1. 1. SSP Rao*, MH Huntley*, NC Durand, EK Stamenova, ID Bochkov, JT Robinson, AL Sanborn, I Machol, AD Omer, ES Lander, EL Aiden. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159 (2014).
    (*) Co-First Authors. Supplemental: Data, Browser, Video Abstract

    Press: NPR's All Things Considered, NIH Director's Blog, Science (2), New Scientist (2), Scientific American, The Scientist, Forbes, Biotechniques (Lab Grammy), Wired, Science News (2, 3), and over 50 other venues.
  2. 2. AL Sanborn*, SSP Rao*, S-C Huang, NC Durand, MH Huntley, AI Jewett, ID Bochkov, D Chinnappan, A Cutkosky, J Li, KP Geeting, A Gnirke, A Melnikov, D McKenna, EK Stamenova, ES Lander, EL Aiden. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. PNAS (2015).
    (*) Co-First Authors. Supplemental: Data, Video Abstract. News & Views.

    Press: The Atlantic, U.S. House of Representatives, Science, TIME, The Independent, The Scientist, and over 20 other venues.
  3. 3. SSP Rao, S-C Huang, BG St Hilaire, JM Engreitz, EM Perez, K-R Kieffer-Kwon, AL Sanborn, SE Johnstone, GD Bascom, ID Bochkov, X Huang, MS Shamim, J Shin, D Turner, Z Ye, AD Omer, JT Robinson, T Schlick, BE Bernstein, R Casellas, ES Lander, EL Aiden. Cohesin Loss Eliminates All Loop Domains. Cell 171-2 (2017).
    Supplemental: Data, Interactive Figures

    Press: Science, Nature
  4. 4. NC Durand, MS Shamim, I Machol, SSP Rao, MH Huntley, ES Lander, EL Aiden. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments Cell Systems 3-1 (2016).
    Supplemental: Code
  5. 5. A Canela, Y Maman, S Jung, N Wong, E Callen, A Day, K-R Kieffer-Kwon, A Pekowska, H Zhang, SSP Rao, S-C Huang, PJ McKinnon, PD Aplan, Y Pommier, EL Aiden, R Casellas, A Nussenzweig. Genome Organization Drives Chromosome Fragility. Cell 170-3 (2017).
    Supplemental: Data
  6. 6. L Vian*, A Pekowska*, SSP Rao*, K-R Kieffer-Kwon*, S Jung*, L Baranello, S-C Huang, L El Khattabi, M Dose, N Pruett, AL Sanborn, A Canela, Y Maman, A Oksanen, W Resch, X Li, B Lee, AL Kovalchuk, Z Tang, S Nelson, MD Pierro, RR Cheng, I Machol, BG St Hilaire, NC Durand, MS Shamim, EK Stamenova, JN Onuchic, Y Ruan, A Nussenzweig, D Levens, EL Aiden, R Casellas. The Energetics and Physiological Impact of Cohesin Extrusion. Cell 173-5 (2018).
    (*) Co-First Authors.
  7. 7. K-R Kieffer-Kwon*, K Nimura*, SSP Rao*, J Xu*, S Jung, A Pekowska, M Dose, E Stevens, E Mathe, P Dong, S-C Huang, MA Ricci, L Baranello, Y Zheng, FT Ardori, W Resch, D Stavreva, S Nelson, M McAndrew, A Casellas, E Finn, C Gregory, BG St. Hilaire, SM Johnson, W Dubois, MP Cosma, E Batchelor, D Levens, RD Phair, T Misteli, L Tessarollo, G Hager, M Lakadamyali, Z Liu, M Floer, H Shroff, EL Aiden, R Casellas. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Molecular Cell 67-4 (2017).
    (*) Co-First Authors. Supplemental: Data
  8. 8. G Nir, I Farabella, CP Estrada, CG Ebeling, BJ Beliveau, HM Sasaki, SH Lee, SC Nguyen, RB McCole, S Chattoraj, J Erceg, JA Abed, NMC Martins, HQ Nguyen, MA Hannan, S Russell, NC Durand, SSP Rao, JY Kishi, P Soler-Vila, MD Pierro, JN Onuchic, SP Callahan, JM Schreiner, JA Stuckey, P Yin, EL Aiden, MA Marti-Renom, C-T Wu. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLOS Genetics 14-12 (2018).
  9. 9. TJ Henrich, NRP Lewine, S-H Lee, SSP Rao, R Berro, RM Gulick, JP Moore, AMN Tsibris, DR Kuritzkes. Differential Use of CCR5 by HIV-1 Clinical Isolates Resistant to Small-Molecule CCR5 Antagonists. Antimicrobial Agents and Chemotherapy 56 (2012).
  10. 10. TJ Henrich, PJ McLaren, SSP Rao, NH Lin, E Hanhauser, F Giguel, RM Gulick, H Ribaudo, PIW DeBakker, DR Kuritzkes. Genome-Wide Association Study of Human Immunodeficiency Virus (HIV)-1 Coreceptor Usage in Treatment-Naive Patients from An AIDS Clinical Trials Group Study. Open Forum Infectious Diseases 1 (2014).
  11. 11. L El Khattabi, H Zhao, J Kalchschmidt, N Young, S Jung, P Van Blerkom, P Kieffer-Kwon, K-R Kieffer-Kwon, S Park, X Wang, J Krebs, S Tripathi, N Sakabe, DR Sobreira, S-C Huang, SSP Rao, N Pruett, D Chauss, E Sadler, A Lopez, MA Nobrega, EL Aiden, FJ Asturias, R Casellas. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. Cell 178-5 (2019).