March 2025 --
Our manuscript describing the Alzheimer's disease genetic risk pattern we discovered was
selected for Biomolecules cover story!
October 2024 --
We've identified a genetic pattern that is significantly associated with Alzheimer's disease
and validated it in two independent data sets! Read more here.
August 2024 --
Congratulations to Ken for successfully defending his dissertation! Ken is moving on to a
postdoc position in Dan Jacobson's lab at Oak Ridge National Laboratory.
December 2023 --
Sharlee is awarded Sabbatical Leave for the Fall 2024 semester.
August 2023 --
Sharlee receives UMSL's Mid-Career Award to support her research on plasma diagnostics
for Alzheimer disease subtypes.
April 2023 --
Sharlee is an invited speaker for the St. Louis Chapter of Graduate Women in Science Annual
Conference.
September 2022 --
Sharlee is promoted to Associate Professor and receives tenure.
March 2022 --
Sharlee receives the 2022 Trailblazer Award award.
February 2022 --
Building on our UMSL-sponsored research, the Alzheimer's Association awards us a 3-year
$150k grant to identify fine-scaled genetic patterns flanking known risk markers.
January 2022 --
Our critiques of network modeling are published in Patterns.
May 2021 --
Our UMSL Research grant to sift out combinations of genetic factors associated with Alzheimer
disease has been funded!
April 2021 --
Alina Nguyen creates a video for WomenCAN.
December 2020 --
Ken is featured in UMSL Magazine (page 29).
September 2020 --
Our NIH grant to study patterns of proteins in plasma associated with varying outcomes of
COVID-19 has been funded! Read more here.
March 2020 --
Sharlee receives UMSL's Junior Faculty Investigator of the Year Award.
May 2019 --
Our Duo metric is used to create the world's largest climatype map.
May 2019 --
Sharlee receives the 2019 Outstanding Research Award from UMSL's Department of
Mathematics and Computer Science.
May 2019 --
Our WomenCAN website is launched.
January 2019 --
Our lab is featured in UMSL Magazine (pp. 10-12).
November 2018 --
We won ACM's Gordon Bell Prize!! More information can
be found here.
August 2018 --
Our team has been selected as a finalist for ACM's Gordon Bell Prize. The winner will be
announced at SC18.
July 2018 --
Graduate Research Assistant Michael Chan assumes multiple roles at the Platform for Scientific
Computing Conference (PASC18).
June 2018 --
Our custom correlation coeffient is the first scientific metric in the world to be computed at
exascale speed!
May 2018 --
Graduate Research Assistant Aditya Karnam Gururaj Rao delivers oral presentation at
MWAIS.
May 2018 --
Graduate Research Assistant Michael Chan wins prize at the
2018 Open Programming Competition.
April 2018 --
Graduate Research Assistants Michael Chan and Aditya Karnam Gururaj Rao present their
research at the
2018 Midwest Bioinformatics Conference
and the 2018 Hope Center Retreat.
April 2018 --
Graduate Research Assistant Aditya Karnam Gururaj Rao wins award at the
University of
Missouri - St. Louis
2018 Graduate Research Fair.
June 2017 --
Ayoubi et al. have applied cut-and-solve
to Virtualized Network Functions (VNF) and achieved a
700 times speedup over
conventional approaches.
April 2017 --
Graduate Research Assistants Matt Lane and John Brandenburg win awards at the
University of
Missouri - St. Louis
Graduate Research Fair.
December 2016 --
Our NIH grant to study plasma and CSF proteins associated with Alzheimer's disease has
been funded!
November 2016 --
Sharlee is the newest faculty member of the
Center for Neurodynamics
at the
University
of Missouri - St. Louis.
August 2016 --
Sharlee has accepted an Assistant Professor position in the
Department of Mathematics and
Computer Science
at the
University of Missouri - St. Louis!
April 2016 --
Sune Gadegaard has integrated cut-and-solve
with semi-Lagrangean based dual ascent while
tackling a
facility location problem.
August 2015 --
A new combined cut-and-solve
approach has been shown to outperform
IBM's CPLEX in
IEEE Transactions on Intelligent Transportation Systems.
June 2015 --
Sharlee is the newest faculty member at the
Hope Center for Neurological Disorders
and has
joined the
Neurogenetics
Group.
