Publications

Author ID

2019 Publications

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

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