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Bustamante, Carlos D.
Cornell Faculty Member
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Positions
- Adjunct Professor, Biological Statistics and Computational Biology (BSCB), College of Agriculture and Life Sciences (CALS)
My research focuses on developing statistical methods for inference in population and comparative genomics. I am particularly interested in approaches for testing evolutionary hypothesis regarding the importance of natural selection and demographic history in patterning genetic variation. Much of my group`s research deals with development of population genetic theory as well as application of our tools to make inference from genome-wide data sets. We have recently become very interested in methods for association mapping in natural and domesticated populations. We work on a variety of organisms including humans, macaques, Canines, rodents, rice, Arabidopsis, and fruit files.
Research Areas
- bioinformatics
- biometry
- computational biology
- evolution
- genetics
- genomics
- information science
- new life sciences
- plant breeding and genetics
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Affiliations
Research
research overview
- My research is focused on four major areas: Population genetic theory ================ My primary research focuses on developing statistical methods for parameter estimation and hypothesis testing in population genetics and molecular phylogenetics. I am particularly interested in developing methods for estimating the relative contributions of demographic forces (e.g., population structure, population size expansion / contraction) and selective forces on the history of natural populations using data from standing genetic variation as well fixed differences between populations. Human population genetics ================= The completion of the human, chimpanzee, and macaque genomes coupled with large-scale experiments to document human genetic variation provide us an unprecedented opportunity to study the evolution of our species. In collaboration with Andy Clark and Rasmus Nielsen, our group has been developing novel tools to facilitate this study as well as applying the tools to novel and interesting data sets. For example, as a joint effort between our three groups, we recently completed the first genome-wide comparison of human genetic variation within protein-coding genes to the genetic differences between humans and chimpanzees (Bustamante et al., 2005; Nature 437:1153-7) Evolutionary genomics of domestication ========================= Ever since Darwin, evolutionary biologists have sought to use human-driven evolutionary change as a model for understanding organic evolution. Some of the most profound and rapid changes in character evolution have been driven by farmers, enthusiasts, and plant and animal breeders using artificial selection to modify the phenotypes of hundreds of domesticated species. This type of intense and focused selection has invariably altered the genomes of domesticated species, affording us both an opportunity for understanding patterns of genetic variation in species subject to intense selection as well as the raw material from population samples for identifying genes of large phenotypic effect. As part of this work, we are analyzing large scale genetic variation data from diferent domesticated plant and animal species including the domestic dog and rice. Association mapping in natural populations =========================== The ease of rapid genotyping coupled with massive phenotyping (such as measuring gene expression simultaneously across tens of thousands of gene) presents an exiting challenge for evolutionary statistical genomics. By developing and deploying tools for linking genetic variation with agronomic or medical phenotypes of interest, my group hopes to help experimental geneticists identify genomic regions, genes, and specific mutations underlying complex traits. Several statistical problems that arise in this endeavor include: detecting cryptic population structure in samples of cases and controls, multiple testing from scanning many markers and many phenotypes, and disentangling correlations due to shared regulatory networks of co-regulated genese.
