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                                Adam Zemla, Ph.D.

Lawrence Livermore National Laboratory                    Phone:   (925) 423-5571
Computing Applications & Research                         Fax:     (925) 423-6437
Global Security Computing Applications Division, L-174    E-mail:  adamz@llnl.gov
7000 East Ave., Livermore, CA 94550, USA                  Bldg: 132S,  Room: 1704

Home address:
986 Country Glen Ln., Brentwood, CA 94513                  Phone:  (925) 516-4682

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Research Interest

-  protein structure analysis and modeling (applications of protein structure
   analysis/modeling to research efforts in biology)
-  mathematical modeling, biological applications
-  scientific computing, programming and database development
-  numerical analysis, partial differential equations with local singularities

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Professional experience

[09/03-present] Computing Applications & Research (CAR), Global Security 
Computing Applications Division (GSCAD), LLNL, USA., computer scientist

[2002-03] Computing Applications & Research (CAR), Chemical & Biological
National Security Program (CBNP), Biology & Biotechnology Research Program 
(BBRP), Biodefense Division, Bioinformatics, LLNL, USA., computer scientist 

[1999-02] Biology & Biotechnology Research Program (BBRP), Protein Structure 
Prediction Center at LLNL, USA., biomedical scientist/computer scientist

[1998-99] Applied Science, UC Davis, USA., (Protein Structure Prediction Center 
at LLNL) research associate

[1996-98] Center of Advanced Research in Biotechnology (CARB), University of 
Maryland, USA., (Protein Structure Prediction Center at LLNL) research associate  

[1994-95] Danish Computer Center for Research and Education, Danish Institute of 
Mathematical Modelling, UNI*C, Copenhagen, Lyngby, Denmark, computer scientist

[1992-95] BAZA Ltd., Computer company, Warsaw, Poland, manager of UNIX systems 
dept., also responsible for marketing and trade of UNIX computers 

[1992-94] The Mathematical Institute of the Polish Academy of Sciences (IM PAN), 
Warsaw, Poland, UNIX system administrator

[1987-90] Computational Center of the Mathematical Institute of Soviet Academy 
of Sciences, Moscow, Russia, mathematician 

[1986-99] Numerical Analysis Laboratory of the Mathematical Institute of the 
Polish Academy of Sciences (IM PAN), Warsaw, Poland, professor associate, 
researcher

[1981-86] Computational Center of Institute of Nuclear Research (CYFRONET),
Swierk, Poland, mathematician, programmer

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Education

M.Sc. Numerical Analysis, Department of Mathematics, Informatics and Mechanics, 
      Warsaw University, Poland

Ph.D. Computational Mathematics and Physics, Department of Computational 
      Mathematics, Moscow University, Russia

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Other professional skills

-  Programming languages: C, Fortran, Pascal, PVM, MPI, Java, Perl, HTML 
-  Operating systems: UNIX, LINUX, Windows

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Involved in projects

-  [2006-present] PI on the LLNL LDRD 06-ERD-059 project: A novel structure-driven 
approach to sequence pattern definition for remote homology detection. 
Cooperation with: C. Zhou from LLNL.

-  [2004-2005] Co-Investigator on the project: "Plague Plasminogen Activator
as a Vaccine Component". The goal of this project is to investigate whether or
not the recombinant plasminogen activator of Yersinia pestis can protect against
plague infection. Sponsor of the project: Sealy Center for Vaccine Development,
University of Texas Medical Branch at Galveston.
Cooperation with: V. Motin from UTMB.

-  [2003-2005] PI on the LDRD-ER project: Protein Classification Based on
Analysis of Local Sequence-Structure Correspondence.
Cooperation with: T. Slezak and C. Zhou from LLNL.

-  [2002-present] Development of a fully automated system for 3D protein
structure predictions, development of computational bioinfrastructure at Lawrence
Livermore National Laboratory (LLNL).
Cooperation with: T. Slezak (LLNL, USA).

