Publications

Author ID

2022 Publications

Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M. 2022. Publisher Correction: Single-sequence protein structure prediction using a language model and deep learning.. Nat Biotechnol. ▶ Go to Pubmed

Coutinho DF, Mundi PS, Marks LJ, Burke C, Ortiz MV, Diolaiti D, Bird L, Vallance KL, Ibáñez G, You D, Long M, Rosales N, Grunn A, Ndengu A, Siddiquee A, Gaviria ES, Rainey AR, Fazlollahi L, Hosoi H, Califano A, Kung AL, Cruz FSDela. 2022. Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors.. Med (N Y). ▶ Go to Pubmed

Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M. 2022. Single-sequence protein structure prediction using a language model and deep learning.. Nat Biotechnol. ▶ Go to Pubmed

Zhong W, Chen L, Li X, Chen Y, Zhang Y, Guo C, Shen Y, Chen H. 2022. Disability-adjusted life years and the trends of the burden of colorectal cancer: a population-based study in Shanghai, China during 2002 to 2016.. Chin Med J (Engl). ▶ Go to Pubmed

Zhou Y, Yang Y, Guo L, Qian J, Ge J, Sinner D, Ding H, Califano A, Cardoso WV. 2022. Airway basal cells show regionally distinct potential to undergo metaplastic differentiation.. Elife. 11▶ Go to Pubmed

Guo C, Figueiredo I, Gurel B, Neeb A, Seed G, Crespo M, Carreira S, Rekowski J, Buroni L, Welti J, Bogdan D, Gallagher L, Sharp A, de la Maza MDFenor, Rescigno P, Westaby D, Chandran K, Riisnaes R, Ferreira A, Miranda S, Calì B, Alimonti A, Bressan S, Nguyen AHT, Shen MM, Hawley JE, Obradovic A, Drake CG, Bertan C, Baker C, Tunariu N, Yuan W, de Bono JS. 2022. B7-H3 as a Therapeutic Target in Advanced Prostate Cancer.. Eur Urol. ▶ Go to Pubmed

Laise P, Bosker G, Califano A, Alvarez MJ. 2022. A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture.. Curr Protoc. 2(9):e544.▶ Go to Pubmed

Boni N, Shapiro L, Honig B, Wu Y, Rubinstein R. 2022. On the formation of ordered protein assemblies in cell-cell interfaces.. Proc Natl Acad Sci U S A. 119(34):e2206175119.▶ Go to Pubmed

Zhong G, Shen Y. 2022. Statistical models of the genetic etiology of congenital heart disease.. Curr Opin Genet Dev. 76:101967.▶ Go to Pubmed

Lutomski CA, El-Baba TJ, Robinson CV, Riek R, Scheres SHW, Yan N, AlQuraishi M, Gan L. 2022. The next decade of protein structure.. Cell. 185(15):2617-2620.▶ Go to Pubmed

Laise P, Stanifer ML, Bosker G, Sun X, Triana S, Doldan P, La Manna F, De Menna M, Realubit RB, Pampou S, Karan C, Alexandrov T, de Julio MKruithof-, Califano A, Boulant S, Alvarez MJ. 2022. A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection.. Commun Biol. 5(1):714.▶ Go to Pubmed

Feng S, Rastogi C, Loker R, Glassford WJ, H Rube T, Bussemaker HJ, Mann RS. 2022. Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors.. Nat Commun. 13(1):3808.▶ Go to Pubmed

Lipman AR, Fan X, Shen Y, Chung WK. 2022. Clinical and genetic characterization of CACNA1A-related disease.. Clin Genet. 102(4):288-295.▶ Go to Pubmed

Sun J, Guo F, Tang Q, Chen G, Peng J, Shen Y, Zhang J, Hu J, Yang C. 2022. Identification of a novel immune gene panel in tongue squamous cell carcinoma.. Am J Transl Res. 14(5):2801-2824.▶ Go to Pubmed

