Publications

Author ID

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

Cerezo-Wallis D, Contreras-Alcalde M, Troulé K, Catena X, Mucientes C, Calvo TG, Cañón E, Tejedo C, Pennacchi PC, Hogan S, Kölblinger P, Tejero H, Chen AX, Ibarz N, Graña-Castro O, Martinez L, Muñoz J, Ortiz-Romero P, Rodriguez-Peralto JL, Gómez-López G, Al-Shahrour F, Rabadan R, Levesque MP, Olmeda D, Soengas MS. 2020. Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state.. Nat Med. 26(12):1865-1877.▶ Go to Pubmed

Wang G, Anastassiou D. 2020. Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis.. Sci Rep. 10(1):17199.▶ 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

Wang XS, Zhao J, Wu-Baer F, Shao Z, Lee BJ, Cupo OM, Rabadan R, Gautier J, Baer R, Zha S. 2020. CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.. Proc Natl Acad Sci U S A. 117(41):25700-25711.▶ Go to Pubmed

Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. 2020. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human.. Circulation. 142(21):2060-2075.▶ Go to Pubmed

Diaz JEl, Ahsen MEren, Schaffter T, Chen X, Realubit RB, Karan C, Califano A, Losic B, Stolovitzky G. 2020. The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies.. Elife. 9▶ Go to Pubmed

Bowen C, Shibata M, Zhang H, Bergren SK, Shen MM, Gelmann EP. 2020. CRISPR/Cas9-Mediated Point Mutation in Prolongs Protein Half-Life and Reverses Effects Allelic Loss.. Cancer Res. 80(21):4805-4814.▶ 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

Crowley L, Cambuli F, Aparicio L, Shibata M, Robinson BD, Xuan S, Li W, Hibshoosh H, Loda M, Rabadan R, Shen MM. 2020. A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors.. Elife. 9▶ Go to Pubmed

Nguyen A-P, Nicoletti P, Arnol D, Califano A, Martínez MRodríguez. 2020. Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN.. Front Bioeng Biotechnol. 8:798.▶ Go to Pubmed

Oldrini B, Vaquero-Siguero N, Mu Q, Kroon P, Zhang Y, Galán-Ganga M, Bao Z, Wang Z, Liu H, Sa JK, Zhao J, Kim H, Rodriguez-Perales S, Nam D-H, Verhaak RGW, Rabadan R, Jiang T, Wang J, Squatrito M. 2020. MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.. Nat Commun. 11(1):3883.▶ Go to Pubmed

Rabadan R, Mohamedi Y, Rubin U, Chu T, Alghalith AN, Elliott O, Arnes L, Cal S, Obaya ÁJ, Levine AJ, Camara PG. 2020. Identification of relevant genetic alterations in cancer using topological data analysis.. Nat Commun. 11(1):3808.▶ Go to Pubmed

Scotto L, Kinahan C, Casadei B, Mangone M, Douglass E, Murty VV, Marchi E, Ma H, George C, Montanari F, Califano A, O'Connor OA. 2020. Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers.. Genes Chromosomes Cancer. 59(11):639-651.▶ Go to Pubmed

Stokes ME, Small JCandice, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell BR. 2020. Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation.. Sci Rep. 10(1):10748.▶ Go to Pubmed

Fiore D, Cappelli LVincenzo, Zumbo P, Phillips JM, Liu Z, Cheng S, Yoffe L, Ghione P, Di Maggio F, Dogan A, Khodos I, de Stanchina E, Casano J, Kayembe C, Tam W, Betel D, Foa' R, Cerchietti L, Rabadan R, Horwitz S, Weinstock DM, Inghirami G. 2020. A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries.. Cancers (Basel). 12(6)▶ Go to Pubmed

Comay O, Ben Yehuda O, Benyamini D, Schwartz-Tzachor R, Pe'er I, Melochna T, Pe'er G. 2020. Analysis of monitoring data where butterflies fly year-round.. Ecol Appl. 30(8):e02196.▶ Go to Pubmed

