1991-96           University of Arizona, Tucson, AZ               B.S.     Ecology & Evolutionary Biology

1997-99           Los Alamos National Laboratory                   (post-grad)      Evolutionary Virology

1999-2005       University of California, San Diego                Ph.D.   Biology  (Douglas Richman, MD)

2005-07           University of California, San Francisco          Postdoctoral Fellow    Medicine





1997-99            Los Alamos National Laboratory                   GRA               Theoretical Biology (T-10)

1999-2005        University of California, San Diego                Doctoral Student         Biology

2005-07            University of California, San Francisco          Postdoctoral Fellow    Medicine

2008-present     University of California, San Francisco          Asst. Adj. Professor   Medicine (Infect. Dis.)





2007-present            Teaching Fellow [UCSF Medical School]

2007-2012                Guest Lecturer [UC Berkeley Department of Bioengineering]

2008-2009                Visiting Scientist [Gladstone Institute of Virology and Immunology]

2008-present            Staff Investigator [San Francisco Veterans Affairs Medical Center]

2009-present            Steering Committee member [UCSF Junior Faculty AIDS Research (JFAR)]

2011-present            Research Associate [Center for Comparative Genomics, California Academy of Sciences]





1999    GAANN Predoctoral Fellow

2002    Keystone Symposia Scholarship

2002    9th Conference on Retroviruses and Opportunistic Infections Travel Grant [Seattle, WA]

2003    10th Conference on Retroviruses and Opportunistic Infections Travel Grant [Boston, MA]

2004    11th Conference on Retroviruses and Opportunistic Infections Travel Grant [San Francisco, CA]

2004    11th International Workshop on HIV Dynamics & Evolution Scholarship [Stockholm, Sweden]

2004    Neal Nathanson, M.D. Investigator in Training award, presented by the International Society for Neurovirology [Sardinia, Italy]

2005    NIH AIDS Training Award (T32)

2006    Prize winner, Nano-Sciences and Biology Award Program [UC Berkeley Nanotechnology Club]

2007    3rd International Workshop on Targeting HIV Entry Scholarship [Washington, DC]

2008    NIH / NIDA Mentored Research Scientist Development Award (K01)

2011    UCSF REAC General Pilot Award in HIV/AIDS

2012    Center for AIDS Research Highly Innovative High Risk Research Award

2013    UCSF Center for AIDS Research Early-Career Award of Excellence in Basic Science





HIV, virology, molecular biology, evolution, population genetics, anatomic compartmentalization, drug resistance, coreceptor usage phenotype, immune escape, innate immunity, cytidine deaminases, pathogenesis, neuropathogenesis, machine learning, biostatistics, point-of-care diagnostics, endogeouns retroviruses







2005-present, American Association for the Advancement of Science


Service to Professional Organizations


2009 - present    UCSF Resource Allocation Program, Basic HIV/AIDS, Infectious Diseases, Global Health Review Committee member.

2010 - present    International Workshop on HIV Dynamics & EvolutionConference Chair, Organizing Committee member

2010 - present    UCSF Junior Faculty AIDS Researchers (JFAR)Chair, Steering Committee

2010 - present    UCSF AIDS Research Institute (ARI) Executive CommitteeCommittee Member

2011 - 2013        San Francisco VA Medical Center Biosafety CommitteeCommittee Member

2013 - present    UCSF CFAR Grant Review Conflict of Interest Committee    Committee Member

2013 - present    UCSF CFAR Internal Advisory Board   Committee Member




2006 - present   Ad hoc referee for AIDS, AIDS Research and Human Retroviruses, AIDS Research and Therapy, Bioinformatics, BMC Research Notes, Future Virology, In Silico Biology, International Journal of Bioinformatics Research and Applications, Journal of Acquired Immune Deficiency Syndromes, Journal of Infection, Journal of Infectious Diseases, Journal of Virology, Molecular Therapy, PLoS Computational Biology, PLoS Medicine, PloS One, PLoS Pathogens, Retrovirology, Virus Adaptation and Treatment.

