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Items: 1 to 50 of 51

1.

Functional data analysis for computational biology.

Cremona M, Xu H, Makova K, Reimherr M, Chiaromonte F, Madrigal P.

Bioinformatics. 2019 Jan 22. doi: 10.1093/bioinformatics/btz045. [Epub ahead of print] No abstract available.

PMID:
30668667
2.

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate.

Guiblet WM, Cremona MA, Cechova M, Harris RS, Kejnovská I, Kejnovsky E, Eckert K, Chiaromonte F, Makova KD.

Genome Res. 2018 Dec;28(12):1767-1778. doi: 10.1101/gr.241257.118. Epub 2018 Nov 6.

3.

Child Weight Gain Trajectories Linked To Oral Microbiota Composition.

Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD.

Sci Rep. 2018 Sep 19;8(1):14030. doi: 10.1038/s41598-018-31866-9.

4.

IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales.

Cremona MA, Pini A, Cumbo F, Makova KD, Chiaromonte F, Vantini S.

Bioinformatics. 2018 Jul 1;34(13):2289-2291. doi: 10.1093/bioinformatics/bty090.

PMID:
29474526
5.

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.

6.

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

Liu Y, Chiaromonte F, Li B.

Biometrics. 2017 Jun;73(2):529-539. doi: 10.1111/biom.12579. Epub 2016 Sep 20.

PMID:
27649087
7.

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. eCollection 2016 Jun.

8.

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.

9.

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.

PMID:
25660222
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

Human-macaque comparisons illuminate variation in neutral substitution rates.

Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F.

Genome Biol. 2008 Apr 30;9(4):R76. doi: 10.1186/gb-2008-9-4-r76.

29.

Support vector machines categorize the scaling of human grip configurations.

Cesari P, Chiaromonte F, Newell KM.

Behav Res Methods. 2007 Nov;39(4):1001-7.

PMID:
18183918
30.

The genome-wide determinants of human and chimpanzee microsatellite evolution.

Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD.

Genome Res. 2008 Jan;18(1):30-8. Epub 2007 Nov 21.

31.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD.

PLoS Comput Biol. 2007 Sep;3(9):1772-82. Epub 2007 Jul 27.

32.

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J; ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis, Chiaromonte F, Miller W, Hardison RC.

Genome Res. 2007 Jun;17(6):775-86.

33.

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.

Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM.

Genome Biol. 2007;8(1):R7.

34.

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F.

Genome Res. 2006 Dec;16(12):1596-604. Epub 2006 Oct 19.

35.

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC.

Genome Res. 2006 Dec;16(12):1480-92. Epub 2006 Oct 12.

36.

Genomic environment predicts expression patterns on the human inactive X chromosome.

Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD.

PLoS Genet. 2006 Sep 29;2(9):e151. Epub 2006 Aug 3.

37.

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.

Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD.

Mol Biol Evol. 2006 Mar;23(3):565-73. Epub 2005 Nov 9.

PMID:
16280537
38.

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC.

Genome Res. 2005 Aug;15(8):1051-60. Epub 2005 Jul 15.

39.

Global predictions and tests of erythroid regulatory regions.

Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W.

Cold Spring Harb Symp Quant Biol. 2003;68:335-44. No abstract available.

PMID:
15338635
40.

The share of human genomic DNA under selection estimated from human-mouse genomic alignments.

Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D.

Cold Spring Harb Symp Quant Biol. 2003;68:245-54. No abstract available.

PMID:
15338624
41.

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison R, Chiaromonte F.

Genome Res. 2004 Apr;14(4):700-7.

42.

Insertions and deletions are male biased too: a whole-genome analysis in rodents.

Makova KD, Yang S, Chiaromonte F.

Genome Res. 2004 Apr;14(4):567-73.

43.

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC.

Genome Res. 2004 Apr;14(4):517-27.

44.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium.

Nature. 2004 Apr 1;428(6982):493-521.

PMID:
15057822
45.

Gene length and proximity to neighbors affect genome-wide expression levels.

Chiaromonte F, Miller W, Bouhassira EE.

Genome Res. 2003 Dec;13(12):2602-8. Epub 2003 Nov 12.

46.

Distinguishing regulatory DNA from neutral sites.

Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F.

Genome Res. 2003 Jan;13(1):64-72.

47.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D.

Genome Res. 2003 Jan;13(1):13-26.

48.

Initial sequencing and comparative analysis of the mouse genome.

Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES.

Nature. 2002 Dec 5;420(6915):520-62.

PMID:
12466850
49.

Scoring pairwise genomic sequence alignments.

Chiaromonte F, Yap VB, Miller W.

Pac Symp Biocomput. 2002:115-26.

50.

Dimension reduction strategies for analyzing global gene expression data with a response.

Chiaromonte F, Martinelli J.

Math Biosci. 2002 Mar;176(1):123-44.

PMID:
11867087

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