Program Director/Principal Investigator (Last, First, Middle):
Willman, Cheryl L.
BIOGRAPHICAL SKETCH
Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
POSITION TITLE
Atlas, Susan Rachel
Research Associate Professor, Physics & Astronomy
Director, UNM Center for Advanced Research Computing
Co-Director, UNM Cancer Center Shared Resource for
Genomics and Bioinformatics
eRA COMMONS USER NAME (credential, e.g., agency login)
Susan.Atlas
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and
residency training if applicable.)
DEGREE
INSTITUTION AND LOCATION
MM/YY
FIELD OF STUDY
(if applicable)
City Univ. New York, Queens College, NY,NY
Harvard University, Cambridge, MA
Harvard University, Cambridge, MA
Los Alamos National Laboratory
B.A.
A.M.
Ph.D.
Postdoc
1979
1981
1988
19881990
Mathematics/Physics
Physics
Chemical Physics
Chemical Physics
A. Personal Statement
As a PI and co-PI leading a large group at UNM with research projects in bioinformatics, computational
biology, molecular biophysics, and theoretical nanoscience, I have the necessary technical and leadership
expertise to serve as co-Director of the UNM Cancer Center Shared Resource for Genomics and Bioinformtics.
My background includes 25+ years of training and expertise in applied mathematics and computational
science, including molecular and statistical physics, statistical machine learning techniques for high-throughput
genomic analysis, and parallel programming for developing and implementing new scientific models and
pattern recognition algorithms on large-scale supercomputers. In 2001, as co-PI on large NIH/NCI and Keck
Foundation grants aimed at constructing a microarray-based molecular taxonomy of acute leukemia, I initiated
and led a large interdisciplinary group of faculty and students in developing advanced machine learning and
bioinformatic analysis methods, including the GenomeDW data warehouse, SawTooth framework for fast nextgeneration resequencing analysis, ZincGrep relational database for zinc finger structure/function prediction,
and a novel biclustering algorithm for identifying cancer subtypes from gene expression data. These successful
projects have led to long-term support from the NCI and Leukemia and Lymphoma Society, 7 Ph.D., master’s,
and undergraduate honors theses, and co-authorship on publications in Blood, PNAS, and other journals.
B. Positions and Honors
Positions
1983-1988
Graduate Research Assistant; Department of Chemistry, Harvard University
1988-1990
Postdoctoral Research Fellow, Los Alamos National Laboratory
1990-1994
Scientist; Thinking Machines Corporation, Cambridge, MA and Santa Fe, NM
1994-1995
Adjunct Assistant Professor; Department of Physics and Astronomy, UNM
1995-1999
Research Assistant Professor; Department of Physics and Astronomy, UNM
1999-2003
Associate Director; High Performance Computing Education and Research Center, UNM
1999Research Associate Professor; Department of Physics and Astronomy, UNM
2003Associate Member, UNM Cancer Center
2004- 2009 Founding Director, UNMCC Shared Resource for Bioinformatics and Computational Biology
2007Research Associate Professor, Department of Electrical and Computer Engineering, UNM
2009-2012
Co-Director, UNMCC Shared Resource for Biostatistics and Bioinformatics
2009Director, UNM Center for Advanced Research Computing
2012Co-Director, UNMCC Shared Resource for Genomics and Bioinformatics
Professional Experience
1996NSF proposal referee, Divisions of Materials Research (Materials Theory, Metallurgy),
Chemistry, Mathematical Sciences, Office of Cyberinfrastructure; Petroleum Research Fund;
1996Referee, Phys. Rev. A, B, E; Phys. Rev. Lett.; Lecture Notes in Comp. Sci; Bioinformatics
1997-2009
Lecturer, UNM NSF/Los Alamos Summer School in Atomic, Molecular, and Optical Physics
PHS 398/2590 (Rev. 06/09)
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Program Director/Principal Investigator (Last, First, Middle):
1999-
2001
2002, 2003
20072012
Willman, Cheryl L.
DOE Office of Science Panelist and Reviewer (Complex and Collective Phenomena; Modeling
and Simulation in Nanoscience; Condensed Matter Physics and Materials Physics; SciDAC
Advanced Computing; Condensed Matter Physics and Scattering, Materials Physics)
NSF Panelist and Committee of Visitors, Information Technology Research Program
Lecturer in Genomics, National Center for Genome Resources/Promega Corp.
