Bringing together researchers in medicine, genomics, molecular biology and statistics to advance basic genomic research and translate that research into new diagnostic, therapeutic, and preventive medical strategies


About Us

Collaborative Publications

2014 Chiaromonte, Makova Using Statistics to Shed Light on the Dynamics of the Human Genome: A Review. Advances in Complex Data Modeling and Computational Methods in Statistics Contributions to Statistics
2014 Paul, I. M., J. S. Williams, S. Anzman-Frasca, J. S. Beiler, K. D. Makova, M. E. Marini, L. B. Hess, S. E. Rzucidlo, N. Verdiglione, J. A. Mindell, L. L. Birch The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study. BMC pediatrics
2014 Ananda, G., S. E. Hile , A. Breski, Y. Wang, Y. Kelkar,K. D. Makova, K. A. Eckert Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes. PLoS Genet
2014 McElhoe, J. A., M. M.Holland. K. D. Makova,M.S.-W. Su, I. M. Paul, C. H. Baker, S. A. Faith, B. Young Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Science International: Genetics
2014 Campos-Sanchez, R., A. Kapusta, C. Feschotte, F. Chiaromonte, K.D. Makova Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations Molecular Biology and Evolution
2014 Dickins, B., B. Rebolledo-Jaramillo, M. Shu-Wei Su, I. M. Paul, D. Blankenberg, N. Stoler, K. Makova, and A. Nekrutenko. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BioTechniques
2013 Kuruppumullage Don, P., G. Ananda , F. Chiaromonte, K.D. Makova Segmenting the human genome based on states of neutral genetic divergence. Proceedings of the National Academy of Sciences
2013 Baptiste, B., G. Ananda, N. Strubczewski, A. Lutzkanin, S. J. Khoo, A. Srikanth, N. Kim, K. D. Makova, M. M. Krasilnikova, and K. A. Eckert. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells. Genes, Genomes, and Genetics
2013 Ananda, G., E. Walsh, K. D. Jacob, M. Krasilnikova, K. A. Eckert, F. Chiaromonte, K. D. Makova. Distinct mutational behaviors distinguish short tandem repeats from microsatellites in the human genome. Genome Biology and Evolution
2012 Wagstaff, B., D.J. Hedges, R.S. Derbes, R.C. Sanchez, F. Chiaromonte, K.D. Makova, and A.M. Roy-Engel. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genetics
2012 Fungtammasan, A., E. Walsh, F. Chiaromonte, K. A. Eckert, K. D. Makova. A Genome-wide Analysis of Common Fragile Sites: What Features Determine Chromosomal Instability in the Human Genome? Genome Research
2011 Kelkar, Y., K. Eckert, F. Chiaromonte, and K.D. Makova A matter of life or death: How microsatellites emerge in and vanish from the human genome. Genome Research
2011 Afgan, E., D. Baker, N. Coraor, H. Goto, I.M. Paul, K.D. Makova, A. Nekrutenko, and J. Taylor Harnessing cloud-computing for biomedical research with Galaxy Cloud Nature Biotechnology
2011 Goto, H., B. Dickins, E. Afgan, I.M. Paul, J. Taylor, K.D. Makova, and A. Nekrutenko Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study Genome Biology
2011 Ananda, G., F. Chiaromonte, and K.D. Makova. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biology
2010 Simeonov I., X. Gong, O. Kim, M. Poss, F. Chiaromonte and J. Fricks Exploratory spatial analysis of in vitro Respiratory Syncytial Virusco-infections Viruses
2010 Kelkar Y.D., N. Strubczewski , S. E. Hile , F. Chiaromonte, K.A. Eckert, and K.D. Makova What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats. Genome Biol. Evol.
2010 Park, C., L. Carrel, and K.D. Makova Strong Purifying Selection at Genes Escaping X Chromosome Inactivation Molecular Biology and Evolution
2010 Schuster, S.,.., K. D. Makova (one of 48 co-authors),.., V. Hayes Complete Khoisan and Bantu genomes from southern Africa Nature
2009 Kvikstad, E.M., F. Chiaromonte, and K. D. Makova. Ride the wavelet: a multi-scale analysis of genomic contexts flanking small insertions and deletions. Genome Research
2009 Roy S.,J. Lavine, F. Chiaromonte, J. Terwee, S. VandeWoude, O. Bjornstad and M. Poss Multivariate statistical analyses demonstrate uniquehost immune responses to single and dual lentiviral infection. PLoS ONE
2008 Tyekucheva, S., K. D. Makova, J. E. Karro, R. C. Hardison, W. Miller, and F. Chiaromonte Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology
2008 Kelkar, Y., S. Tyekucheva, F. Chiaromonte, and K. D. Makova The genome-wide determinants of microsatellite evolution Genome Research
2007 Kvikstad, E. M., S. Tyekucheva, F. Chiaromonte, and K. D. Makova A macaque's-eye view of human insertions and deletions: differences in mechanisms PLoS Computational Biology
2006 Carrel, L., C. Park, S. Tyekucheva, J. Dunn, F. Chiaromonte, and K. D. Makova Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genet
2006 Taylor, J., S. Tyekucheva, M. Zody, F. Chiaromonte, and K. D. Makova Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison Molecular Biology and Evolution
2004 Makova, K.D., S. Yang, and F. Chiaromonte Indels are male-biased too: a whole genome analysis in rodents Genome Research


