughput cancer drug screenings: an end-to-end approach.. Biostatistics. ▶ Go to Pubmed

Sato M, Liebau AWalter, Liu Z, Liu L, Rabadan R, Gautier J. 2021. The UVSSA complex alleviates MYC-driven transcription stress.. J Cell Biol. 220(2)▶ Go to Pubmed

Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. 2021. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.. EMBO J. 40(2):e106696.▶ Go to Pubmed

Anghileri E, Di Ianni N, Paterra R, Langella T, Zhao J, Eoli M, Patanè M, Pollo B, Cuccarini V, Iavarone A, Rabadan R, Finocchiaro G, Pellegatta S. 2021. High tumor mutational burden and T-cell activation are associated with long-term response to anti-PD1 therapy in Lynch syndrome recurrent glioblastoma patient.. Cancer Immunol Immunother. 70(3):831-842.▶ Go to Pubmed

Chiang AH, Chang J, Wang J, Vitkup D. 2021. Exons as units of phenotypic impact for truncating mutations in autism.. Mol Psychiatry. 26(5):1685-1695.▶ Go to Pubmed

Lasso G, Honig B, Shapira SD. 2021. A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease.. Cell Syst. 12(1):82-91.e3.▶ Go to Pubmed

Liu B, Liu Z, Chen S, Ki M, Erickson C, Reis-Filho JS, Durham BH, Chang Q, de Stanchina E, Sun Y, Rabadan R, Abdel-Wahab O, Chandarlapaty S. 2021. Mutant SF3B1 promotes AKT- and NF-κB-driven mammary tumorigenesis.. J Clin Invest. 131(1)▶ Go to Pubmed

Bhuyan MShariful I, Pe'er I, M Rahman S. 2021. SICaRiO: short indel call filtering with boosting.. Brief Bioinform. 22(4)▶ Go to Pubmed

Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, E Sweet-Cordero A, Honig B, Califano A. 2021. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.. Nat Biotechnol. 39(2):215-224.▶ Go to Pubmed

Ogundijo OE, Zhu K, Wang X, Anastassiou D. 2021. Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption.. IEEE/ACM Trans Comput Biol Bioinform. 18(6):2271-2280.▶ Go to Pubmed

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