Publications

Original Articles as a PI at the University of Pennsylvania:

Verma P, Zhou Y, Cao Z, Deraska PV, Deb M, Arai E, Li W, Shao Y, Puentes L, Li Y, Patankar S, Mach RH, Faryabi RB, Shi J, Greenberg RA, ‘‘ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells’’, Nature Cell Biology, February 2021.
Kahn BM, Lucas A, Alur GR, Wengyn MD, Schwartz GW, Li J, Sun K, Maurer HC, Olive KP, RB Faryabi^, Stanger BZ^, ‘‘The vascular landscape of human cancer’’, Jornal of Clinical Investigation, December 2020. ^co-corresponding author.
Schwartz GW, Petrovic J, Fasolino M, Zhou Y, Xu L, Pear WS, Vahedi G, Faryabi RB, ‘‘TooManyCells Identifies and Visualizes Relationships of Single-cell Clades’’, Nature Methods, March 2020.
Rome KS, Stein SJ, Kurachi M, Petrovic J, Schwartz GW, Mack EA, Uljon S, Ms. Wu WW, DeHart AG, Xu L, Gimotty PA, Blacklow SC, Faryabi RB, Wherry EJ, Jordan MS, Pear WS, ‘‘Trib1 Regulates T Cell Differentiation During Chronic Infection by Restraining the Effector Program’’. Journal of Experimental Medicine, March 2020.
Fasolino M^, Goldman N^, Wang W, Cattau B, Zhou Y, Petrovic J, Link, VM, Cote A, Chandra A, Silverman, M, Joyce EF, Little SC, the HPAP Consortium, Kaestner KH, Naji A, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G, ‘‘Genetic Variation in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells’’, Immunity, February 2020. ^co-first author.
Petrovic J^, Zhou Y^, Fasolino M, Goldman N, Schwartz GW, Mumbach MR, Nguyen SC, Rome KS, Sela Y, Zapataro Z, Blacklow SC, Kruhlak MJ, Shi J, Aster JC, Joyce EF, Little SC, Vahedi G, Pear WS, Faryabi RB, ‘‘Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques’’, Molecular Cell, March 2019, ^co-first author.
Schwartz GW, Manning BS, Zhou Y, Velu PD, Bigdeli A, Astles R, Lehman AW, Morrissette JJ, Perl AE, Li M, Carroll M, Faryabi RB, ‘‘Classes of ITD predict outcomes in AML patients treated with FLT3 inhibitors’’, Clinical Cancer Research, July 2018.
Li J, Byrne KT, Yan F, Yamazoe T, Chen Z, Baslan T, Richman LP, Lin JH, Sun YH, Rech AJ, Balli D, Hay CA, Sela Y, Merrell AJ, Liudahl SM, Gordon N, Norgard RJ, Yuan S, Yu S, Chao T, Ye S, Eisinger-Mathason TSK, Faryabi RB, Tobias JW, Lowe SW, Coussens LM, Wherry EJ, Vonderheide RH, Stanger BZ, ‘‘Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy’’, Immunity, July 2018.
Schwartz G, Petrovic J, Zhou Y, Faryabi RB, ‘‘Differential integration of transcriptome and proteome identifies pan-cancer prognostic biomarkers’’, Frontiers in Genetics, June 2018.
Pajcini KV, Xu L, Shao L, Petrovic J, Palasiewicz K, Ohtani Y, Bailis W, Lee C, Wertheim GB, Mani R, Muthusamy N, Li Y, Meijerink JPP, Blacklow SC, Faryabi RB, Cherry S, Pear WS, ‘‘MAFB Enhances Oncogenic Notch Signaling in T Cell Acute Lymphoblastic Leukemia’’, Science Signaling, November 2017.
Ryan RJH^, Petrovic J^, Rausch DM, Zhou Y, Lareau C, Kluk MJ, Christie AL, Lee W, Guo B, Donohue LKH, Gillespie S, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS, ‘‘A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas’’, Cell Reports, October 2017. ^co-first author.
Rolland DC, Basrur V, Jeon Y-K, McNeil-Schwalm C, Fermin D, Conlon K, Zhou Y, Ng SY, Tsou C-C, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ, ‘‘Functional Proteogenomics Reveals Biomarkers and Therapeutic Targets in Lymphomas’’, PNAS, May 2017.
Stein SJ, Mack EA, Rome KS, Pajcini KV, Ohtani T, Xu L, Li Y, Meijerink JP, Faryabi RB, Pear WS, ‘‘Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL’’, PLoS ONE, May 2016.