2013 - present    Editorial Board Member, Journal of Acquired Immune Deficiency Syndromes (JAIDS)






2004               International Workshop on HIV Dynamics and Evolution; Stockholm, Sweden (invited talk)

2004               International Symposium on Neurovirology; Sardinia, Italy (invited talk)

2006               International Workshop on HIV Dynamics and Evolution; Woods Hole, MA (invited talk)

2007               International Workshop on Targeting HIV Entry; Washington, DC (invited talk)

2008               International Workshop on HIV Dynamics and Evolution; Santa Fe, NM (invited talk)

2009               International Workshop on HIV Dynamics and Evolution; Oxford, UK (invited talk)

2010               International Workshop on HIV Dynamics and Evolution; Asilomar, CA (invited talk)

2010               International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies; Dubrovnik, Croatia (poster)

2010               International AIDS Conference; Vienna, Austria (poster)




2002               Conference on Retroviruses and Opportunistic Infections, Seattle, WA (invited talk)

2004               Conference on Retroviruses and Opportunistic Infections, San Francisco, CA (poster)

2008               Conference on Retroviruses and Opportunistic Infections, Boston, MA (poster)

2013               CEPHIA (Consortium for the Evaluation and Performance of HIV Incidence Assays) Symposium, Atlanta, GA (invited talk)

2013               Conference on Retroviruses and Opportunistic Infections, Atlanta, GA (invited talk)




2004               Virologic, Inc. (now Monogram Biosciences), South San Francisco, CA

2007               Division of Experimental Medicine Inter-Lab Meeting

2007               CFAR Mentoring Symposium, UCSF-Gladstone Institute

2008               City College of San Francisco, Dept. of Chemistry

2008               Mills College, Oakland, CA

2008               Burton High School, San Francisco, CA

2008               Museum of Vertebrate Zoology, University of California, Berkeley

2009               California Academy of Sciences Research Seminar Series, San Francisco, CA

2009               De Anza College, Cupertino, CA

2011               California Academy of Sciences Research Seminar Series, San Francisco, CA

2012               UCSF Evolution Seminar Series

2012               World AIDS Day Symposium, J. David Gladstone Institutes, San Francisco, CA

2013               San Francisco VA Medical Center Research Seminar Series, San Francisco, CA

2013               Illumina, Inc., San Diego, CA

2013               UCSF Center for AIDS Research Mentoring Symposium, San Francisco, CA





1.     Eigenbrode SD, Pillai S. Neonate Plutella xylostella Responses to Surface Wax Components of a Resistant Cabbage (Brassica oleracea). J Chem Ecol. 1998 Oct; 24(10):1611-1627


2.     Korber B, Foley BT, Kuiken C, Pillai S, Sodroski JG. Numbering positions in HIV relative to HXB2CG. pp. III-102-111 in Human Retroviruses and AIDS 1998. Edited by: Korber B, Kuiken CL, Foley B, Hahn B, McCutchan F, Mellors JW, and Sodroski J. Published by: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM. (1998)


3.     Spencer JL, Pillai S, Bernays EA. Synergism in the oviposition behavior of Plutella xylostella: sinigrin and wax compounds. J Insect Behav. 1999 Jul;12(4):483-500.


4.     Thakallapally R, Rose P, Vasil S, Pillai S, Kuiken C. Reagents for HIV/SIV vaccine studies. pp. 506-516 in Human Retroviruses and AIDS 1999. Edited by: Kuiken CL, Foley B, Hahn B, Korber B, McCutchan F, Marx PA, Mellors JW, Mullins JI, Sodroski J, and Wolinksy S. Published by: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM. (1999)


5.     Good B, Peay J, Pillai S, Corbeil J. Class prediction based on gene expression: applying neural networks via a genetic algorithm wrapper. pp. 122-130 in Proceedings of the 2001 Genetic and Evolutionary Computing Conference (San Francisco, CA.)


6.     Kalish ML, Korber BT, Pillai S, Robbins KE, Leo YS, Saekhou A, Verghese I, Gerrish P, Goh CL, Lupo D, Tan BH, Brown TM, Chan R. The sequential introduction of HIV-1 subtype B and CRF01AE in Singapore by sexual transmission: accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology. 2002 Dec 20;304(2):311-29.


7.     Pillai S, Good B, Richman D, Corbeil J. A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses. 2003 Feb;19(2):145-9.


8.     Ali A, Pillai S, Ng H, Lubong R, Richman DD, Jamieson BD, Ding Y, McElrath MJ, Guatelli JC, Yang OO. Broadly increased sensitivity to cytotoxic T lymphocytes resulting from Nef epitope escape mutations. J Immunol. 2003 Oct 15;171(8):3999-4005.


9.     Kunstman KJ, Puffer B, Korber BT, Kuiken C, Smith UR, Kunstman J, Stanton J, Agy M, Shibata R, Yoder AD, Pillai S, Doms RW, Marx P, Wolinsky SM. Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea. J Virol. 2003 Nov;77(22):12310-8.


10.   Yu Q, Konig R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin J, Landau NR. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol. 2004 May;11(5):435-42.