Ganapathi M, Argyriou L, Martínez-Azorín F, Morlot S, Yigit G, Lee TM, Auber B, von Gise A, Petrey DS, Thiele H, Cyganek L, Sabater-Molina M, Ahimaz P, Cabezas-Herrera J, Sorlí-García M, Zibat A, Siegelin MD, Burfeind P, Buchovecky CM, Hasenfuss G, Honig B, Li Y, Iglesias AD, Wollnik B. 2020. Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis.. Hum Genet. 139(11):1443-1454.▶ Go to Pubmed

Laise P, Bosker G, Sun X, Shen Y, Douglass EF, Karan C, Realubit RB, Pampou S, Califano A, Alvarez MJ. 2020. The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States.. bioRxiv. ▶ 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.. bioRxiv. ▶ Go to Pubmed

Blattman SB, Jiang W, Oikonomou P, Tavazoie S. 2020. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing.. Nat Microbiol. 5(10):1192-1201.▶ Go to Pubmed

Kane JR, Zhao J, Tsujiuchi T, Laffleur B, Arrieta VA, Mahajan A, Rao G, Mela A, Dmello C, Chen L, Zhang DY, González-Buendia E, Lee-Chang C, Xiao T, Rothschild G, Basu U, Horbinski C, Lesniak MS, Heimberger AB, Rabadan R, Canoll P, Sonabend AM. 2020. CD8 T-cell-Mediated Immunoediting Influences Genomic Evolution and Immune Evasion in Murine Gliomas.. Clin Cancer Res. 26(16):4390-4401.▶ Go to Pubmed

Galanti M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Shittu A, Tagne E, Birger R, Ud-Dean M, Filip I, Morita H, Rabadan R, Anthony S, Freyer GA, Dayan P, Shopsin B, Shaman J. 2020. Active surveillance documents rates of clinical care seeking due to respiratory illness.. Influenza Other Respir Viruses. 14(5):499-506.▶ Go to Pubmed

Honig B, Shapiro L. 2020. Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition.. Cell. 181(3):520-535.▶ Go to Pubmed

Sergeeva AP, Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S, Shapiro L, Honig B. 2020. DIP/Dpr interactions and the evolutionary design of specificity in protein families.. Nat Commun. 11(1):2125.▶ Go to Pubmed

Liu Z, Zhang J, Sun Y, Perea-Chamblee TE, Manley JL, Rabadan R. 2020. Pan-cancer analysis identifies mutations in that recapitulate mutant SF3B1 splicing dysregulation.. Proc Natl Acad Sci U S A. 117(19):10305-10312.▶ Go to Pubmed

Yuan Q, He Y, Xiang P-Y, Wang S-P, Cao Z-W, Gou T, Shen M-M, Zhao L, Qin W, Gan R-Y, Wu D-T. 2020. Effects of simulated saliva-gastrointestinal digestion on the physicochemical properties and bioactivities of okra polysaccharides.. Carbohydr Polym. 238:116183.▶ Go to Pubmed

Ji BW, Sheth RU, Dixit PD, Tchourine K, Vitkup D. 2020. Macroecological dynamics of gut microbiota.. Nat Microbiol. 5(5):768-775.▶ Go to Pubmed

Liu Z, Yoshimi A, Wang J, Cho H, Lee SChun-Wei, Ki M, Bitner L, Chu T, Shah H, Liu B, Mato AR, Ruvolo P, Fabbri G, Pasqualucci L, Abdel-Wahab O, Rabadan R. 2020. Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization.. Cancer Discov. 10(6):806-821.▶ Go to Pubmed

Orenbuch R, Filip I, Rabadan R. 2020. HLA Typing from RNA Sequencing and Applications to Cancer.. Methods Mol Biol. 2120:71-92.▶ Go to Pubmed

Jiang W, Oikonomou P, Tavazoie S. 2020. Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.. Cell. 180(5):1002-1017.e31.▶ Go to Pubmed

Zhu K, Anastassiou D. 2020. 2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions.. Bioinformatics. 36(11):3588-3589.▶ Go to Pubmed

Indra I, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM. 2020. Sensing Actin Dynamics through Adherens Junctions.. Cell Rep. 30(8):2820-2833.e3.▶ Go to Pubmed