March 2015 --
Our discovery of yin-yang
sequences
on human chromosome 14 has been
published in
Nature
Communications.
This discovery suggests that two completely divergent evolutionary
paths rapidly progressed
in our past, presumably achieving the shared
goal of enhancing gephyrin, a gene that is vital for signal
transmissions in the human brain.
February 2015 --
More applications of cut-and-solve
have been shown to outperform
IBM's CPLEX in
Mathematical Problems in Engineering
and
Computers and Industrial Engineering.
January 2015 --
Our
grant to study combinatorial genetics underlying Alzheimer's
Disease has been funded!
November 2014 --
Our BlocBuster C++ code is now available
at
www.blocbuster.org.
October 2014 --
Application of cut-and-solve
is shown to outperform
IBM's CPLEX
in a presentation at the
IEEE 17th International Conference on Intelligent Transportation Systems.
January 2014 --
A cut-and-solve implementation described in
the
International Journal of Production Research
is shown to
outperform
IBM's CPLEX.
June 2013 --
Our new approach for finding combinations of genes with highly synchronized expression
will
be put to the test in an analysis of the remarkably
adaptive talents of fire salamanders.
January 2013 --
A limit-crossing approach is applied to
semi-supervised clustering in Jiang et al.'s manuscript
appearing in
Neurocomputing.
January 2013 --
A cut-and-solve approach for optimally
solving the
automated truck freight transportation
problem is shown to
outperform
IBM's CPLEX.
November 2012 -- A second R package has been implemented (by others)
for our
TSP+k rearrangement
clustering algorithm. It is available
here.
(The first package is available
here.)
August 2012 -- Our NIH R01 grant (PI: Weixiong Zhang)
has been funded! (Just in the nick of time!)
August 2012 -- Our limit-crossing
strategy has been applied to the
p-median problem by Ren et al.
June 2012 -- Cut-and-solve was
shown to outperform
IBM's CPLEX
for a transportation
problem in Fang et al.'s
manuscript in
IEEE Transactions on Intelligent Transportation Systems.
May 2012 -- Our abstract Co-adaptation of the vitamin D receptor (VDR) and
colour-determining genes during
humans' venture out of Africa has
been selected out of 1,012 abstracts (blinded review)
for the Henning
Andersen prize
for highest rated basic abstract at
the European Society for Paediatric
Endocrinology
51st Annual Meeting.
April 2012 -- Cut-and-solve is
utilized for a facility location problem in Yang et al.'s manuscript
in
European
Journal of Operational Research.
November 2011 -- Our TSP+k approach to the rearrangement
clustering problem, which was published in
J.Machine Learning Research,
is summarized (and described as 'elegant') in
William J. Cook's book
In
Pursuit
of the Traveling Salesman: Mathematics at the Limits of
Computation.
April 2011 -- Cut-and-solve
reduces computation time for optimally solving a transportation
problem in Fang
et al.'s presentation at the
2011 IEEE International Conference on Networking, Sensing and
Control.
February 2010 -- An example of a pitfall in current
clustering methods that we presented in Rearrangement
clustering: Pitfalls, remedies, and
applications is included as SF Myth 1 in
Harvey J. Greenberg's
Myths
and
Counterexamples in
Mathematical Programming.
January 2010 -- Our search strategy for solving combinatorial
optimization problems, cut-and-solve, is
featured
in Boris
Goldengorin's plenary lecture
at
the 2010 American
Conference on Applied Mathematics.
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Sharlee Climer, Ph.D. My primary research interest is the development of combinatorial methods for biological applications. A key focus is to identify patterns in genetic and other omics data, such as the genetic anomaly shown at the top of this webpage, and determine associations of these patterns with traits of interest, with a particular interest in Alzheimer disease. |
email: Office: |
climer at umsl.edu 319 ESH |
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Elaina Rohlfing Graduate Research Assistant |
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Zach Valleroy Graduate Researcher |
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Kenneth Smith Graduate Research Assistant |
Previous Lab Members:
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Elizabeth Whitmore Undergraduate Researcher |
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Daniel Cross Undergraduate Research Assistant |
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Jamie Lea Graduate Researcher |
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James Smith Graduate Research Assistant |
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Aaron Heumphreus Graduate Research Assistant |
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Zeran Li Currently a postdoc at GSK (Co-mentored with Carlos Cruchaga) |
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Alberto Maiocco Research Assistant |
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Emily Chan Currently at GotSoccer |
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Aditya Karnam Gururaj Rao Currently at ePlata |
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John Brandenburg Currently at Norfolk Southern |
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Matthew Lane Currently at Oak Ridge National Laboratory |
Scott Hulver (NSF Summer REU), currently graduate student at Loyola University.