AlQuraishi M, Chahed S, Alani D, Puckett DL, Dowker PD, Hubbard K, Zhao Y, Kim JYeon, Nodit L, Fatima H, Donohoe D, Voy B, Chowanadisai W, Bettaieb A. 2022. Podocyte specific deletion of PKM2 ameliorates LPS-induced podocyte injury through beta-catenin.. Cell Commun Signal. 20(1):76.▶ Go to Pubmed

H Rube T, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BViet, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. 2022. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.. Nat Biotechnol. ▶ Go to Pubmed

Gartrell RD, Enzler T, Kim PS, Fullerton BT, Fazlollahi L, Chen AX, Minns HE, Perni S, Weisberg SP, Rizk EM, Wang S, Oh EJeong, Guo XV, Chiuzan C, Manji GA, Bates SE, Chabot J, Schrope B, Kluger M, Emond J, Rabadan R, Farber D, Remotti HE, Horowitz DP, Saenger YM. 2022. Neoadjuvant chemoradiation alters the immune microenvironment in pancreatic ductal adenocarcinoma.. Oncoimmunology. 11(1):2066767.▶ Go to Pubmed

Abate-Shen C, de Almeida FNunes. 2022. Establishment of the LNCaP Cell Line - The Dawn of an Era for Prostate Cancer Research.. Cancer Res. 82(9):1689-1691.▶ Go to Pubmed

Papachristodoulou A, Abate-Shen C. 2022. Precision intervention for prostate cancer: Re-evaluating who is at risk.. Cancer Lett. 538:215709.▶ Go to Pubmed

Cortes JR, Filip I, Albero R, Patiño-Galindo JA, S Quinn A, Lin W-HW, Laurent AP, Shih BB, Brown JA, Cooke AJ, Mackey A, Einson J, Zairis S, Rivas-Delgado A, Laginestra MAntonella, Pileri S, Campo E, Bhagat G, Ferrando AA, Rabadan R, Palomero T. 2022. Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma.. Cell Rep. 39(3):110695.▶ Go to Pubmed

Schoenfeld DA, Zhou R, Zairis S, Su W, Steinbach N, Mathur D, Bansal A, Zachem AL, Tavarez B, Hasson D, Bernstein E, Rabadan R, Parsons R. 2022. Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma.. Mol Cancer Res. 20(8):1193-1207.▶ Go to Pubmed

Xu S, Sergeeva AP, Katsamba PS, Mannepalli S, Bahna F, Bimela J, S Zipursky L, Shapiro L, Honig B, Zinn K. 2022. Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules.. Cell Rep. 39(1):110618.▶ Go to Pubmed

Middelhoff M, Valenti G, Tomassoni L, Ochiai Y, Belin B, Takahashi R, Malagola E, Nienhüser H, Finlayson M, Hayakawa Y, Zamechek LB, Renz BW, C Westphalen B, Quante M, Margolis KG, Sims PA, Laise P, Califano A, Rao M, Gershon MD, Wang TC. 2022. Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury.. Am J Physiol Gastrointest Liver Physiol. 322(6):G583-G597.▶ Go to Pubmed

Obradovic A, Graves D, Korrer M, Wang Y, Roy S, Naveed A, Xu Y, Luginbuhl A, Curry J, Gibson M, Idrees K, Hurley P, Jiang P, X Liu S, Uppaluri R, Drake CG, Califano A, Kim YJ. 2022. Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer.. Clin Cancer Res. 28(10):2094-2109.▶ Go to Pubmed

Cambuli F, Foletto V, Alaimo A, De Felice D, Gandolfi F, Palumbieri MDilia, Zaffagni M, Genovesi S, Lorenzoni M, Celotti M, Bertossio E, Mazzero G, Bertossi A, Bisio A, Berardinelli F, Antoccia A, Gaspari M, Barbareschi M, Fiorentino M, Shen MM, Loda M, Romanel A, Lunardi A. 2022. Intra-epithelial non-canonical Activin A signaling safeguards prostate progenitor quiescence.. EMBO Rep. 23(5):e54049.▶ Go to Pubmed