UNM NSF/NCI IGERT Nanoscience and Microsystems Program, Management Committee
NSF panelist, Chemical Theory, Models and Computational Methods/Quantum Chemistry
Professional Memberships
American Physical Society; Materials Research Society; American Chemical Society; Society for Industrial and
Applied Mathematics; Mathematical Association of America; International Society for Computational Biology;
American Society of Hematology; American Association for the Advancement of Science
Honors
2011
2004
2002
2001
1979-1982
1979
1979
1977
Qforma Thesis Prize (as mentor), Outstanding Dissertation or Master’s Thesis in Computational
Science/Engineering to N Sakhavand (parallel molecular biophysics and engineering code PDQ)
Cray Award, First Place (as mentor), NM Supercomputing Challenge (molecular biophysics)
Siemens Westinghouse Competition in Math, Science and Technology, Regional Finalist Team,
Outstanding Mentor (computational genomics)
Cray Award, First Place (as mentor), NM Supercomputing Challenge (computational genomics)
National Science Foundation Three Year Predoctoral Fellowship
Phi Beta Kappa; Pi Mu Epsilon National Honor Society in Mathematics; B.A. summa cum laude;
Departmental Honors in Mathematics and Physics, Queens College, CUNY
Samuel Jacobs Memorial Award in Mathematics; Physics Prize; Queens College, CUNY
Karyn Kupcinet International Science School Scholar, Weizmann Institute of Science
C. Relevant/significant publications (in chronological order)
1. P Helman, R Veroff, SR Atlas, and C Willman. A Bayesian network classification methodology for gene
expression data, J. Comp. Biol. 11(4):581-615, 2004.
2. CS Wilson, GS Davidson, SB Martin, E Andries, J Potter, R Harvey, K Ar, Y Xu, KJ Kopecky, DP
Ankerst, H Gundacker, ML Slovak, M Mosquera-Caro, I-M Chen, M Murphy, FA Schultz, H Kang, X
Wang, DL Stirewalt, JP Radich, FR Appelbaum, SR Atlas, J Godwin, and CL Willman. Gene expression
profiling of adult acute myeloid leukemia identifies novel biologic clusters for risk classification and
outcome prediction. Blood 108:685, 2006.
3. SM Valone and SR Atlas. Energy dependence on fractional charge for strongly interacting subystems,
Phys. Rev. Lett. 97:256402, 2006.
4. H Kang, EJ Bedrick, SR Atlas, and CL Willman. ROC curve of a generalized odds-rate model,
Proceedings of the Joint Statistical Meeting, Salt Lake City, UT, July 29-August 7, 2007.
5. SB Martin, M P Mosquera-Caro, J W Potter, G S Davidson, E Andries, H Kang, P Helman, R L Veroff,
SR Atlas, M Murphy, X Wang, K Ar, Y Xu, I-M Chen, F A Schultz, C S Wilson, R Harvey, E Bedrick, J
Shuster, A J Carroll, B Camitta, and CL Willman, Gene expression overlap affects karyotype prediction
in pediatric acute lymphoblastic leukemia, Leukemia 21:1341, 2007.
6. E Andries, T Hagstrom, SR Atlas, and CL Willman. Regularization strategies for hyperplane classifiers:
application to cancer classification with gene expression data, J. Bioinf. Comp. Biol. 5:79-104, 2007.
7. CG Mullighan, J Zhang, RC Harvey, BA Schulman, LA Phillips, X Su, M Devidas, SR Atlas, I-M Chen, D
Gerhard, WL Carroll, GH Reaman, M Smith, JR Downing, SP Hunger, and CL Willman. JAK mutations
in high-risk childhood acute lymphoblastic leukemia, Proc. Natl. Acad. Sci. (USA) 106:9414, 2009.
8. H Kang, I-M Chen, CS Wilson, EJ Bedrick, RC Harvey, SP Hunger, M Devidas, SR Atlas, et al. Gene
expression classifiers for minimal residual disease and relapse free survival improve outcome prediction
and risk classification in children with high risk acute lymphoblastic leukemia: A Children’s Oncology
Group study, Blood 115:1994, 2010.
9. RC Harvey, CG Mullighan, X Wang, KK Dobbin, GS Davidson, EJ Bedrick, IM Chen, SR Atlas, H Kang,
K Ar, et al. Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic
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Program Director/Principal Investigator (Last, First, Middle):
Willman, Cheryl L.
leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations,
clinical characteristics, and outcome. Blood 116(23):4874-84, 2010.
10. X Meng, K Matlawska-Wasowska, F Girodon, T Mazel, CL Willman, S Atlas, I-M Chen, RC Harvey, SP
Hunger, SA Ness, SS Winter, BS Wilson. GSI-I (Z-LLNle-CHO) inhibits -secretase and the proteosome
to trigger cell death in precursor-B acute lymphoblastic leukemia. Leukemia 25:1135–1146, 2011.
11. A Ho, M Murphy, S Wilson, SR Atlas, and J Edwards. Sequencing by ligation variation with
Endonuclease V digestion and deoxyinosine-containing query oligos, BMC Genomics 12:598, 2011.
12. H Kang, CS Wilson, RC Harvey, I-M Chen, MH Murphy, SR Atlas, et al. Gene expression profiling
reveals genes predictive of outcome in infant Acute Lymphoblastic Leukemia and distinctive age-rrelated
gene expression profiles: A Children’s Oncology Group Study, Blood 119:1872-1881, 2012.
13. X Wang, D Chee, CL Willman, and SR Atlas. Robust semi-supervised biclustering for discovery of novel
phenotypes in cancer expression data, arXiv:q-bio for submission to Bioinformatics, 2013.
