Bioinformatics & Genomics


Most of my research occurs at the interfaces between statistics, bioinformatics and genomics. Over the years, this work has comprised NIH and NSF funded collaborations with Ross Hardison, Kateryna Makova, Webb Miller, Anton Nekrutenko, Mary Poss and other researchers at the Center for Comparative Genomics and Bioinformatics, the Center for Medical Genomics,  and the Center for Infectious Disease Dynamics of Penn State, as well as other institutions (e.g. the Center for Biomolecular Science and Engineering of UC Santa Cruz).

Starting with our participation in several genome Consortia (e.g. Mouse, Rat, Chicken), we used sequence and alignment data to investigate various aspects of evolution and function – which we continue to explore now taking advantage of a vast and diverse array of information on sequence, epigenomic signatures and transcription produced by next generation sequencing technologies.

Among others, I have been involved in projects concerning alignment scoring methodology, estimation of the share of the human genome under purifying selection, genome-wide computational prediction of noncoding functional elements (ESPERR and RP scores), and genome dynamics – studying the local variation and co-variation of different processes of mutagenesis and their associations with features of the genomic landscape. I also work on projects in which genomic information is linked to aspects of the spatio-temporal dynamics of infectious diseases in in vitro and in vivo systems.


  • Kuruppumullage Don P., Andanda G., Chiaromonte F. and Makova K.D. (2013) Segmenting the human genome based on states of neutral genetic divergence. Proceedings of the National Academy of Sciences USA. 110(36), 14699–14704. doi:10.1073/pnas.1221792110
  • Ananda G., Walsh E., Jacob K.D., Krasilnikova M., Eckert K.A., Chiaromonte F., Makova K.D. (2012) Distinct mutational behaviors distinguish simple tandem repeats from microsatellites in the human genome. Genome Biology and Evolution. 5(3) 606-620. doi: 10.1093/gbe/evs116.
  • Wagstaff B.J., Hedges D.J., Derbes R.S., Campos Sanchez R., Chiaromonte F., Makova K.D. and Roy-Engel A.M.(2012) Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genetics 8(8) e1002842.
  • FungtammasanA., Walsh E., Chiaromonte F., Eckert K.A., Makova K.D. (2012) A Genome-Wide Analysis of Common Fragile Sites: What Features determine chromosomal instability in the human genome? Genome Research 22, 993-1005.
  • Kelkar Y.D., Eckert K.A. Chiaromonte F. and Makova K.D. (2011) A matter of life and death: how microsatellites emerge in and vanish from the human genome. Genome Research 21(12), 2038-2048.
  • Wu W., Cheng Y., Keller C.A., Kumar S.A., Ernst J., Mishra T., Morrissey C., Dorman C.M., Chen K.B., Drautz D., Giardine B., Shibata Y., Song L., Crawford G.E., Furey T.S., Kellis M., Miller W., Taylor J., Schuster S.C., Zhang Y., Chiaromonte F., Blobel G.L., Weiss M.J. and Hardison R.C. (2011) Dynamics of the Epigenetic Landscape During Erythroid Differentiation after GATA1 Restoration. Genome Research 21(10), 1659-1671.
  • Ananda G., Chiaromonte F. and Makova K.D. (2011) A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biology. 12(3):R27. doi:10.1186/gb-2011-12-3-r27.
  • Simeonov I., Gong X., Kim O., Poss M., Chiaromonte F. and Fricks J. (2010) Exploratory spatial analysis of in vitro Respiratory Syncytial Virus co-infections. Viruses. 2(12), 2782-2802; doi:10.3390/v2122782.
  • Kelkar Y.D., Strubczewski N., Hile S.E., Chiaromonte F., Eckert K.A. and Makova K.D. (2010) What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats. Genome Biology and Evolution. doi: 10.1093/gbe/evq046.
  • Schuster S., Miller W. et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature, 463, 943-947.
  • Cheng Y., Wu W., Kumar S.A., Yu D., Deng W., Tripic T., King D.C., Chen K.B.,  Zhang Y., Drautz D., Giardine B., Schuster S.C., Miller W., Chiaromonte F., Zhang Yu, Blobel G.A., Weiss M.J. and Hardison R.C. (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications and mRNA expression. Genome Research, 19, 2172-2184.
  • Kosakovsky Pond S., Wadhawan S., Chiaromonte F., Ananda G., Chung W.Y., Taylor J., Nekrutenko A. and The Galaxy Team. (2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research, 19, 2144-2153.
  • Roy S., Lavine J., Chiaromonte F., Terwee J., VandeWoude S., Bjornstad O. and Poss M. (2009) Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection. PLoS ONE, 4(10) e7359. doi:10.1371/journal.pone.0007359
  • Zhang Y., Wu W., Cheng Y., King D.C., Harris R.S., Taylor J., Chiaromonte F. and Hardison R.C. (2009) Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Research. doi: 10.1093/nar/gkp747.
  • Kvikstad E.M., Chiaromonte F. and Makova K.D. (2009) Ride the wavelet: a multi-scale analysis of genomic context flanking small insertions and deletions. Genome Research, 19, 1153-1164.