Harrison OJ, Brasch J, Katsamba PS, Ahlsen G, Noble AJ, Dan H, Sampogna RV, Potter CS, Carragher B, Honig B, Shapiro L. 2020. Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.. Cell Rep. 30(8):2655-2671.e7.▶ 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

Lyashenko E, Niepel M, Dixit PD, Lim SKyun, Sorger PK, Vitkup D. 2020. Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.. Elife. 9▶ Go to Pubmed

Öberg K, Califano A, Strosberg JR, Ma S, Pape U, Bodei L, Kaltsas G, Toumpanakis C, Goldenring JR, Frilling A, Paulson S. 2020. A meta-analysis of the accuracy of a neuroendocrine tumor mRNA genomic biomarker (NETest) in blood.. Ann Oncol. 31(2):202-212.▶ Go to Pubmed

Gartrell-Corrado RD, Chen AX, Rizk EM, Marks DK, Bogardus MH, Hart TD, Silverman AM, -Audrey Y Bayan C, Finkel GG, Barker LW, Komatsubara KM, Carvajal RD, Horst BA, Chang R, Monod A, Rabadan R, Saenger YM. 2020. Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma.. Cancer Res. 80(5):1078-1087.▶ Go to Pubmed

Dixit PD, Lyashenko E, Niepel M, Vitkup D. 2020. Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.. Cell Syst. 10(2):204-212.e8.▶ Go to Pubmed

Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. 2020. Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma.. Clin Cancer Res. 26(5):1094-1104.▶ Go to Pubmed

Ji BW, Sheth RU, Dixit PD, Huang Y, Kaufman A, Wang HH, Vitkup D. 2019. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.. Nat Methods. 16(8):731-736.▶ Go to Pubmed

Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. 2019. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.. Annu Rev Cell Dev Biol. 35:357-379.▶ Go to Pubmed

Cook SJ, Jarrell TA, Brittin CA, Wang Y, Bloniarz AE, Yakovlev MA, Nguyen KCQ, Tang LT-H, Bayer EA, Duerr JS, Bülow HE, Hobert O, Hall DH, Emmons SW. 2019. Whole-animal connectomes of both Caenorhabditis elegans sexes.. Nature. 571(7763):63-71.▶ Go to Pubmed

Nam AS, Kim K-T, Chaligne R, Izzo F, Ang C, Taylor J, Myers RM, Abu-Zeinah G, Brand R, Omans ND, Alonso A, Sheridan C, Mariani M, Dai X, Harrington E, Pastore A, Cubillos-Ruiz JR, Tam W, Hoffman R, Rabadan R, Scandura JM, Abdel-Wahab O, Smibert P, Landau DA. 2019. Somatic mutations and cell identity linked by Genotyping of Transcriptomes.. Nature. 571(7765):355-360.▶ Go to Pubmed

Joseph TA, Pe'er I. 2019. Inference of Population Structure from Time-Series Genotype Data.. Am J Hum Genet. 105(2):317-333.▶ Go to Pubmed

van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Võsa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B. 2019. High-throughput identification of human SNPs affecting regulatory element activity.. Nat Genet. 51(7):1160-1169.▶ Go to Pubmed

Ma W, Lee J, Backenroth D, Zhou YJerry, Bush E, Sims P, Liu K, Shen Y. 2019. Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose.. BMC Mol Cell Biol. 20(1):20.▶ Go to Pubmed

Feng H, Bao S, Rahman MAlinoor, Weyn-Vanhentenryck SM, Khan A, Wong J, Shah A, Flynn ED, Krainer AR, Zhang C. 2019. Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.. Mol Cell. 74(6):1189-1204.e6.▶ Go to Pubmed

Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna V, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ. 2019. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.. Bioinformatics. ▶ Go to Pubmed

Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. 2019. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.. Cancer Discov. 9(8):1102-1123.▶ Go to Pubmed

Shenhav L, Thompson M, Joseph TA, Briscoe L, Furman O, Bogumil D, Mizrahi I, Pe'er I, Halperin E. 2019. FEAST: fast expectation-maximization for microbial source tracking.. Nat Methods. 16(7):627-632.▶ Go to Pubmed

Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R. 2019. arcasHLA: high resolution HLA typing from RNAseq.. Bioinformatics. ▶ Go to Pubmed

