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-present               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)]





1999-2001          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)





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







2005-present, American Association for the Advancement of Science


Service to Professional Organizations


2005-present   CNS HIV Anti-Retroviral Effects Therapy Research Group                        Bioinformaticist


2008-present   Junior Faculty AIDS Research (JFAR)                                  Steering Committee member





2006-present   Ad hoc referee for PLoS Medicine, PLoS Computational Biology, AIDS Research and Therapy, Journal of Infection, AIDS Research and Human Retroviruses, In Silico Biology, Virus Adaptation and Treatment, Journal of Acquired Immune Deficiency Syndromes.






International Workshop on HIV Dynamics and Evolution; Stockholm, 2004 (invited talk); Woods Hole, 2006 (invited talk); Santa Fe, 2008 (invited talk) ); Oxford, 2009 (poster)

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

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




Conference on Retroviruses and Opportunistic Infections; 2002 (talk); 2004 (poster); 2008 (poster)




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






K01 DA024654 (PI)                                                                                       5/01/2008 - 4/30/2013

NIH/NIDA                                                                                                     $167,000 direct/yr 1

Antiviral Role of APOBEC3 in HIV/HCV Coinfected Patients                    $835,000 direct/yrs 1-5





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.


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. (in press)


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.


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 (in press)


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 Pathogens (in press)


30.  Kuiken C, Kunstman K, Kunstman J, Bhattacharya T, Kommander K, Good B, Pillai SK, Wolinsky S. Successive dominance of human immunodeficiency virus type 1 sequences in patients receiving combination antiretroviral therapy. (submitted)


31.  Kosakovsky Pond SL, Scheffler K, Poon AFY, Gravenor MB, Woelk CH, Zarate S, Nickle DC, Pillai SK, Leigh Brown AJ, Richman DD, Frost SDW. Evolutionary fingerprinting of viral genes: searching for patterns in a sea of change. (submitted)


32.  Rempel H, Sun B, Calosing C, Pillai SK, Pulliam L. Interferon-α drives monocyte gene expression in chronic unsuppressed HIV-1 infection. (submitted)




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)





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)