11.  Strain MC, Letendre S, Pillai S, Russell T, Ignacio CC, Gunthard HF, Good B, Smith DM, Wolinsky SM, Furtado M, Marquie-Beck J, Durelle J, Grant I, Richman DD, Marcotte T, McCutchan JA, Ellis RJ, Wong JK. Genetic composition of HIV-1 in CSF and plasma without treatment and during failing combination antiretroviral therapy. J Virol. 2005 Feb;79(3):1772-88.


12.  Pillai S, Good B, Kosakovsky Pond S, Wong JK, Strain MC, Richman DD, Smith DM. Semen-specific genetic characteristics of HIV-1 env. J Virol. 2005 Feb;79(3):1734-42.


13.  Pillai S, Woelk C, Kosakovsky Pond S, Richman D, Smith D. “Codon volatility” does not reflect selective pressure on the HIV-1 genome. Virology. 2005 Jun 5;336(2):137-43.


14.  Coleman S, Madrid R, Van Damme N, Bouchet J, Servant C, Pillai S, Benichou S, Guatelli J. HIV-1 Nef uses different AP complex family members to modulate specific cellular proteins. J Virol. 2006 Feb;80(4):1837-49.


15.  Pillai S, Kosakovsky Pond SL, Wrin T, Good B, Strain MC, Ellis R, Letendre S, Smith DM, Gunthard H, Grant I, Marcotte T, McCutchan JA, Richman DD, Wong JK. Genetic attributes of cerebrospinal fluid-derived HIV-1. Brain. 2006 Jul;129(7):1872-83.


16.  Smith DM, Strain MC, Frost SD, Pillai SK, Wong JK, Wrin T, Liu Y, Petropolous CJ, Daar ES, Little SJ, Richman DD. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology. 2006 Nov 10;355(1):1-5.


17.  Noviello CM, Kosakovsky Pond S, Lewis MJ, Richman DD, Pillai SK, Yang O, Little SJ, Smith DM, Guatelli JC. Maintenance of Nef-mediated modulation of MHC I and CD4 after sexual transmission of HIV-1. J Virol. 2007 May;81(9):4776-86.


18.  Willberg CB, Pillai SK, Sharp E, Rosenberg M, Agudelo JD, Barbour J, Nixon DF. Rational epitope selection for T cell specificity under resource limited conditions. Clin Vaccine Immunol. 2007 Jun;14(6):785-8.


19.  Low AJ, Dong W, Chan D, Sing T, Swanstrom R, Jensen M, Pillai SK, Good B, Harrigan PR. Current V3 Genotyping Algorithms are Inadequate for Predicting X4 Co-receptor Usage in Clinical Isolates. AIDS. 2007 Sep 12;21(14):F17-24.


20.  Pillai SK, Wong JK, Barbour JD. Turning up the volume on mutational pressure: is more of a good thing always better? (a case study of HIV-1 Vif and APOBEC3). Retrovirology. 2008 Mar 13;5(1):26.


21.  Pilcher CD, Wong JK, Pillai SK. Inferring HIV transmission dynamics from phylogenetic sequence relationships. PLoS Med. 2008 Mar 18;5(3):e69.


22.  Kosakovsky Pond SL, Poon AFY, Zarate CS, Smith DM, Little SJ, Pillai SK, Ellis RJ, Wong JK, Leigh Brown AJ, Richman DD, Frost SDW. Estimating selection pressures on HIV-1 using phylogenetic likelihood models. Stat Med. 2008 Oct 15;27(23):4779-89.


23.  Joos B, Fischer M, Kuster H, Pillai SK, Wong J, Boni J, Hirschel B, Weber R, Trkola A, Gunthard H. HIV rebounds from latently infected cells, rather than from continuing low-level replication. Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16725-30.


24.  Smith DM, Zárate S, Shao H, Pillai SK, Letendre SL, Wong JK, Richman DD, Frost SDW, Ellis RO. Pleocytosis Is Often Associated with Disruption of HIV Compartmentalization between Blood and Cerebral Spinal Fluid Viral Populations. Virology. 2009 Mar 1;385(1):204-8.


25.  Yukl S, Pillai SK, Chang K, Li P, Pasutti W, Ahlgren C, Havlir D, Richman DD, Little S, Daar E, Rice A, Wong JK. Latently-Infected CD4+ T Cells are Enriched for HIV-1 Tat Variants with Impaired Transactivation Activity. Virology. 2009 Apr 25;387(1):98-108.


  1. 26. Joos B, Rieder P, Fischer M, Kuster H, Rusert P, Trkola A, Pillai SK, Wong JK, Weber R, Günthard HF. Association between Specific HIV-1 Env Traits and Virologic Control in vivo. Infect Genet Evol. 2010 Apr;10(3):365-72.