Hanoun M, Arnal-Estapé A, Maryanovich M, Zahalka AH, Bergren SK, Chua CW, Leftin A, Brodin PN, Shen MM, Guha C, Frenette PS. 2019. NestinNG2 Cells Form a Reserve Stem Cell Population in the Mouse Prostate.. Stem Cell Reports. 12(6):1201-1211.▶ Go to Pubmed

Farber DL, Sims PA. 2019. Dissecting lung development and fibrosis at single-cell resolution.. Genome Med. 11(1):33.▶ Go to Pubmed

Hobson BD, Sims PA. 2019. Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry.. eNeuro. 6(3)▶ Go to Pubmed

Beh LY, Debelouchina GT, Clay DM, Thompson RE, Lindblad KA, Hutton ER, Bracht JR, Sebra RP, Muir TW, Landweber LF. 2019. Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.. Cell. 177(7):1781-1796.e25.▶ Go to Pubmed

Ahalt SC, Chute CG, Fecho K, Glusman G, Hadlock J, Taylor COverby, Pfaff ER, Robinson PN, Solbrig H, Ta C, Tatonetti N, Weng C. 2019. Clinical Data: Sources and Types, Regulatory Constraints, Applications.. Clin Transl Sci. 12(4):329-333.▶ Go to Pubmed

Nicoletti P, Barrett S, McEvoy L, Daly AK, Aithal G, M Lucena I, Andrade RJ, Wadelius M, Hallberg P, Stephens C, Bjornsson ES, Friedmann P, Kainu K, Laitinen T, Marson A, Molokhia M, Phillips E, Pichler W, Romano A, Shear N, Sills G, Tanno LK, Swale A, Floratos A, Shen Y, Nelson MR, Watkins PB, Daly MJ, Morris AP, Alfirevic A, Pirmohamed M. 2019. Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.. Clin Pharmacol Ther. 106(5):1028-1036.▶ Go to Pubmed

Zhang J, Caruso FP, Sa JK, Justesen S, Nam D-H, Sims P, Ceccarelli M, Lasorella A, Iavarone A. 2019. The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival.. Commun Biol. 2:135.▶ Go to Pubmed

Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. 2019. Overlooked roles of DNA damage and maternal age in generating human germline mutations.. Proc Natl Acad Sci U S A. 116(19):9491-9500.▶ Go to Pubmed

Cascione L, Rinaldi A, Bruscaggin A, Tarantelli C, Arribas AJ, Kwee I, Pecciarini L, Mensah AA, Spina V, Chung EYL, di Bergamo LTerzi, Dirnhofer S, Tzankov A, Miranda RN, Young KH, Traverse-Glehen A, Gaidano G, Swerdlow SH, Gascoyne R, Rabadan R, Ponzoni M, Bhagat G, Rossi D, Zucca E, Bertoni F. 2019. Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses.. Haematologica. ▶ Go to Pubmed

Echeverria GV, Ge Z, Seth S, Zhang X, Jeter-Jones S, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Sun Y, Qiu H, Chang Q, Bristow C, Carugo A, Shao J, Ma X, Harris A, Mundi P, Lau R, Ramamoorthy V, Wu Y, Alvarez MJ, Califano A, Moulder SL, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. 2019. Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.. Sci Transl Med. 11(488)▶ Go to Pubmed

Blasco MTeresa, Navas C, Martín-Serrano G, Graña-Castro O, Lechuga CG, Martín-Díaz L, Djurec M, Li J, Morales-Cacho L, Esteban-Burgos L, Perales-Patón J, Bousquet-Mur E, Castellano E, Jacob HKC, Cabras L, Musteanu M, Drosten M, Ortega S, Mulero F, Sainz B, Dusetti N, Iovanna J, Sanchez-Bueno F, Hidalgo M, Khiabanian H, Rabadan R, Al-Shahrour F, Guerra C, Barbacid M. 2019. Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.. Cancer Cell. 35(4):573-587.e6.▶ Go to Pubmed

Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E. 2019. Structural variation in the gut microbiome associates with host health.. Nature. 568(7750):43-48.▶ Go to Pubmed