Brittany Scheid (NSF Summer REU), currently graduate student at University of Pennsylvania.
David Marango (undergraduate intern), currently student at Harris-Stowe State University.
Peter Holly (NSF Summer REU), currently Software Engineer at National Instruments.
Dhevi Rajendran (NSF Summer REU), currently Software Engineer at Two Sigma Investments.
Papers/Book
Book - Journals/Book Chapters - Conferences - Abstracts/posters - Theses - Reports
Book
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Limit Crossing
A Guide for Solving Combinatorial Problems by Exploiting Bounds Sharlee Climer VDM Verlag, 2008, ISBN: 978-3-639-05796-6 View book on Amazon |
| Combinatorial problems are ubiquitous in the sciences, engineering, and industry. These problems tend to be difficult to solve optimally as they typically have an exponential number of feasible solutions. Bounds have been used to prune away large numbers of feasible solutions, thus allowing the computation to optimality for some problems. Limit Crossing reflects on the history of the use of bounds and observes that the major focus has been on bounds derived from relaxations of constraints. Neglected opportunities to exploit bounds are subsequently identified, explored, and tabulated. Furthermore, a methodology for the use of these bounds is formulated as a two-step procedure, referred to as limit crossing. Direct instantiations of the limit-crossing method have produced two unconventional search strategies: Cut-and-Solve and BBF. These strategies are presented and their power is demonstrated for solving difficult, real-world problems. |
Journals / Book Chapters / Preprints
Capturing biomarkers associated with Alzheimer disease subtypes using data distribution characteristics Kenneth Smith and Sharlee Climer Frontiers in Neuroscience, vol. 18, 2024 journal link |
A machine-learning evaluation of biomarkers designed for the future of precision medicine Sharlee Climer medRxiv, preprint, doi: 10.1101/2023.07.09.23292430, 2023 preprint link |
Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer`s and coronary disease pathways Lihua Wang et al. iScience, vol. 26, issue 4, 2023 journal link |
Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder David Kainer, et al. Human Genetics and Genomics Advances, vol. 4, issue 1, 1000150, 2023 journal link |
Heterogeneity impacts biomarker discovery for precision medicine Kenneth Smith Jr. and Sharlee Climer medRxiv, preprint, doi: 2022.02.14.22270972, 2022 preprint link |
Climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics John Lagergren, et al. Phytobiomes Journal, 2022 journal link |
Connecting the dots: The boons and banes of network modeling Sharlee Climer Patterns, vol. 2, issue 12, 100374, 2021 journal link |
COVID-19 and the differential dilemma Sharlee Climer Patterns, vol. 2, issue 5, 100260, 2021 journal link |
Eyeing the Patterns: Data Visualization Using Doubly-Seriated Color Heatmaps Matthew Lane, Alberto Maiocco, Sanjiv K. Bhatia, Sharlee Climer Advances in Computers, vol. 119, pp. 121-156, 2020 book chapter link |
Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Erik Alexandersson, et al. BMC Plant Biology, vol. 20, 120, 2020 journal link |
Synchronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis Sharlee Climer, et al. bioRxiv, preprint, doi: 2020.01.28.923730, 2020 preprint link |
Network Modeling of Complex Data Sets Piet Jones, et al. Metabolic Pathway Engineering: Methods and Protocols, Springer Methods in Molecular Biology series M. Himmel and Y. Bomble, Eds. Springer, 2019 book chapter link |
Parallel accelerated Custom Correlation Coefficient calculations for genomics applications Wayne Joubert, James Nance, Sharlee Climer, Deborah Weighill, and Daniel Jacobson Parallel Computing, vol. 84, pp. 15-23, 2019 journal link |
Phytobiome and transcriptional adaptation of Populus deltoides to acute progressive drought and cyclic drought Benjamin James Garcia, et al. Phytobiomes Journal, vol. 2, no. 4, pp. 249-260, e-ISSN: 2471-2906, 2019 journal link |
Complete parsimony haplotype inference problem and algorithms based on integer programming, branch-and-bound and Boolean satisfiability Gerold Jäger, Sharlee Climer, and Weixiong Zhang Journal of Discrete Algorithms, vol. 37, pp. 68-83, 2016 journal link |
Latitudinal clines of the human vitamin D receptor and skin color genes Dov Tiosano, et al. (joint first author) G3: Genes, Genomes, Genetics, vol. 6, pp. 1251-1266, 2016 journal link |
