Susanna L. Lamers
susanna@hivanalysis.net
Ph: 985-493-3487
Research Background
and Interests
For almost 20 years Susanna has worked in the area of molecular
evolution with an emphasis on the epidemiology of the Human
Immunodeficiency Virus within individuals, populations and upon
transmission events. To allow for the simultaneous work between
laboratories, she started her first scientific consulting firm in 1995.
She has been contracted individually by researchers at the University
of Florida in Gainesville, FL, The University of Massachusetts,
Worchester, MA and the University of California in San Francisco. In
2000, she initiated a plan to develop the first virus-specific data
management and analysis software, called HIVbase. She successfully
funded the project through several NSF and NIH Small Business Innovated
Research grants. The software is now in its third release and
used internationally. Susanna is currently a consultant for
the AIDS and Cancer Specimen Resource, Michael McGrath at the
University of California in San Francisco, a partner at BioInfoExperts
and the scientific director at Gene Johnson Inc.
Current projects include marketing/licensing of HIVbase software
and the development of a web-based version of HIVbase for the AIDS and
Cancer Specimen Resource at UCSF (with Gene Johnson Inc.), the
study of the evolution of HIV in the central nervous system of patients
that develop dementia (with BioInfoExperts), utilizing HIV as a
biomarker to study metastasis (with BioInfoExperts), the integration of
HIVbase with an evolving neural network application to identify genetic
aspects of HIV responsible for viral tropism (with Gene Johnson
in cooperation with Natural Selection Inc.), and other exploratory
research projects at the AIDS and Cancer Specimen Resource.
Publications
Book Chapters
1. Goodenow, MM, JW Sleasman, and SL Lamers. Persistence of
multiple maternal genotypes in infants infected by perinatal
transmission. In Vaccines 93 Modern Approaches to New Vaccines
including Prevention of AIDS. pp. 125-129, 1993.
Journal Articles
1. Salemi M, Lamers S, Yu S, Oliveira T, Fitch W,
McGrath MS. Phylodynamic Analysis of Human Immunodeficiency Virus
Type 1 in Distinct Brain Compartments Provides a Model for the
Neuropathogenesis of AIDS. Journal of Virology 79 (17):11343-11352. 2005
2. Lamers SL., Scott Beason, Luke Dunlap, Robert
Compton, Marco Salemi. Specialized PC/Windows-based software that
offers powerful data management and exploration tools for locally held
HIV-1 genetic, experimental, and clinical data. Bioinformatics, 20(3)
Feb, 2004.
3. Tuttle, DL, CB. Anders, MJ Acquino-de Jesus, PP
Poole, SL Lamers, DR Briggs, SM Pomeroy, L Alexander, KWC Peden, WA
Andiman, JW Sleasman, and MM Goodenow. Increased replication by
nonsyncytium-inducing HIV-1 isolates in monocyte-derived macrophages is
linked to clinical decline in patients. AIDS Res Hum Retroviruses. 2002
Mar 20;18(5):353-62.
4. Perez EP, Rose SL, Peyser B, Lamers SL, Burkhardt
B, Dunn BM, Hutson AD, Sleasman JW, Goodenow MM. Human
Immunodeficiency Virus Type 1 Protease Genotype Predicts Immune and
Viral Responses to Combination Therapy with Protease Inhibitors (Pis)
in PI-Naïve Patients. J. Inf. Diseases 2001;183:579-88
5. Ping LH, Nelson JA, Hoffman IF, Schock J, Lamers
SL, Goodman M, Vernazza P, Kazembe P, Maida M, Zimba D, Goodenow MM,
Eron JJ Jr, Fiscus SA, Cohen MS, Swanstrom R. Characterization of V3
sequence heterogeneity in subtype C human immunodeficiency virus type 1
isolates from Malawi: underrepresentation of X4 variants. J Virol. 1999
Aug;73(8):6271-81.
6. Skinner, L.M., S.L. Lamers, J.C. Sanders, M.E.
Eyster, M.M. Goodenow, and M. Katzman. Analysis of a large collection
of natural HIV-1 Integrase Sequence, Including Those From Long-Term
Nonprogressors. J. Acq. Imm. Def. Synd.and Hum. Ret. 19:99-110, 1998.
7. White G.B., A. Pfahnl, S. Haddock, S.L. Lamers,
Robert M. Greenberg, and P. Anderson. Structure of a Putative
Sodium Channel from the Sea Anenome Aiptasia pallida. Invertebrate
Neuroscience 3, 317-326, 1998.
