Francesca Chiaromonte: representative publications in Bioinformatics and Genomics

 

 

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.

Carrel L., Park C., Tyekucheva S., Dunn J., 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.

Yang S., Smit A.F., Schwartz S., Chiaromonte F., Roskin K. M., Haussler D., Miller W. and Hardison R.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.

Elnitski L., Hardison R., Li J., 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.

 


(last updated Nov 2008)