Sharma SDas, Metz JB, Li H, Hobson BD, Hornstein N, Sulzer D, Tang G, Sims PA. 2019. Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice.. Cell Rep. 26(12):3313-3322.e5.▶ Go to Pubmed

Slotkin EK, Diolaiti D, Shukla NN, Cruz FSDela, Clark JJ, Gundem G, Yellapantula VD, Levine MF, You D, Ma P, Pachhal S, Sanchez GIbanez, Benayed R, Jungbluth AA, Smyth LM, Mauguen A, Gushterova I, Ding H, Spraggon L, Darnell R, Califano A, Ladanyi M, Papaemmanuil E, Kung AL, Hyman DM, Roberts SS. 2019. Patient-driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-driven Cancer.. Cancer Discov. ▶ Go to Pubmed

Snyder ME, Finlayson MO, Connors TJ, Dogra P, Senda T, Bush E, Carpenter D, Marboe C, Benvenuto L, Shah L, Robbins H, Hook JL, Sykes M, D'Ovidio F, Bacchetta M, Sonett JR, Lederer DJ, Arcasoy S, Sims PA, Farber DL. 2019. Generation and persistence of human tissue-resident memory T cells in lung transplantation.. Sci Immunol. 4(33)▶ Go to Pubmed

Venkatasubramanian L, Mann RS. 2019. The development and assembly of the Drosophila adult ventral nerve cord.. Curr Opin Neurobiol. 56:135-143.▶ Go to Pubmed

Wang C, Hobert O. 2019. Sex-specific pheromone responses in .. EMBO Rep. 20(3)▶ Go to Pubmed

Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J. 2019. Longitudinal active sampling for respiratory viral infections across age groups.. Influenza Other Respir Viruses. ▶ Go to Pubmed

Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R. 2019. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.. Nat Med. 25(3):462-469.▶ Go to Pubmed

Anzalone AV, Zairis S, Lin AJ, Rabadan R, Cornish VW. 2019. Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection.. Biochemistry. 58(8):1167-1178.▶ Go to Pubmed

Bhattacharya A, Aghayeva U, Berghoff EG, Hobert O. 2019. Plasticity of the Electrical Connectome of C. elegans.. Cell. 176(5):1174-1189.e16.▶ Go to Pubmed

Ganapathi M, Padgett LR, Yamada K, Devinsky O, Willaert R, Person R, Au P-YBillie, Tagoe J, McDonald M, Karlowicz D, Wolf B, Lee J, Shen Y, Okur V, Deng L, Leduc CA, Wang J, Hanner A, Mirmira RG, Park MHee, Mastracci TL, Chung WK. 2019. Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder.. Am J Hum Genet. 104(2):287-298.▶ Go to Pubmed

Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP. 2019. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes.. Gut. ▶ Go to Pubmed

Klein HL, Bačinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gómez-González B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miné-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AAit, Sakofsky CJ, Shim EYong, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JLucas, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SAe, Lee SEun, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A. 2019. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.. Microb Cell. 6(1):1-64.▶ Go to Pubmed

Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A. 2019. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.. PLoS One. 14(1):e0208646.▶ Go to Pubmed

Yuan J, Sheng J, Sims PA. 2018. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.. Genome Biol. 19(1):227.▶ Go to Pubmed

Wendorff AA, S Quinn A, Rashkovan M, Madubata CJ, Ambesi-Impiombato A, Litzow MR, Tallman MS, Paietta E, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Rabadan R, Van Vlierberghe P, Ferrando AA. 2018. Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL.. Cancer Discov. ▶ Go to Pubmed

Sa JK, Choi SWon, Zhao J, Lee Y, Zhang J, Kong D-S, Choi JWon, Seol HJun, Lee J-I, Iavarone A, Rabadan R, Nam D-H. 2018. Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.. Int J Cancer. ▶ Go to Pubmed

Moretti A, Stirn A, Marks G, Pe'er I. 2018. Autoencoding Topographic Factors.. J Comput Biol. ▶ Go to Pubmed

Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C. 2018. NSD2 is a conserved driver of metastatic prostate cancer progression.. Nat Commun. 9(1):5201.▶ Go to Pubmed