Moving from Capstones towards Cornerstones: Successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders Nathan Kopp, Sharlee Climer, and Joseph D. Dougherty Frontiers in Genetics, vol. 6, no. 00301, doi:10.3389/fgene.2015.00301, 2015 journal link |
Human gephyrin is encompassed within giant functional noncoding yin-yang sequences Sharlee Climer, Alan R. Templeton, and Weixiong Zhang Nature Communications, vol. 6, no. 6534, doi:10.1038/ncomms7534, 2015 journal link | PMC link |
Allele-specific network reveals combinatorial interaction that transcends small effects in psoriasis GWAS Sharlee Climer, Alan R. Templeton, and Weixiong Zhang PLoS Computational Biology, vol. 10, no. 9, e1003766, 2014 pdf | suppl |
A custom correlation coefficient (CCC) approach for fast identification of multi-SNP association patterns in genome-wide SNPs data Sharlee Climer, Wei Yang, Lisa de las Fuentes, Victor G. Davila-Roman, and C. Charles Gu Genetic Epidemiology, vol. 38, no. 7, pp. 610-621, 2014 pdf | suppl |
How frugal is Mother Nature with Haplotypes? Sharlee Climer, Gerold Jäger, Alan R. Templeton, and Weixiong Zhang Bioinformatics, vol. 25, no. 1, pp. 68-74, 2009 |
Cut-and-solve: An iterative search strategy for combinatorial optimization problems Sharlee Climer and Weixiong Zhang Artificial Intelligence, vol. 170, pp. 714-738, June 2006 pdf | ps |
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Rearrangement clustering: Pitfalls, remedies, and applications Sharlee Climer and Weixiong Zhang Journal of Machine Learning Research, vol. 7, pp. 919-943, June 2006 pdf | ps |
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Local
Lines: A linear time line detector Sharlee Climer and Sanjiv K. Bhatia Pattern Recognition Letters, vol. 24, pp. 2291-2300, October 2003 pdf | ps |
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Image
database indexing using JPEG coefficients Sharlee Climer and Sanjiv K. Bhatia Pattern Recognition, vol. 35, pp. 2479-2488, November 2002 pdf | ps |
Refereed conference manuscripts
Following are full-length conference manuscripts that were competitively peer reviewed (with acceptance rates noted
when available).
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Mr. Clean: An Ensemble of Data Cleaning Algorithms for Increased Data Retention
Kenneth Smith and Sharlee Climer 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Istanbul, Turkey, December 2023 |
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Predicting COVID-19 Severity Using a Cut-and-Solve Feature Selection Approach
Kenneth Smith, et al. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Istanbul, Turkey, December 2023 |
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Finding Single and Multi-Gene Expression Patterns for Psoriasis Using Sub-Pattern Frequency Pruning
Kenneth Smith, Jamie Lea, and Sharlee Climer Workshop on Machine Learning and Artificial Intelligence in Bioinformatics and Medical Informatics (MABM 2021) in conjunction with IEEE BIBM 2021 Virtual, December 2021 |
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Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for
Chronic Pain and Opioid Addiction Wayne Joubert, et al. International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'18), No. 57, Dallas, Texas, November 2018 (24% acceptance rate) |
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Efficient reduced-bias genetic algorithm (ERBGA) for generic community detection objectives
Aditya Karnam Gururaj Rao, Cezary Janikow, Sanjiv Bhatia, and Sharlee Climer Midwest United States Association for Information Systems 13th Annual Conference, No. 32, St. Louis, MO, May 2018 link |
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SplittingHeirs: Inferring haplotypes by optimizing resultant dense graphs
Sharlee Climer, Alan R. Templeton, and Weixiong Zhang ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), pp. 127-136, Niagara Falls, New York, August 2010 (28% acceptance rate) |
Complete parsimony haplotype inference problem and algorithms Gerold Jäger, Sharlee Climer, and Weixiong Zhang 17th Annual European Symposium on Algorithms (ESA), Lecture Notes in Computer Science, vol. 5757, pp. 337-348, Copenhagen, September 2009 (25% acceptance rate) |