keywords
- Computational Genomics
- Evolutionary Genomics
- Molecular Evolution
- Population Genetics
submitted impact statement
Publications
individual publications
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academic article
- High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. . Plant, Cell and Environment. 36:454-466. 2013
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2. 2011
- Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping. PLoS Genetics. 7:e1002221. 2011
- Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genetics. 7. 2011
- Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2:467. 2011
- High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875-886. 2011
- ALCHEMY: A Reliable Method for Automated SNP Genotype Calling for Small Batch Sizes and Highly Homozygous Populations. Bioinformatics. 26:2952-2960. 2010
- Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice. 3:205-217. 2010
- A genome-wide linkage scan in German shepherd dogs localizes canine platelet procoagulant deficiency (Scott Syndrome) to canine chromosome 27. Gene. 450:70-75. 2010
- A simple genetic architecture underlies morphological variation in dogs. PLoS Biology. 8. 2010
- Balancing selection maintains a form of ERAP2 tat undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genetics. 6. 2010
- Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach. Genetics. 186:493-503. 2010
- Development of genome-wide SNP assays for rice. Breeding Science. 60:524-535. 2010
- Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One. 5. 2010
- Successful Computational Prediction of Novel Imprinted Genes From Epigenomic Features. Molecular and Cellular Biology. 30. 2010
- The Baker's Yeast Diploid Genome is Remarkably Stable in Vegetative Growth and Meiosis. PLoS Genetics. 6. 2010
- The effect of recent admixture on inference of ancient human population history. Genetics. 185. 2010
- CCL3L copy number variation is a common host immune factor for SIV/HIV/AIDS in Humans and Macaques. PLoS Genetics. 5. 2009
- Darwinian and demographic forces affecting human protein coding genes. Genome Research. 19:838-849. 2009
- Evaluating genomic signatures of sexspecific processes. Nature Genetics. 41:8-10. 2009
- Evolutionary processes acting on non‐coding DNA in humans inferred from patterns of polymorphism and divergence. PLoS Genetics . PLoS Genetics. 5. 2009
- Methods for human demographic inference using haplotype patterns from genome‐wide SNP data. Genetics. 182:217-231. 2009
- Molecular and Evolutionary History of Melanism in North American Gray Wolves. Science. 323:1339-43. 2009
- Targets of balancing selection in the human genome. Molecular Biology and Evolution. 26:2755-2764. 2009
- Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genetics. 4. 2008
- Exclusion of ABCA-1 as a candidate gene for canine Scott syndrome. J Thromb Haemost. 6:1608-10. 2008
- Exploring population genetic models with recombination using efficient forward-time simulations. Genetics. 178:2417-2427. 2008
- Genetics mirrors geography within Europe. Nature. 456:98-101. 2008
- Natural selection on genes that underlie human disease susceptibility. Current Biology. 18:883-9. 2008
- Patterns of positive selection in six mammalian genomes. PLoS Genetics. 4. 2008
- Population genetics of polymorphism and divergence under fluctuating selection. Genetics. 178:325-37. 2008
- Proportionally More Deleterious Variation in European than in African Populations. Nature. 451:994-997. 2008
- The Population Reference Sample (POPRES): a resource for population, disease, and pharmacological genetics research. Am J Hum Gen. 83:347-58. 2008
- A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs. PLoS-Genetics. 3. 2007
- A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs. Science. 316:112-5. 2007
- Context Dependence, Ancestral Misidentification, and Spurious Signatures of Selection. Molecular Biology and Evolution. 24:1792-800. 2007
- Context-Dependent Mutation Rates May Cause Spurious Signatures of a Fixation Bias Favoring Higher GC-Content in Humans. Molecular Biology and Evolution. 24:2196-202. 2007
- Genetic Variation Reveals Diametric Demographic Histories for Chinese and Indian Rhesus Macaques. Science. 316:240-3. 2007
- Genome-wide patterns of nucleotide polymorphism in domesticated Asian rice (Oryza sativa). PLoS Genetics. 3:1745-56. 2007
- Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics. 3. 2007
- Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis. Nature Genetics. 39:153-5. 2007
- Joint Inference of Self-Fertilization Rate and Population Structure. Genetics. 176:1635-51. 2007
- Localizing recent adaptive evolution in the human genome. PLoS Genetics. 3. 2007
- On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics. 176:2371-9. 2007
- Recent and ongoing selection in the human genome. Nat Rev Genet.. 8:857-68. 2007
- A composite-likelihood approach for detecting directional selection from DNA sequence data. Genetics. 170:1411-21. 2005
- A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology. 3. 2005
- A statistical characterization of consistent patterns of Human Immunodeficiency Virus evolution within infected patients. Molecular Biology and Evolution. 22:456-468. 2005
- Ascertainment bias in studies of human genome-wide polymorphism. Genome Research. 15:1496-1502. 2005