-  [2001-present] Application of AS2TS (automated protein structure modeling
system) and LGA (protein structure comparison program) to:
a) facilitate the molecular replacement (MR) phasing technique in experimental
   X-ray crystallographic determination of protein structure.
   Collaboration with B. Rupp, B. Segelke from LLNL.
b) modeling proteins in pathogens such as foot and mouth disease virus, west
   nile virus, and variola virus (smallpox). These models are being used for
   studies and starting a new effort in designing protein-based pathogen
   detection signatures.
   Collaboration with T. Slezak, P. Fitch, P. McCready and R. Balhorn from LLNL.

-  [2001-2003] PI on the LDRD-LW project: Automated 3-D Protein Structure
Predictions Based on Sensitive Identification of Sequence Homology (AS2TS).
Cooperation with: T. Slezak and D. Barsky from LLNL.

-  [1996-2003] Organizing the CASP process (Critical Assessment of Protein
Structure Prediction). Development of a protein structure prediction facility
(LLNL & UC Davis & University of Maryland, USA). The project is to establish a
Center for the assessment and development of computational methods of determining
protein structure (for more details see http://PredictionCenter.llnl.gov).
Structure prediction is a 'grand challenge' problem in high performance computing. 
The Center is intended to directly support the CASP meetings and to build
foundations for the CASP process in general.
Cooperation with: J. Moult (CARB, University of Maryland, USA), T. Hubbard
(Sanger Centre, Hinxton, UK), K. Fidelis (LLNL, USA).

-  [1994-1995] LAPACK-90. Development of FORTRAN-90 interface for LAPACK 
(Linear Algebra PACKage), a library of Fortran-77 subroutines for solving the 
most commonly occurring problems in numerical linear algebra.
Cooperation with: J.J. Dongarra (Oak Ridge Nat. Lab., USA), 
J.Du Croz & S. Hammarling (Numerical Algorithm Group, Oxford, UK), 
J. Wasniewski (UNI*C, Denmark). 

-  [1993-1994] Parallel computing using PVM (Parallel Virtual Machine) and its 
practical application in image processing when applying methods of wavelets 
theory. 
Cooperation with A. Wakulicz (IM PAN, Poland).

-  [1992-1994] Computer Modeling of Stochastic Control Problems. Applying simulated 
annealing algorithm to search for the solution of an ergodic control cost 
problem (the results are published in the monograph: W. Runggaldier, L. Stettner
"Approximations of discrete time partially observed control problems", Applied 
Mathematics Monographs, Pisa, 1994).
Cooperation with: L. Stettner (IM PAN, Poland) and W. Runggaldier (Math. Dept. 
of Padova University, Italy). 

-  [1990-1992] Computer Modeling of Demografics & Epidemiologics Processes. 
Applying a nonlinear system of integro - differential equations for modeling
demographic and epidemiologic processes. Hypothetical development of the HIV 
infection in Poland was computed. 
Collaboration to Main School of Planning and Statistics, Warsaw, Poland.

-  [1987-1990] Difference methods to solve semilinear parabolic equations with 
nonsmooth initial data. 
Cooperation with A. A. Abramov (Computational Center of the Mathematical 
Institute of Soviet Academy of Sciences, Russia).

-  [1985] The Ph.D. thesis "The grid approximation of the diffusion equation 
with local singularities" (supervisor: A. A. Samarskii and V. B. Andreev, 
Computational Mathematics, Moscow University, Russia).

-  [1981] The M.Sc. thesis "An analysis of some methods of solving parabolic 
obstacle variational inequalities" (supervisor: M. Dryja, Faculty of Mathematics, 
Mechanics and Informatics, Warsaw University, Poland). 

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Other activities

-  member of the organizing committee of CASP (Critical Assessment of Protein 
   Structure Prediction; CASP4 - 2000, CASP5 - 2002) 
-  member of New York Academy of Sciences
-  member of Polish Mathematical Society

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Awards

2002, LLNL 2002 Science and Technology Award for "Rapid Development
      of Nucleic Acid Diagnostics"

1999, BBRP Achievement Award for CASP project

1994, TEMPUS award for LAPACK-90 project

1982, first prize for the thesis "An analysis of some methods of solving 
      parabolic obstacle variational inequalities" at the competition 
      organized by Polish Mathematical Society

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Selected publications:

S. W. Singer, C. S. Chan, A. Zemla, N. C. VerBerkmoes, M. Hwang, R. L. Hettich, 
  J. F. Banfield, and M. P. Thelen: "Characterization Of Cytochrome 579, An Unusual 
  Cytochrome Isolated From An Iron Oxidizing Microbial Community", Applied and 
  Environmental Microbiology, 2008, v. 74, pp. 4454-4462.

