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Results: 1 to 20 of 44


Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.

Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M.

BMC Bioinformatics. 2015 Jun 30;16:202. doi: 10.1186/s12859-015-0607-z.


An attraction-repulsion point process model for respiratory syncytial virus infections.

Goldstein J, Haran M, Simeonov I, Fricks J, Chiaromonte F.

Biometrics. 2015 Jun;71(2):376-85. doi: 10.1111/biom.12267. Epub 2015 Feb 6.


Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15474-9. doi: 10.1073/pnas.1409328111. Epub 2014 Oct 13.


Genomic landscape of human, bat, and ex vivo DNA transposon integrations.

Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD.

Mol Biol Evol. 2014 Jul;31(7):1816-32. doi: 10.1093/molbev/msu138. Epub 2014 Apr 22.


Segmenting the human genome based on states of neutral genetic divergence.

Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14699-704. doi: 10.1073/pnas.1221792110. Epub 2013 Aug 19.


Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome.

Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F, Makova KD.

Genome Biol Evol. 2013;5(3):606-20. doi: 10.1093/gbe/evs116.


Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion.

Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, Roy-Engel AM.

PLoS Genet. 2012;8(8):e1002842. doi: 10.1371/journal.pgen.1002842. Epub 2012 Aug 9.


A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD.

Genome Res. 2012 Jun;22(6):993-1005. doi: 10.1101/gr.134395.111. Epub 2012 Mar 28.


Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections.

Simeonov I, Gong X, Kim O, Poss M, Chiaromonte F, Fricks J.

Viruses. 2010 Dec;2(12):2782-802. doi: 10.3390/v2122782. Epub 2010 Dec 22.


A matter of life or death: how microsatellites emerge in and vanish from the human genome.

Kelkar YD, Eckert KA, Chiaromonte F, Makova KD.

Genome Res. 2011 Dec;21(12):2038-48. doi: 10.1101/gr.122937.111. Epub 2011 Oct 12.


Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2011 Oct;21(10):1659-71. doi: 10.1101/gr.125088.111. Epub 2011 Jul 27.


A genome-wide view of mutation rate co-variation using multivariate analyses.

Ananda G, Chiaromonte F, Makova KD.

Genome Biol. 2011;12(3):R27. doi: 10.1186/gb-2011-12-3-r27. Epub 2011 Mar 22.


What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats.

Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD.

Genome Biol Evol. 2010;2:620-35. doi: 10.1093/gbe/evq046. Epub 2010 Jul 28.


Complete Khoisan and Bantu genomes from southern Africa.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM.

Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.


Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.

Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2009 Dec;19(12):2172-84. doi: 10.1101/gr.098921.109. Epub 2009 Nov 3.


Windshield splatter analysis with the Galaxy metagenomic pipeline.

Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

Genome Res. 2009 Nov;19(11):2144-53. doi: 10.1101/gr.094508.109. Epub 2009 Oct 9.


Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection.

Roy S, Lavine J, Chiaromonte F, Terwee J, VandeWoude S, Bjornstad O, Poss M.

PLoS One. 2009 Oct 6;4(10):e7359. doi: 10.1371/journal.pone.0007359.


Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC.

Nucleic Acids Res. 2009 Nov;37(21):7024-38. doi: 10.1093/nar/gkp747. Epub .


Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.

Kvikstad EM, Chiaromonte F, Makova KD.

Genome Res. 2009 Jul;19(7):1153-64. doi: 10.1101/gr.088922.108. Epub 2009 Jun 5.


Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC.

Genome Res. 2008 Dec;18(12):1896-905. doi: 10.1101/gr.083089.108. Epub 2008 Sep 25.

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