Hat Seminar

Mitonuclear linkage disequilibrium in human populations, Sloan et. al.

Link to Paper

Dr. Prabhani Kuruppumullage, Postdoctoral Fellow, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. Boston, MA

Statistical analyses of expression measurements in RNA from archival formalin-fixed, paraffin embedded tissues

519 Wartik video-conferenced to CG628 Hershey

Dr. Giovanni Felici (Istituto di Analisi dei Sistemi ed Informatica, Consiglio Nazionale delle Ricerche, Roma, Italy)

DNA barcoding for species classification: methods, algorithms, results

519 Wartik video-conferenced to CG628 Hershey

Presenters will be chosen using the Hat procedure.

Genomics Journal Club - RNA editing

307 Wartik Lab

Erika Kvikstad (Centre for Human Genetics, University of Oxford)

On nuisance events, junk DNA, and determining the impact of genomic pariah on human disease

519 Wartik video-conferenced to CG623 Hershey

Marta Tomaszkiewicz (Penn State)

Deciphering the Sequence of Gorilla Y Chromosome and "amplicomics" of fertility genes

519 Wartik Lab with connection to CG 624F in Hershey

David Koslicki (Oregon State University)

New Techniques to Analyze the Microbiome: analyze thousands of samples, compare without a reference, and profile a community down to the strain level

519 Wartik, with video connection to CG628 in Hershey

Michael Schatz (Cold Springs Harbor Lab)

The Resurgence of Reference Quality Genomes using 3rd Generation Sequencing Technologies

519 Wartik Lab at University Park; with video to room CG628 at Hershey


Children born to older mothers have greater rates of mitochondrial mutations.

The discovery of a "maternal age effect" by a team of Penn State scientists that could be used to predict the accumulation of mitochondrial DNA mutations in maternal egg cells - and the transmission of these mutations to children - could provide valuable insights for genetic counseling.

Full Article

New characterization of human genome mutability catalyzes biomedical research.

A crucial development for personalized genomic medicine researchers at the Center for Medical Genomics elucidate intricacies of mutagenesis.

Full Article

Genome instability studies could change treatment for cancer and other diseases.

Making steps toward the realization of personalized genomic medicine, Huck Institutes affiliates at the Center for Medical Genomics are finding and analyzing hotspots of genomic instability and mutation known as microsatellites.

Full Article

Galaxy genome-analysis system now available for cloud computing

Development provides vast increases in computational power for researchers worldwide.

Full Article