  • Cheng Y., King D.C., Dore L.C., Zhang X., Zhou Y., Zhang Y., Dorman C., Abebe D., Kumar S., Chiaromonte F., Miller W., Green R.D., Weiss M.J. and Hardison R.C. (2008) Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Research, 18, 1896-1905.
  • Kelkar Y., Tyekucheva S., Chiaromonte F. and Makova K.D. (2008) The genome-wide determinants of microsatellite evolution. Genome Research, 18, 30-38.
  • Tyekucheva S., Makova K.D., Karro J. Hardison R.C., Miller W. and Chiaromonte F. (2008) Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology, 9(4): R76.
  • Gutiérrez R.A., Lejay L., Chiaromonte F., Shasha D.E. and Coruzzi G.M. (2007) Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biology, 8(1): R7.
  • King D.C., Taylor J., Zhang Y., Cheng Y., Lawson H.A., Martin J., ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Chiaromonte F., Miller W. and Hardison R.C. (2007) Finding cis-regulatory modules using comparative genomics: some lessons from ENCODE data. Genome Research, 17, 775-786.
  • Kvikstad E.M., Tyekucheva S., Chiaromonte F. and Makova K.D. (2007) A macaque’s-eye view of human insertions and deletions: differences in mechanisms. PLoS Computational Biology, 3(9) e176, 1772-1782.
  • Taylor J., Tyekucheva S., King D.C., Hardison R., Miller W. and Chiaromonte F. (2006) ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Research, 16, 1596-1604.
  • Wang H., Zhang Y., Petrykowska H., Cheng Y., Zhou Y., King D., Kasturi J., Taylor J. Chiaromonte F., Miller W., Welch J., Weiss M. and Hardison R. (2006) Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Research, 16, 1480-1492.
  • CarrelL., ParkC., TyekuchevaS., DunnJ., Chiaromonte F. and Makova K.D. (2006) Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genetics, 2(9) e151.
  • Taylor J., Tyekucheva S., Zody M., Chiaromonte F. and Makova K.D. (2006) Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Molecular Biology and Evolution, 23(3), 565-573.
  • King D.C., Taylor J., Elnitski L., Chiaromonte F., Miller W. and Hardison R.C. (2005) Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Research, 15, 1051-1060.
  • Gibbs R. et al., Rat Genome Sequencing Project Consortium. (2004) Genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature, 428, 493-521.
  • Hillier L. et al. International Chicken Genome Sequencing Consortium (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716.
  • Makova K.D., Yang S. and Chiaromonte F. (2004) Insertions and deletions are male-biased too: a whole-genome analysis in rodents. Genome Research, 14, 567-573.
  • Kolbe D., Taylor J., Elnitski L., Eswara P., Li J., Miller W., Hardison R.C. and Chiaromonte F. (2004) Regulatory potential scores from genome-wide 3-way alignments of human, mouse and rat. Genome Research, 14, 700-707.
  • YangS., Smit A.F., Schwartz S., Chiaromonte F., Roskin K. M., Haussler D., Miller W. and HardisonR.C. (2004) Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome Research, 14, 517-527.
  • Hardison R.C., Chiaromonte F., Kolbe D., Wang H., Petrykowska H., Elnitski L., Yang S., Giardine B., Zhang Y., Riemer C., Schwartz S., Haussler D., Roskin K., Weber R., Diekhans M., Kent W.J., Weiss M.J., Welch J. and Miller W. (2004) Global prediction and tests for erythroid regulatory regions. Cold Spring Harbor Symposia in Quantitative Biology: The Genome of Homo Sapiens, 68, 335-345.
  • Chiaromonte F., Weber R. J., Roskin K.M., Diekhans M., Kent W.J. and Haussler D. (2004) The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harbor Symposia in Quantitative Biology: The Genome of Homo Sapiens, 68, 245-255.
  • ElnitskiL., HardisonR., LiJ., Yang S., Kolbe D., Eswara P., O’Connor M., Schwartz S., Miller W. and Chiaromonte F. (2003) Distinguishing regulatory DNA from neutral sites. Genome Research, 13, 64-72.
  • Hardison R., Roskin K.M., Yang S., Diekhans M., Kent J.W., Weber R., Elnitski L., Li J., O’Connor M., Kolbe D., Schwartz S., Furey T.S., Whelan S., Goldman N., Smit A., Miller W., Chiaromonte F. and Haussler D. (2003) Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Research, 13, 13-26.
  • Chiaromonte F., Miller W. and Bouhassira E. (2003) Gene length and proximity to neighbors affect genome-wide expression levels. Genome Research, 13, 2602-2608.
  • Waterston, R. et al., International Mouse Genome Sequencing consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature. 420, 520-562.
  • Chiaromonte F., Bing Yap V. and Miller W. (2002) Scoring pairwise genomic sequence alignments. Proceedings of the Pacific Symposium on Biocomputing 2002.
  • Chiaromonte F., Yang S., Elnitski L., Bing Yap V., Miller W. and Hardison R. (2001). Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proceedings National Academy of Sciences USA, 98(25), 14503-14508.

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