  1. 27. Jha AR, Pillai SK, York VA, Sharp ER, Storm EC, Wachter DJ, Martin JN, Deeks SG, Rosenberg MG, Nixon DF, Garrison KE. Cross sectional dating of novel haplotypes of HERV-K 113 and HERV-K 115 indicate these proviruses originated in Africa before Homo sapiens. Mol Biol Evol. 2009 Nov;26(11):2617-26.

  1. 28. Manosuthi W, Butler DM, Perez J, Poon A, Kosakovsky Pond S, Pillai SK, Mehta SR, Pacold ME, Richman DD, Smith DM. Protease Polymorphisms in HIV-1 Subtype CRF01_AE Represent Selection by Antiretroviral Therapy and Host Immune Pressure. AIDS. 2010 Jan 28;24(3):411-6.

  1. 29. Wong JK, Strain MC, Porrata R, Reay E, Sankaran-Walters S, Ignacio CC, Russell T, Pillai SK, Looney DJ, Dandekar S. In vivo CD8+ T-cell suppression of SIV viremia is not mediated by CTL clearance of productively infected cells. PLoS Pathog. 2010 Jan 29;6(1):e1000748.

  1. 30. Rempel H, Sun B, Calosing C, Pillai SK, Pulliam L. Interferon-α drives monocyte gene expression in chronic unsuppressed HIV-1 infection. AIDS. 2010 Jun 19;24(10):1415-23.

  1. 31. Skasko M, Tokarev A, Cheng-Chang C, Fischer WB, Pillai SK, Guatelli J. BST-2 is rapidly down-regulated from the cell surface by the HIV-1 protein Vpu: evidence for a post-ER mechanism of Vpu-action. Virology. 2011 Mar 1;411(1):65-77.

  1. 32. Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK. Human Endogenous Retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans. PLoS One. 2011 May 25; 6(5): e20234. doi:10.1371/journal.pone.0020234.

  1. 33. Pillai SK, Abdel-Mohsen M, Guatelli J, Skasko M, Monto A, Fujimoto K, Yukl S, Greene W, Kovari H, Rauch A, Fellay J, Battegay M, Hirschel B, Witteck A, Bernasconi E, Ledergerber B, Gunthard H, Wong JK. Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3035-3040.

  1. 34. Yukl SA, Boritz E, Busch M, Bentsen C, Chun TW, Douek D, Eisele E, Haase A, Ho YC, Hütter G, Justement JS, Keating S, Lee TH, Li P, Murray D, Palmer S, Pilcher C, Pillai SK, Price RW, Rothenberger M, Schacker T, Siliciano J, Siliciano R, Sinclair E, Strain M, Wong J, Richman D, Deeks SG. Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS Pathog. 2013 May;9(5):e1003347.

  1. 35. Raposo RAS, Abdel-Mohsen M, Holditch SJ, Kuebler PJ, Cheng RG, Eriksson EM, Liao W, Pillai SK*, Nixon DF*. Increased Expression of Intrinsic Antiviral Genes in HLA-B57*-Positive Individuals. J Leukoc Biol. 2013 Aug 8. [Epub ahead of print] *Co-senior authors

  1. 36. Raposo RAS, Abdel-Mohsen M, Bilska M, Montefiori D, Nixon DF, Pillai SK. Effects of Cellular Activation on Anti-HIV-1 Restriction Factor Expression Profile in Primary Cells. J Virol. 2013 Aug 21. [Epub ahead of print]

  1. 37. Abdel-Mohsen M, Raposo RAS, Deng X, Li M, Liegler T, Sinclair E, Salama M, Ghanem H, Hoh R, Wong JK, David M, Nixon DF, Deeks SG, Pillai SK. Expression Profile of Host Restriction Factors in HIV-1 Elite Controllers. Retrovirology. 2013 Oct 16;10(1):106.

  1. 38. Abdel-Mohsen M, Deng X, Liegler T, Guatelli JC, Salama M, Ghanem H, Rauch A, Ledergerber B, Deeks SG, Gunthard HF, Wong JK, Pillai SK. Effects of Alpha Interferon Treatment on Intrinsic Anti-HIV-1 Immunity In Vivo. J Virol. 2014 Jan; 88(1):763-7.

  1. 39. Wang C, Abdel-Mohsen M, Strain MC, Lada SM, Yukl S, Cockerham L, Pilcher CD, Hecht FM, Sinclair E, Liegler T, Richman DD, Deeks SG, Pillai SK. Decreased HIV-1 Transcription in CCR5 Delta-32 Heterozygotes On Suppressive Antiretroviral Therapy. J Infect Dis. 2014 Jun 16. pii: jiu338.