8. Barrie, K.A., E. Perez, S.L. Lamers, W.F.
Farmerie, B.M. Dunn, J.W. Sleasman, and M.M. Goodenow. Natural
Variation in HIV-1 Protease, Gag p7 and p6, and Protease Cleavage
Sites Within Gag/Pol Polyproteins: Amino Acid Substitutions in the
Absence of Protease Inhibitors in Mothers and Children Infected by
Human Immunodeficiency Virus Type 1. Virology. 219:407-416. 1996.
9. Lamers S.L., J.W. Sleasman, and M.M.
Goodenow. A Model for Alignments of env V1 and V2 Hypervariable
Domains from Human Immunodefiviency Viruses. Aids Research and Human
Retroviruses. 12:1169-1177, 1996.
10. Lamers, SL. J.W. Sleasman, K.A. Barrie, S.M.
Pomeroy, D.J. Barrett, and M.M. Goodenow. Persistence of Multiple
Maternal HIV-1 Genotypes in Infants Infected by Perinatal Transmission.
J. Clin. Invest. 93:380-390, 1994.
11. Lamers SL, JW Sleasman, KA Barrie, SM Pomeroy, DJ
Barrett, and MM Goodenow. Independent Variation and Positive Selection
in env V1 and V2 Domains Within Maternal-Infant Strains of Human
Immunodeficiency Virus Type 1 in vivo. J. Virol. 67:3951-3960, 1993.
Publications under review or in preparation:
1. Lamers S.L., Marco Salemi, Michael M. McGrath,
Gary B. Fogel, Prediction of HIV Phenotype Using Evolved Neural
Networks. IEEE/ACM Transactions on Computational Biology and
Bioinformatics. Manuscript Submitted
2. Lamers S. de Oliveria, T., Beason S. Compton R.
Dunlap, L. McGrath, M.S., Salemi, M. Large-Scale Sequence Screening of
drug resistance mutations. Journal of Biomedical Informatics.
Manuscript Submitted.
3. Lamers S. L. , Derek Galligan, Li Zhao, Stephanie
Yu, Lamia Shagrun, Tulio De Oliveira, Marco Salemi, Michael S.
McGrath. HIV in AIDS Related Lymphoma Represents a Homogeneous
Population In Vivo. Manuscript in Preparation.
4. Salemi M, Lamers, S.L., de Oliveria, T, Galligan,
D., Zhao, L., Shagrun, L., McGrath, M.S. Phylodynamic analysis of HIV
in mulisite tissue biopsies. Manuscript in preparation.
5. Lamers S. L. de Oliveria, T, Galligan, D. Salemi,
M. and MS McGrath. HIV as a Viral Biomarker to Track Metastasis.
Manuscript in preparation.
1., SL Lamers, Galligan D, Zhao L, Yu S, Shagrun L, De Oliveria
T, Salemi M, McGrath MS. Multi-site tissue autopsy samples from
patients with dementia and AIDS related lymphoma show distinct patterns
of HIV evolution in vivo. International AIDS Conference, Toronto,
Canada, August 13-18, 2006
2. SL Lamers, Salemi M, de Oliveira T, Beason S, Compton R, Goodenow M,
McGrath MS. A protocol for HIV-1 env alignments assists in
determining the evolutionary dynamics of the V1, V2 and V4
hypervariable domains. Keystone Symposia, HIV Pathogenesis
Meeting, Keystone, CO, March, 2006.
3. MS McGrath, Lamers SL, Salemi M. Evolutionarily distinct forms
of HIV in AIDS lymphoma and dementia. 9th International
Conference on Malignancies in AIDS and Other Acquired
Immunodeficiencies: Basic, Epidemiologic and Clinical Research, North
Bethesda, MD, September 26-27, 2005. (Selected for presentation).
4. MS McGrath, Salemi M, Lamers SL. Genetic analysis of HIV in
AIDS malignancies. 2005 International Meeting of the Institute of
Human Virology, Baltimore, MD, August 29-September 2, 2005. (Selected
for presentation)
5. SL Lamers, Salemi M, McGrath MS. HIV-1 envelope domains
derived from AIDS related lymphoma tissues display unique substitution
patterns as compared to published envelope domains. 3rd
International AIDS Society Conference on HIV Pathogenesis and
Treatment, Rio de Janeiro, Brazil, July 24-27, 2005.
