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Items: 1 to 20 of 47

1.

Corrigendum: 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. 2016 Oct;26(10):1451. No abstract available.

2.

Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units.

Liu Y, Chiaromonte F, Li B.

Biometrics. 2016 Sep 20. doi: 10.1111/biom.12579. [Epub ahead of print]

PMID:
27649087
3.

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.

Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD.

PLoS Comput Biol. 2016 Jun 16;12(6):e1004956. doi: 10.1371/journal.pcbi.1004956.

4.

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.

5.

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.

PMID:
25660222
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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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. Erratum in: Genome Res. 2016 Oct;26(10 ):1451.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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