  1. 40. Dynamic regulation of host restriction factor expression over the course of HIV-1 infection in vivo. Saraiva Raposo RA, Abdel-Mohsen M, Deng X, Hecht FM, Pilcher CD, Pillai SK, Nixon DF. J Virol. 2014 Jul 16. pii: JVI.01771-14.

  1. 41. Abdel Mohsen M, Deng X, Danesh A, Liegler T, Jacobs ES, Rauch A, Ledergerber B, Norris PJ, Günthard HF, Wong JK, Pillai SK. Role of MicroRNA Modulation in the Interferon-α/Ribavirin Suppression of HIV-1 In Vivo. PLoS One. (in press)

  1. 42. Abdel-Mohsen M, Wang C, Strain MC, Lada SM, Deng X, Yukl S, Cockerham L, Pilcher CD, Hecht FM, Sinclair E, Liegler T, Richman DD, Deeks SG, Pillai SK. Select Host Restriction Factors Are Associated with HIV Persistence during Antiretroviral Therapy. (under review) 



Web-based software


Creator of: several applications on the Los Alamos National Lab HIV Sequence Database website

            Available for public use at:


Creator of: WetCat (Prediction of Coreceptor Usage for HIV-1)

   Available for public use at:


Co-Creator of: Virus Evolution (An Evolutionary Rates Database)

            Available for public use at:


Musical Performance


Singer/Songwriter/Pianist in 3 Bay Area bands:

            The Satish Collective (

            Black Mahal (

            Boy In The Bubble (





1.     Pillai SK, Pasutti WD, McCutchan JA, Collier AC, Clifford D, Gelman B, Morgello S, McArthur J, Grant I, Ellis R, Letendre S, Wong JK. Validation of a V3-Based Genetic Biomarker of HIV-1 Neurovirulence. (in prep)


2.     Pillai SK, Günthard HF, Ellis RJ, Letendre S, Kee K, Denison B, Hsia K, Spector S, Grant I, Richman DD, McCutchan JA, Wong JK. Effects of anatomic compartmentalization on HIV-1 population dynamics and evolution of antiretroviral resistance. (in prep)


3.     Pillai SK, Pasutti W, Li P, Ahlgren C, Yukl S, Fujimoto K, Ellis R, Masliah E Wong JK. Genetic characterization of contemporaneous HIV-1 RNA and DNA variants in the brain and lymphoid tissue (in prep)


4.     Pillai SK, Porrata R, Good B, Low A, Harrigan R, Wong JK. Enhanced Prediction of HIV-1 Coreceptor Phenotype using BaTCLaW (Bayesian Triplet Classification Widget). (in prep)


5.     Porrata RA, Pillai SK, Reay E, Sankaran S, Dandekar S, Wong JK. CD8+ T Cells Suppress Simian Immunodeficiency Virus Replication by Increasing the Intracellular Delay of Infected CD4+ T Cells. (in prep)





Effects of Interferon-alpha Treatment on Anti-HIV-1 Intrinsic Immunity in vivo

20th Conference on Retroviruses and Opportunistic Infections (3/2013, Atlanta, GA)

Acquisition of Enfuvirtide Resistance Attenuates HIV-1 Virulence

International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies (6/2010, Dubrovnik, Croatia)

Role of Host Restriction in the Interferon-α-Mediated Suppression of HIV-1 in vivo

17th International Workshop on HIV Dynamics & Evolution (4/2010, Asilomar, CA)

Determining the Role of APOBEC3 in the Interferon-α Suppression of HIV-1 in vivo

17th Conference on Retroviruses and Opportunistic Infections (2/2010, San Francisco, CA)

Simulation of residual HIV-1 replication during suppressive therapy: consequences of myopic sampling.

16th International Workshop on HIV Dynamics & Evolution (4/2009, Oxford, UK)


Genotype-based prediction of HIV-1 coreceptor usage via machine learning.

15th International Workshop on HIV Dynamics & Evolution (4/2008, Santa Fe, NM)


Validation of a V3-based genetic biomarker of HIV-1 neurovirulence.

15th Conference on Retroviruses and Opportunistic Infections (2/2008, Boston, MA)


Genotype-based prediction of HIV-1 coreceptor usage: clinical applicability.

3rd International Workshop on Targeting HIV Entry (12/2007, Washington, DC)


Evolution of HIV-1 drug resistance in the CNS: causes and consequences.

13th International Workshop on HIV Dynamics & Evolution (4/2006, Woods Hole, MA)