M. Cosman, J. B. Pesavento, A. Zemla, P. T. Beernink, R. Balhorn, and D. Barsky: 
  "Identification of a thermo-regulated glutamine-binding protein from Yersinia 
  pestis", Protein Peptide Letters, 2008, (in press).

A. Zemla, C. Ecale Zhou: "Structural re-alignment in an immunogenic surface region 
  of ricin A chain", Bioinformatics and Biology Insights, 2008, v. 2, pp. 5-13.

A. Zemla, B. Geisbrecht, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, 
  C.E. Zhou. "STRALCP structure alignment-based clustering of proteins", Nucleic 
  Acids Research, 2007; doi: 10.1093/nar/gkm1049.

R. Balhorn, S. Hok, P. Burke, F. C. Lightstone, M. Cosman, A. Zemla, G. Mirick, 
  J. Perkins, A. Natarajan, M. Corzett, S. J. DeNardo, T. A. Lehner, H. Albrecht, 
  J. P. Gregg, G. L. DeNardo: Selective High Affinity Ligand Antibody Mimics for 
  Cancer Diagnosis and Therapy: Initial Application to Lymphoma/Leukemia, 
  Clinical Cancer Research, 2007, 13, pp: 5621-5628.
	
C. E. Zhou, J. Smith, M. Lam, A. Zemla, M. D. Dyer, and T. Slezak: "MvirDB   
  A microbial database of protein toxins, virulence factors and antibiotic 
  resistance genes for bio-defence applications", Nucleic Acids Research, 2007, 
  Vol. 35, pp: 391-394.

C. L. E. Zhou, M. W. Lam, J. R. Smith, A. Zemla, M. D. Dyer, T. A. Kuczmarski, 
  E. A. Vitalis, T. R. Slezak: "MannDB - A microbial database of automated 
  protein sequence analyses and evidence integration for protein 
  characterization", BMC Bioinformatics, 2006, v. 7, pp. 1-6.

P. J. Beuning, S. M. Simon, A. Zemla, D. Barsky, G. C. Walker: "A Non-cleavable 
  UmuD Variant That Acts as a UmuD' Mimic", J.Biol.Chem, 2006, v. 281, 
  pp. 9633-9640.

R. L. Stanfield, A. Zemla, I. A. Wilson, B. Rupp: "Antibody elbow angles are 
  influenced by their light chain class", J.Mol.Biol., 2006, v. 357, 5, 
  pp. 1566-1574.

B. V. Geisbrecht, B. Y. Hamaoka, B. Perman, A. Zemla, D. J. Leahy: "Crystal 
  Structures of Eap Domains from Staphylococcus Aureus Reveal an Unexpected 
  Homology to Bacterial Superantigens", J.Biol.Chem, 2005, v. 280(17), 
  pp. 17243-50.

C. Ecale Zhou, A. Zemla, D. Roe, M. Young, M. Lam, J. Schoeniger, R. Balhorn: 
  "Computational approaches for identification of conserved/unique binding 
  pockets in the A chain of ricin", Bioinformatics 2005 21: pp. 3089-3096.

A. Zemla, C. Ecale Zhou, T. Slezak, T. Kuczmarski, D. Rama, C. Torres, 
  D. Sawicka, D. Barsky: "AS2TS system for protein structure modeling and 
  analysis", Nucleic Acids Research, 2005, 33, pp. W111-W115.

S. D. Goens, S. Botero, A. Zemla, C. Ecale Zhou, M. Perdue: "Bovine enterovirus 
  type 2. Complete genomic sequence and molecular modeling of the reference 
  strain and a wild type isolate from endemically infected US cattle", Journal 
  of General Virology, 85, 2004, pp. 3195-3203.