Billerbeck S, Brisbois J, Agmon N, Jimenez M, Temple J, Shen M, Boeke JD, Cornish VW. 2018. A scalable peptide-GPCR language for engineering multicellular communication.. Nat Commun. 9(1):5057.▶ Go to Pubmed

Šuštić T, van Wageningen S, Bosdriesz E, Reid RJD, Dittmar J, Lieftink C, Beijersbergen RL, Wessels LFA, Rothstein R, Bernards R. 2018. A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.. Genome Med. 10(1):90.▶ Go to Pubmed

Ta CN, Dumontier M, Hripcsak G, Tatonetti NP, Weng C. 2018. Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records.. Sci Data. 5:180273.▶ Go to Pubmed

Cosmanescu F, Katsamba PS, Sergeeva AP, Ahlsen G, Patel SD, Brewer JJ, Tan L, Xu S, Xiao Q, Nagarkar-Jaiswal S, Nern A, Bellen HJ, S Zipursky L, Honig B, Shapiro L. 2018. Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins.. Neuron. 100(6):1385-1400.e6.▶ Go to Pubmed

Xu S, Xiao Q, Cosmanescu F, Sergeeva AP, Yoo J, Lin Y, Katsamba PS, Ahlsen G, Kaufman J, Linaval NT, Lee P-T, Bellen HJ, Shapiro L, Honig B, Tan L, S Zipursky L. 2018. Interactions between the Ig-Superfamily Proteins DIP-α and Dpr6/10 Regulate Assembly of Neural Circuits.. Neuron. 100(6):1369-1384.e6.▶ Go to Pubmed

Youn A, Kim KIn, Rabadan R, Tycko B, Shen Y, Wang S. 2018. A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.. BMC Med Genomics. 11(1):98.▶ Go to Pubmed

Khatamian A, Paull EO, Califano A, Yu J. 2018. SJARACNe: a scalable software tool for gene network reverse engineering from big data.. Bioinformatics. ▶ Go to Pubmed

Sapienza MRosaria, Abate F, Melle F, Orecchioni S, Fuligni F, Etebari M, Tabanelli V, Laginestra MAntonella, Pileri A, Motta G, Rossi M, Agostinelli C, Sabattini E, Pimpinelli N, Truni M, Falini B, Cerroni L, Talarico G, Piccioni R, Amente S, Indio V, Tarantino G, Brundu F, Paulli M, Berti E, Facchetti F, Dellino GIvan, Bertolini F, Tripodo C, Rabadan R, Pileri SA. 2018. Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target.. Haematologica. ▶ Go to Pubmed

Zagore LL, Sweet TJ, Hannigan MM, Weyn-Vanhentenryck SM, Jobava R, Hatzoglou M, Zhang C, Licatalosi DD. 2018. DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions.. Cell Rep. 25(5):1225-1240.e6.▶ Go to Pubmed

Liang H, Peng B, Dong C, Liu L, Mao J, Wei S, Wang X, Xu H, Shen J, Mao H-Q, Gao X, Leong KW, Chen Y. 2018. Cationic nanoparticle as an inhibitor of cell-free DNA-induced inflammation.. Nat Commun. 9(1):4291.▶ Go to Pubmed

Erlich, iv Y, Shor T, Pe'er I, Carmi S. 2018. Identity inference of genomic data using long-range familial searches.. Science. 362(6415):690-694.▶ Go to Pubmed

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho B-K, Yang C, Palsson BO, Church GM, Lewis NE. 2018. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.. Proc Natl Acad Sci U S A. 115(43):11096-11101.▶ Go to Pubmed

Kratsios P, Hobert O. 2018. Nervous System Development: Flies and Worms Converging on Neuron Identity Control.. Curr Biol. 28(19):R1154-R1157.▶ Go to Pubmed

Li JJ, Shen MM. 2018. Prostate Stem Cells and Cancer Stem Cells.. Cold Spring Harb Perspect Med. ▶ Go to Pubmed

Le Magnen C, Virk RK, Dutta A, Kim JYeji, Panja S, Lopez-Bujanda ZA, Califano A, Drake CG, Mitrofanova A, Abate-Shen C. 2018. Cooperation of loss of and inflammation in prostate cancer initiation.. Dis Model Mech. 11(11)▶ Go to Pubmed

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