- Detecting coevolving amino acid substitutions using Bayesian mutational mapping. ISMB / Bioinformatics. 21 . 2005
- Distinguishing between Selective Sweeps and Demography Using DNA Polymorphism Data. Genetics. 170:1401-10. 2005
- Genomic scans for selective sweeps using SNP data. Genome. 15:1566-75. 2005
- Natural Selection on Protein-Coding Genes in the Human Genome. Nature. 437:1153-7. 2005
- Selective sweep mapping of genes with large phenotypic effects. Genome. 15:1809-19. 2005
- Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences (PNAS). 102:7882-7. 2005
- Darwinian selection on a selfing locus. Science. 306:2081-4. 2004
- Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics. 168:463-75. 2004
- Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. Journal of Molecular Evolution. 57. 2003
- Elevated selection intensities of rapidly-evolving Arabidopsis genes. Genetics. 163:723-33. 2003
- Maximum Likelihood and Bayesian Methods for Estimating the Distribution of Selective Effects among Classes of Mutations Using DNA Polymorphism Data. Theoretical Population Biology. 63:91-103. 2003
- Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am J Hum Gen. 73:489-501. 2003
- A Maximum Likelihood Method for Analyzing Pseudogene Evolution: Implications for Silent Site Evolution in Humans and Rodents. Molecular Biology and Evolution. 19:110-7. 2002
- The Cost of Inbreeding: Fixation of Deleterious Genes in Arabidopsis. Nature. 416:531-534. 2002
- Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science. 291:128-130. 2001
- Directional Selection and the Site-Frequency Spectrum. Genetics. 159:1779-88. 2001
- Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coliand Salmonella enterica. Molecular Biology and Evolution. 17:301-308. 2000
- The Glean Machine: What can we learn from DNA sequence polymorphism?. Symp. Genomics & Proteomics. 4:37-49. 2000
- Crystal structure of 1,1-trimethylenebis[4-(hydroxyiminomethyl)pyridinium bromide] hydrate, (C15H18N4O2)Br2 · H2O. New Crystal Structures. 214:141. 1999
- Pretreatment with 1; 25(OH)2D3 protects from Cytoxan-induced alopecia without protecting the leukemic cells from Cytoxan. Am J Med Sci. 310:43-47. 1995
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booksection
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chapter
- Population Genetics of Molecular Evolution. Statistical Methods in Molecular Evolution. 63-99. 2005
- Selective Sweep in the Evolution of a New Sperm-Specific Gene in Drosophila. Selective Sweep. 2005
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document part
selected publications listing
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Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 2008 Feb 21;451(7181):994-7.
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Huerta-Sanchez E, Durrett R, Bustamante CD. Population genetics of polymorphism and divergence under fluctuating selection. Genetics. 2008 Jan;178(1):325-37. Epub 2007 Oct 18.
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Santos, V.J., C. D. Bustamante, and F. J. Valero-Cuevas. Improving the Fitness of High-Dimenstional Biomechanical Models via Data-driven Stochastic Exploration. IEEE Transac-tions on Biomedical Engineering. (in press).
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Boyko, A. R., S. H. Williamson, A. R. Indap, J. D. Degenhardt, R. D. Hernandez, K.E. Lohmueller, M. D. Adams, S. Schmidt, J. J. Sninsky, S. R. Sunyaev, T. J. White,R. Nielsen, A. G. Clark, and C. D. Bustamante. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS-Genetics 4(5):e1000083.
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Blekhman, R., O. Man, L. Herrmann, A. R. Boyko, A. Indap, C. Kosiol, C. D. Bustamante, K. M. Teshima, and M. Przeworski. 2008. Natural selection on genes that underlie human disease susceptibility. Current Biology. (in press).
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Kosiol, C., T. Vinar, R. R. Da Fonseca, M. J. Hubisz, C. D. Bustamante, R. Nielsen, and A. Siepel. 2008. Patterns of positive selection in six mammalian genomes. PLoS- Genetics. (in press).
- Padhukasahasram, B., P. Marjoram, J. D. Wall, C. D. Bustamante, and M. Nord-borg. 2008. Exploring population genetic models with recombination using efficientforward-time simulations. Genetics 178(4):2417-27.
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Teaching
teaching overview
- Statistical analysis of genetic and molecular data is a central component of research in every branch of the biological sciences. As a consequence, there is a tremendous need on campus (and beyond) for training in statistical and computational genomics at both the undergraduate and graduate level. In the past three years, I have developed and/or revamped four courses relevant to this mission. In the next three to five years, I hope to continue development of these courses as well as to add at least two new courses to the curriculum in BSCB.
teaching activities
Background
education and training
- Ph.D. in Biology, Harvard University 2001
- M.A. in Statistics, Harvard University 2001
- B.A. in Biology, Harvard University 1997
awards and honors
Other
college
- CALS
research keyword
- Computational Genomics
- Evolutionary Genomics
- Molecular Evolution
- Population Genetics