K. A. Kanterdjieff, Ch. Y. Kim, C. Naranjo, G. S. Waldo, T. P. Lekin,
  B. W. Segelke, A. Zemla, M. S. Park, T. C. Terwilliger, B. Rupp: "Mycobacterium
  tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the
  rhamnose pathway", Acta Cryst., 2004, D60, pp. 895-902.

T. Slezak, T. Kuczmarski, L. Ott, C. Torres, D. Medeiros, J. Smith, B. Truitt,
  N. Mulakken, M. Lam, E. Vitalis, A. Zemla, C. Zhou, S. Gardner: "Comparative
  genomics tools applied to bioterrorism defense", Briefings in Bioinformatics,
  Vol. 4. No. 2, 2003, pp. 133-149.

A. Zemla: "LGA - a method for finding 3D similarities in protein structures",
  Nucleic Acids Research, Vol. 31, No. 13, 2003, pp. 3370-3374.

J. Moult, K. Fidelis, A. Zemla, T. Hubbard: "Critical assessment of methods
  of protein structure prediction (CASP)-round V", PROTEINS: Structure,
  Function, and Genetics, Vol. 53, Issue S6, 2003, pp. 334-339.

C. Venclovas, A. Zemla, K. Fidelis, J. Moult: "Assessment of progress over the
  CASP experiments", PROTEINS: Structure, Function, and Genetics, Vol. 53,
  Issue S6, 2003, pp. 585-595.

J. P. Fitch, S. N. Gardner, T. A. Kuczmarski, S. Kurtz, R. Myers, L. Ott,
  T. R. Slezak, E. A. Vitalis, A. T. Zemla, P. M. McCready: "Rapid Development 
  of Nucleic Acid Diagnostics", Proceedings of the IEEE (Institute of the 
  Electronic and Electrical Engineers), Vol. 90, No. 11, 2002, 1708-1721.

J. Moult, K. Fidelis, A. Zemla, T. Hubbard, A. Tramontano: "The significance
  of performance ranking in CASP--response to Marti-Renom et al.",
  Structure (Camb), 2002, 10(3), 291-2.

B. Rupp, B. W. Segelke, H. I. Krupka, T. P. Lekin, J. Schafer, A. Zemla,
  D. Toppani, G. Snell, T. Earnest: "The TB structural genomics consortium
  crystalization facility: towards automation from protein to electron
  density", Acta Cryst., 2002, D58, pp. 1514-1518.

J. Moult, K. Fidelis, A. Zemla, T. Hubbard: "Critical assessment of methods
  of protein structure prediction (CASP): Round IV", PROTEINS: Structure,
  Function, and Genetics, Vol. 45, Issue S5, 2001, pp. 2-7.

A. Zemla, C. Venclovas, J. Moult, K. Fidelis: "Processing and evaluation of
  predictions in CASP4", PROTEINS: Structure, Function, and Genetics,
  Vol. 45, Issue S5, 2001, pp. 13-21.

C. Venclovas, A. Zemla, K. Fidelis, J. Moult: "Comparison of performance
  in successive CASP experiments", PROTEINS: Structure, Function, and
  Genetics, Vol. 45, Issue S5, 2001, pp. 163-170.

S. Cristobal, A. Zemla, D. Fischer, L. Rychlewski, A. Elofsson: "A study
  of quality measures for protein threading models", BMC Bioinformatics, 
  2001; 2(1): 5.

A. Zemla, C. Venclovas, J. Moult, K. Fidelis: "Processing and Analysis 
  of CASP3 Protein Structure Predictions", PROTEINS: Structure, Function, 
  and Genetics, Suppl.3, 1999, pp. 22-29. 

C. Venclovas, A. Zemla, K. Fidelis, J. Moult: "Some Measures of Comparative
  Performance in the three CASPs", PROTEINS: Structure, Function, 
  and Genetics, Suppl.3, 1999, pp. 231-237. 