6. SL Lamers, Salemi M., Compton R., Beason S.. Genetic management
software with tools providing novel querying ability and composition
analysis of genetic data. USL bioinformatics symposia, March
2005. (Selected for Presentation)
7. SL Lamers, Salemi M., Yu S., MS McGrath., HIV genomic
variability in LTRS from brain and lymphoma. XV International AIDS
Conference, Bangkok, Thailand, July 2004 (Selected for presentation)
8. M. Salemi, Lamers SL, Yu S., McGrath MS, HIV genomic variability in
LTRS from brain and lymphoma. 11th International Workshop on HIV
Dynamics and Evolution, Stockholm, Sweden, April, 2004 (Selected for
presentation)
9. S. Beason, Dunlap L., Compton R., Lamers SL. Software that
supports novel integration and analysis of locally held genetic,
experimental, and clinical data. Stanford workshop on Molecular
Evolution, July 2003. (Selected for Presentation)
10. SL. Lamers, Salemi M., Burkhardt B, Fitch WF, Goodenow MM.
Compartmentalization and migration rates of HIV-1 sub-populations in
pediatric patients. Stanford workshop on Molecular Evolution, July
2003. (Selected for Presentation)
NSF OII-0610688 SBIR Phase I: Machine learning software for viral
sequence analysis and diagnostics. 7/06-12/06. Amount
$100,000. Grantee Institution: Natural Selection Inc. The goal of
this project is to utilize evolving neural networks to identify novel
genetic attributes of HIV genetic sequences associated with viral
tropism. Role: Consultant
NSF DMI- 0349669 SBIR Phase II and Phase IIb: HIVbase, Data Integration
Software to Support the Study of Chronic Viruses. Dates
1/04- 1/02/07 Amount $598,871 The goal of this project is
to implement new algorithms for alignments, search protocols and data
formatting into HIVbase. Grantee Institution: Gene Johnson . Role:
Principal Investigator.
NIH ZMH1 BRB-S HIV Sequence evolution in AIDS Dementia Pathogenesis.
Dates 12/04- 12/09. Amount $5,000,000. The goal of this project is to
investigate the evolution of HIV sequences present in the CNS and other
tissues of HAD patients. Role: Consultant.
NSF DMI-0349669 SBIR IIB: Matched funding from NSF to support the
development an on-line data resource for the AIDS and Cancer Specimen
Resource Dates 7/06- 7/07. Amount $99,000 Role: Principal Investigator
NSF DMI-0349669 SBIR IICC: Supplemental teaching grant to involve
students at a community college in business research. Dates 9/06 -
10/06. Amount $40,000. Role: Principal Investigator
NSF DMI-0349669 SBIR IICC: Supplemental teaching grant to
involve students at a community college in business research. Dates
10/06 - 12/06. Amount $40,000. Role: Principal Investigator
NIH UO1 CA66259-09 TDC: West Coast AIDS and Cancer Specimen Resource.
Dates 6/02-6/07. Amount $7,515,580. The major goal for this
project is to perserve, supply and perform research on tissues from
autopsies of patients that died with AIDS, cancer or both. Role:
Consultant.
NIH R43-AI-56904 SBIR Phase I: HIVbase: The Genetic Data Solution.
Dates 9/03- 2/04 Amount $100,000 The major goal for this project is to
continue development of HIV-specific software especially designed for
data basing and novel analysis of HIV sequence data and associated
annotations. Grantee Institution: Gene Johnson . Role: Principal
Investigator.
NSF DMI-0232127 SBIR Phase I: HIVBase, Data Integration Software to
Support the Study of Chronic Viruses. Dates 1/03-6/03 Amount
$100,000. The major goal for this project is to develop HIV-specific
software especially designed for data basing and novel analysis of HIV
sequence data and associated annotations. Grantee Institution: Gene
Johnson . Role: Principal Investigator.
1. Introduzione Alle Techniche do Bioinformatica per analisi
epidemiologico-moleculari, con particolare rifermento alla virologia
dell 'HIV. Sept 2003. Instituto Superiore di Sanita Rome, Italy.
2. Advanced Bioinformatics and Virus Molecular Epidemiology Workshop,
FioCruz in Salvador, Bahia, Brazil. June 12 to 18, 2004.
3. Introduzione Alle Techniche do Bioinformatica per analisi
epidemiologico-moleculari, con particolare rifermento alla virologia
dell 'HIV. Oct. 2004 Instituto Superiore di Sanita Rome, Italy.
4. Introduction to HIVbase and analysis of genetic data from viruses.
July, 2005, Stellenbosh University, Cape Town, South Africa
5. HIVbase workshop. September, 2005, FioCruz in Salvador, Bahia, Brazil
6. HIV molecular biology, database development and programming.
September-December 2006, Valencia College, Orlando Florida
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Analysis Group at BioinfoExperts.
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