Goodman KMarie, Katsamba PS, Rubinstein R, Ahlsen G, Bahna F, Mannepalli S, Dan H, Sampogna RV, Shapiro L, Honig B. 2022. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition.. Elife. 11▶ Go to Pubmed

Bartolomé A, Suda N, Yu J, Zhu C, Son J, Ding H, Califano A, Accili D, Pajvani UB. 2022. Notch-mediated Ephrin signaling disrupts islet architecture and β cell function.. JCI Insight. 7(6)▶ 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. 2022. Publisher Correction: ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.. Nat Cancer. 3(3):373.▶ Go to Pubmed

Laise P, Stanifer ML, Bosker G, Sun X, Triana S, Doldan P, La Manna F, De Menna M, Realubit RB, Pampou S, Karan C, Alexandrov T, de Julio MKruithof-, Califano A, Boulant S, Alvarez MJ. 2022. A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection.. Res Sq. ▶ Go to Pubmed

Douglass EF, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-I-Mompel P, Mateo L, Guitart-Pla O, Chung V, Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A. 2022. A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.. Cell Rep Med. 3(1):100492.▶ Go to Pubmed

Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T. 2022. Transcription factor regulation of eQTL activity across individuals and tissues.. PLoS Genet. 18(1):e1009719.▶ Go to Pubmed

Galán-Díez M, Borot F, Ali AMahmood, Zhao J, Gil-Iturbe E, Shan X, Luo N, Liu Y, Huang X-P, Bisikirska B, Labella R, Kurland I, Roth BL, Quick M, Mukherjee S, Rabadan R, Carroll M, Raza A, Kousteni S. 2022. Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia.. Cancer Discov. 12(4):1106-1127.▶ Go to Pubmed

Shilo S, Godneva A, Rachmiel M, Korem T, Bussi Y, Kolobkov D, Karady T, Bar N, Wolf BChen, Glantz-Gashai Y, Cohen M, Zuckerman-Levin N, Shehadeh N, Gruber N, Levran N, Koren S, Weinberger A, Pinhas-Hamiel O, Segal E. 2022. The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control.. Diabetes Care. 45(3):555-563.▶ Go to Pubmed

Christin JR, Shen MM. 2022. Modeling tumor plasticity in organoid models of human cancer.. Trends Cancer. 8(3):161-163.▶ Go to Pubmed

Joseph TA, Chlenski P, Litman A, Korem T, Pe'er I. 2022. Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.. Genome Res. 32(3):558-568.▶ Go to Pubmed

Lassman AB, Wen PY, van den Bent MJ, Plotkin SR, Walenkamp AME, Green AL, Li K, Walker CJ, Chang H, Tamir S, Henegar L, Shen Y, Alvarez MJ, Califano A, Landesman Y, Kauffman MG, Shacham S, Mau-Sørensen M. 2022. A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma.. Clin Cancer Res. 28(3):452-460.▶ Go to Pubmed

Crowley L, Shen MM. 2022. Heterogeneity and complexity of the prostate epithelium: New findings from single-cell RNA sequencing studies.. Cancer Lett. 525:108-114.▶ Go to Pubmed

Shilo S, Godneva A, Rachmiel M, Korem T, Kolobkov D, Karady T, Bar N, Wolf BChen, Glantz-Gashai Y, Cohen M, Levin NZuckerman, Shehadeh N, Gruber N, Levran N, Koren S, Weinberger A, Pinhas-Hamiel O, Segal E. 2022. Prediction of Personal Glycemic Responses to Food for Individuals With Type 1 Diabetes Through Integration of Clinical and Microbial Data.. Diabetes Care. 45(3):502-511.▶ Go to Pubmed

Li W, Shen MM. 2022. Prostate cancer cell heterogeneity and plasticity: Insights from studies of genetically-engineered mouse models.. Semin Cancer Biol. 82:60-67.▶ Go to Pubmed

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