A. Zemla, C. Venclovas, K. Fidelis, B. Rost: "A modified definition of Sov, a 
  segment based measure for protein secondary structure prediction assessment", 
  PROTEINS:  Structure, Function, and Genetics, 34, 1999, pp. 220-223.

C. Venclovas, A. Zemla, K. Fidelis, J. Moult: "Criteria for evaluating protein 
  structures derived from comparative modeling", PROTEINS: Structure, Function, 
  and Genetics, Suppl.1, 1997, pp. 7-13. 

A. Zemla, C. Venclovas, A. Reinhardt, K. Fidelis, T. J. Hubbard: "Numerical 
  criteria for the evaluation of ab initio predictions of protein structure", 
  PROTEINS: Structure, Function, and Genetics, Suppl.1, 1997, pp. 140-150. 

J. J. Dongarra, J. Du Croz, S. Hammarling, J. Wasniewski, A. Zemla: "LAPACK for 
  FORTRAN90", Applied Mathematics and Computer Science Technical University 
  Press, Zielona Gora, Poland Vol. 6, No. 2, ISSN 0867-857X, 1997, pp. 375-382., 
  Proceeding of International Conference and Exhibition High Performance 
  Computing and Networking, Brussels, Belgium, April 1996 Lecture Notes in 
  Computer Science No. 1067 Springer-Verlag, 1996, pp. 826-839. 

J. J. Dongarra, J. Du Croz, S. Hammarling, J. Wasniewski, A. Zemla: "LAPACK 
  Working Note 101. A Proposal for a Fortran-90 Interface for LAPACK", Netlib: 
  http://www.netlib.org/lapack/lawns/lawn101.ps, University of Tennessee 
  (Knoxville) report No. CS-95-295, July 1995 & Scientific Computing Group 
  (UNI*C), report No. UNIC-95-09, August 1995., Applied Parallel Computing, 
  PARA'95 Lyngby, Denmark, August 1995, Lecture Notes in Computer Science, 
  No. 1041 Springer-Verlag, 1996, pp. 158-167. 

A. Zemla: "On the fundamental solutions for the difference Helmholtz operator", 
  SIAM J. Num. Analysis, Vol. 32, No. 2, 1995, pp. 560-570. 

A. Zemla: "Wavelet transforms computing on PVM", Parallel Scientific Computing, 
  PARA'94 Lyngby, Denmark, July 1994, Lecture Notes in Computer Science, No. 879, 
  Springer-Verlag, 1994, pp. 534-546. 

H. V. Lai, T. Zamek-Gliszczynski, A. Zemla: "Predation on Age-dependent Prey 
  Population", ICS PAS Reports No. 707, Warsaw 1991, 1-36. 

A. Zemla: "On lattice approximations of the Helmholtz equation in a singularly 
  perturbed domain", Comput. Math. Math. Phys. Vol. 28, No. 4, 1988, pp. 143-151. 
  English translation from: Zh. Vychisl. Mat. i Mat. Fiz. 8, 1988, pp. 1177-1189.

A. Zemla: "The asymptotic properties of the fundamental solutions for the 
  difference Helmholtz operator", XI International Conference on Nonlinear 
  Oscillations. Budapest 1987, 583-586. 

A. Zemla: "Analysis of a method for calculation of heterogeneous nuclear 
  reactors. Part II: The diffusion equations", Mosc. Univ. Comput. Math. Cybern. 
  1987, No. 3, 20-26 (1988) English translation from: Vestnik Moskov. Univ. XIV, 
  3, 1987, pp. 18-23. 

A. Zemla: "On the fundamental solution of the grid approximation for the 
  Helmholtz equation", Comput. Math. Math. Phys., v. 25, No. 5, 1986, pp. 92-96. 
  English translation from: Zh. Vychisl. Mat. i Mat. Fiz. 9, 1985, pp. 1416-1421.

A. Zemla: "On analysis of a method for solving heterogeneous nuclear reactors. 
  Part I", Vestnik Moskov. Univ. XIV, 2 (1985), 7-13 (in Russian). 

A. Zemla: "The Galerkin's alternating direction method for a parabolic obstacle 
  problem",  Matematyka Stosowana, 23 (1983), 5-22 (in Polish). 

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