D. Research Support
Ongoing Research Support
1P30 CA118100-01
CL Willman (PI)
9/1/10-8/31/15
NIH/NCI
UNM Cancer Center Support Grant
The goal of this grant is to conduct outstanding multidisciplinary and transdisciplinary cancer research and
build on unique institutional and regional scientific strengths to reduce cancer incidence and mortality by
discovering factors contributing to distinct cancer patterns in the multiethnic populations of New Mexico.
Role: Resource co-Director, Biostatistics and Bioinformatics
NCI
CL WIllman (PI)
4/1/11-3/31/16
National Institutes of Health
Strategic Partnerships to Evaluate Cancer Signatures: Molecular Signatures for Outcome
Prediction and Therapeutic Targeting in ALL
This project utilizes gene expression profiling of leukemia cells to yield systematic profiles or “signatures” that
can be evaluated, tested in prospective trials, and used to improve outcome prediction, risk classification, and
therapeutic targeting in acute lymphoblastic leukemia.
Role: co-I
1 R01 HG005852-01
JS Edwards (PI)
9/1/10-8/31/14
NIH/NHGRI
Polony Sequencing and the $1000 Genome
The major goals of this project are to further develop ultra high-throughput polony (polymerase colony)
sequencing with the goal of resequencing a human genome for < $1,000 in one week, by implementing
methods to achieve increased read lengths and numbers of reads, as well as improved pre-sequencing steps,
and improved computational tools for assembling and calling single nucleotide polymorphisms.
Role: co-I
1R01 CA170250-01
SA Ness (PI)
8/1/12-5/31/16
NIH/NCI
Alternative RNA Splicing and Protein Products in Leukemia Outcome (PQ11)
This NCI Provocative Questions grant will use next-generation sequencing and sophisticated bioinformatics
approaches to analyze the alternative RNA splicing in a large cohort of pediatric leukemia patient samples, to
determine whether the enhanced level of RNA splicing observed in leukemias is due to “splicing noise” or
contributes to the disease process.
Role: Collaborator
1R01DE023222-01
SA Ness (PI)
NIH/ NIDCR
Mutations and Target Genes in Adenoid Cystic Carcinoma
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Program Director/Principal Investigator (Last, First, Middle):
Willman, Cheryl L.
This project will focus on the identification of genes that are regulated by Myb-NFIB fusion proteins expressed
in Adenoid Cystic Carcinomas, and a determination of whether the fusion proteins have different and
unique activities than wild type Myb proteins expressed in normal cells.
Role: Collaborator
HDTRA1-09-1-0018
SR Atlas (PI)
4/1/09 – 3/31/13
DoD/Defense Threat Reduction Agency
Coupled Atomistic Modeling and Experimental Studies of Energy Transduction and Catalysis in the
Molecular Motor Protein Kinesin
The goal of this project is to study the mechanochemistry of kinesin catalysis using an approach that tightly
and iteratively couples a novel theoretical framework—charge-transfer atomistic modeling—with data from
experimental single-molecule motility assays.
Role: PI
OCI-1040530
SR Atlas (PI)
9/1/10-8/31/14
National Science Foundation
MRI: Acquisition of a GPU-Accelerated Parallel Supercomputer for Computational Science and
Engineering Research at the University of New Mexico
The goal of this project is to acquire a state-of-the-art GPU-based parallel supercomputer in support of
science and engineering research at UNM.
Role: PI
1 R21 ES021499
LG Hudson (PI)
4/1/12-3/31/14
NIH
Predicting Novel Arsenic Targets in DNA Repair Pathways
The objective of this research is to implement an iterative bioinformatic/experimental approach to identify, test,
and refine the selection of high-affinity arsenic targets in the DNA repair pathway, to gain insights into
mechanisms of arsenic carcinogenicity and DNA repair inhibition.
Role: co-I
206753-1
SR Atlas (PI
10/1/12-9/30/14
DOE (CMIME EFRC subcontract, Valone)
Solution of a One-Dimensional Chain Structure for the Fragment Hamiltonian (FH) Model
The goal of this project is to compute the Green’s function and analyze the electronic properties of a 1D
chain as a prototype system for the FH model of materials, and to determine whether it exhibits a
metal/insulator transition. Other properties of interest relate to electronic spectra, susceptibilities, and timedependent electronic transitions, as expressed in the FH model for the prototype system.
Completed Research Support
NIH/NCI P30 CA118100
CL Willman (PI)
UNM Cancer Center Support Grant
Role: Shared Resource Director, Bioinformatics/Computational Biology
9/26/05-8/31/10
NIH/NCI U01CA114762
CL Willman (PI)
4/1/05-3/30/10
SPECS: Molecular Signatures for Outcome Prediction and Therapeutic Targeting in ALL
Role: Co-I
Leukemia and Lymphoma Society 7388-06
CL Willman (PI)
10/1/05-9/30/10
SCOR in Acute Leukemia: Comprehensive Molecular Technologies for Improved Risk Classification
and Therapy: Core B: Bioinformatics, Computational Biology, and Biostatistics
Role: Core PI
Leukemia and Lymphoma Society 7372-07
C Felix, U Penn/CHOP (PI)
Specialized Center of Research in Targeted Therapies for Infant Leukemias
Core B: Biomedical Informatics and Computational Biology
Role: Collaborator
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