Original Articles Prior to Joining the University of Pennsylvania:

Santos MA, Faryabi RB, Ergen AV, Day AM, Malhowski A, Canela A, Onozawa M, Lee J-E, Callen E, Gutierrez-Martinez P, Chen H-T, Wong N, Finkel N, Deshpande A, Sharrow S, Rossi DJ, Ito K, Ge K, Aplan PD, Armstrong SA, Nussenzweig A, ‘‘DNA-damage-induced Differentiation of Leukaemic Cells as an Anti-cancer Barrier’’, Nature, October 2014.
Callen E, Di Virgilio M, Kruhlak MJ, Nieto-Soler M, Wong N, Chen H-T, Faryabi RB, Polato F, Santos M, Starnes LM, Wesemann DR, Lee J-E, Tubbs A, Sleckman BP, Daniel JA, Ge K, Alt FW, Fernandez-Capetillo O, Nussenzweig MC, Nussenzweig A: ‘‘53BP1 Mediates Productive and Mutagenic DNA Repair Through Distinct Phosphoprotein Interactions’’, Cell, June 2013.
Barlow JH^, Faryabi RB^, Callen E, Wong N, Malhowski A, Chen H-T, Gutierrez-Cruz G, Sun H-W, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A, ‘‘Identification of Early Replicating Fragile Sites that Contribute to Genome Instability’’, Cell, January 2013. ^co-first author.
Bunting SF, Callen E, Kozak ML, Kim JM, Wong N, López-Contreras AJ, Ludwig T, Baer R, Faryabi RB, Malhowski A, Chen H-T, Fernandez-Capetillo O, D’Andrea A, Nussenzweig A, ‘‘BRCA1 Functions Independently of Homologous Recombination in DNA Interstrand Crosslink Repair’’, Molecular Cell, April 2012.
Callen E, Faryabi RB, Luckey M, Hao B, Daniel JA, Yang W, Sun H-W, Dressler G, Peng W, Chi H, Ge K, Krangel MS, Park J-H, Nussenzweig A, ‘‘The DNA Damage- and Transcription-associated Protein Paxip1 Controls Thymocyte Development and Emigration’’, Immunity, December 2012.
Vahedi G, Faryabi RB, Chamberland J-F, Datta A, Dougherty ER, ‘‘Sampling-Rate-Dependent Probabilistic Boolean Networks’’, Journal of Theoretical Biology, December 2009.
Faryabi RB, Vahedi G, Datta A, Chamberland J-F, Dougherty ER, ‘‘Recent Advances in the Control of Markovian Gene Regulatory Networks’’, Current Genomics, November 2009.
Vahedi G, Faryabi RB, Chamberland J-F, Datta A, Dougherty ER, ‘‘Optimal Intervention Strategies for Cyclic Therapeutic Methods’’, IEEE Transactions on Biomedical Engineering, February 2009.
Faryabi RB, Vahedi G, Chamberland J-F, Datta A, Dougherty ER, ‘‘Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited’’, EURASIP Journal on Bioinformatics and Systems Biology, February 2009.
Vahedi G, Faryabi RB, Chamberland J-F, Datta A, Dougherty ER, ‘‘Intervention in Gene Regulatory Networks via a Stationary Mean-First-Passage-Time Control Policy’’, IEEE Transactions on Biomedical Engineering, October 2008.
Faryabi RB, Chamberland J-F, Vahedi G, Datta A, Dougherty ER, ‘‘Optimal Intervention in Asynchronous Genetic Regulatory Networks’’, IEEE Journal of Selected Topics in Signal Processing, June 2008.
Faryabi RB, Vahedi G, Chamberland J-F, Datta A, Dougherty ER, ‘‘Optimal Constrained Stationary Intervention in Gene Regulatory Networks’’, EURASIP Journal on Bioinformatics and Systems Biology, April 2008.
Faryabi RB, Datta A, Dougherty ER, ‘‘On Approximate Stochastic Control in Genetic Regulatory Networks’’, IET Journal of Systems Biology, November 2007.

In collaboration with Dr. Vahedi’s lab, we established IFI Advanced Computational Biology Club. Join us Fridays at 4 pm (BRB 301) to share your experience with the application of cutting-edge technologies in biology and have a beer or two!