Take a walk and cluster genes: A TSP-based approach to optimal rearrangement clustering Sharlee Climer and Weixiong Zhang 21st International Conference on Machine Learning (ICML'04), pp. 169-176, Banff, Canada, July 2004 (32% acceptance rate, double-blind review) pdf | ps |
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A linear search strategy using bounds Sharlee Climer and Weixiong Zhang 14th International Conference on Automated Planning and Scheduling (ICAPS'04), pp. 132-141, Whistler, Canada, June 2004 (31% acceptance rate, double-blind review) pdf | ps |
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Searching
for backbones and fat: A limit-crossing approach with applications Sharlee Climer and Weixiong Zhang Proceedings of the 18th National Conference on Artificial Intelligence (AAAI'02), pp. 707-712, Edmonton, Canada, July 2002 (26% acceptance rate, double-blind review) pdf | ps |
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Searching
for backbones and fat Sharlee Climer and Weixiong Zhang 4th International Conference on the Integration of AI and OR Techniques in Constraint Programming (CP-AI-OR'02), pp. 307-320, Le Croisic, France, March 2002. (77% acceptance rate) pdf | ps |
Abstracts & posters
| The APOE locus: More than two polymorphisms of interest?
Sharlee Climer 2023 Alzheimer's Association International Conference (AAIC) Advancements: APOE`23, St Louis, MO, March 2023 |
| Proteomic profiling identified plasma biomarkers for SARS-COV-2 infection and severity of COVID-19 patients
L. Wang, et al. Annual Program in Quantitative Genomics (PQG) Conference (PQG 2021), Virtual, October 2021 |
| Correlation network analysis of cortical mRNA transcripts in an AD case-control study
Jamie Lea and Sharlee Climer Alzheimer's Association International Conference (AAIC 2021), Denver, July 2021 |
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Evolving to recognize high-dimensional relationships in data: GA operators and representation designed expressly for community detection Kenneth Smith, Cezary Janikow, and Sharlee Climer The Genetic and Evolutionary Computation Conference (GECCO 2019), pp. 308-309, Prague, Czech Republic, July 2019 website |
Co-adaptation of the vitamin D receptor (VDR) and colour-determining genes to latitude during humans' venture out of Aftrica Dov Tiosano, et al. 51st Annual Meeting of the European Society for Paediatric Endocrinology (ESPE 2012), Leipzig, Germany, September 2012 |
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A dense graph model for haplotype inference
Sharlee Climer, Alan R. Templeton, and Weixiong Zhang 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB'08), Poster Book pp. 265-266, Singapore, March 2008 pdf | ps |
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A fast search algorithm to identify communities of interacting SNPs in
GWAS
Sharlee Climer, Lisa de las Fuentes, Victor G. Davila-Roman, and C. Charles Gu 17th Annual Meeting for the International Genetic Epidemiology Society (IGES'08}, Poster Book p. 32, St. Louis, September 2008 |
Theses
Novel search strategies that exploit bounds with applications in engineering and biology Sharlee Climer Doctoral dissertation, Washington University in St. Louis, December 2006 Contact me for a copy of this dissertation |
| Image
database indexing using compressed data Sharlee Climer Master's thesis, University of Missouri - St. Louis, May 2001 Contact me for a copy of this thesis |
Technical reports
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Synchronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis
Sharlee Climer et al. bioRxiv, 2020.01.28.923730v1, 2020 link
These packages are written in C++ and we have run them on Linux. The packages are gzipped tar
files. BlocBuster code download code This code is for optimal rearrangement clustering, as described in Rearrangement clustering: Pitfalls, remedies, and applications. R packages developed by others are available here and here.
Cut-and-solve code for the Traveling Salesman Problem Line detector code Code for converting graphs from .gml
format to .list format
CS 5130: Advanced Data Structures and Algorithms CSE 542T: Advanced Data Structures and Algorithms
CSE 511A: Artificial
Intelligence MTH1035: Trigonometry
MTH1030: College Algebra Techniques for computing and using bounds for
combinatorial optimization problems, Tutorial for the 19th Systematic bounding techniques for combinatorial
optimization, Tutorial for the 20th Conference for the
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