Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 84

1.

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.

Rangavittal S, Stopa N, Tomaszkiewicz M, Sahlin K, Makova KD, Medvedev P.

BMC Genomics. 2019 Aug 9;20(1):641. doi: 10.1186/s12864-019-5996-3.

2.

Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data.

Harris RS, Cechova M, Makova KD.

Bioinformatics. 2019 Jul 10. pii: btz484. doi: 10.1093/bioinformatics/btz484. [Epub ahead of print]

PMID:
31290946
3.

High satellite repeat turnover in great apes studied with short- and long-read technologies.

Cechova M, Harris RS, Tomaszkiewicz M, Arbeithuber B, Chiaromonte F, Makova KD.

Mol Biol Evol. 2019 Jul 2. pii: msz156. doi: 10.1093/molbev/msz156. [Epub ahead of print]

PMID:
31273383
4.

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
5.

Investigating mitonuclear interactions in human admixed populations.

Zaidi AA, Makova KD.

Nat Ecol Evol. 2019 Feb;3(2):213-222. doi: 10.1038/s41559-018-0766-1. Epub 2019 Jan 14.

PMID:
30643241
6.

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.

7.

Correcting palindromes in long reads after whole-genome amplification.

Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D.

BMC Genomics. 2018 Nov 6;19(1):798. doi: 10.1186/s12864-018-5164-1.

8.

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.

Sahlin K, Tomaszkiewicz M, Makova KD, Medvedev P.

Nat Commun. 2018 Nov 2;9(1):4601. doi: 10.1038/s41467-018-06910-x.

9.

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.

10.

High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups.

Ye D, Zaidi AA, Tomaszkiewicz M, Anthony K, Liebowitz C, DeGiorgio M, Shriver MD, Makova KD.

Genome Biol Evol. 2018 May 1;10(5):1333-1350. doi: 10.1093/gbe/evy086.

11.

Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives.

Holland MM, Makova KD, McElhoe JA.

Genes (Basel). 2018 Feb 26;9(3). pii: E124. doi: 10.3390/genes9030124.

12.

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.

13.

A Population Phylogenetic View of Mitochondrial Heteroplasmy.

Wilton PR, Zaidi A, Makova K, Nielsen R.

Genetics. 2018 Mar;208(3):1261-1274. doi: 10.1534/genetics.118.300711. Epub 2018 Jan 17.

14.

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.

Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P.

Bioinformatics. 2018 Apr 1;34(7):1125-1131. doi: 10.1093/bioinformatics/btx771.

15.

Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent.

Baker RJ, Dickins B, Wickliffe JK, Khan FAA, Gaschak S, Makova KD, Phillips CD.

Evol Appl. 2017 Jun 22;10(8):784-791. doi: 10.1111/eva.12475. eCollection 2017 Sep.

16.

Y and W Chromosome Assemblies: Approaches and Discoveries.

Tomaszkiewicz M, Medvedev P, Makova KD.

Trends Genet. 2017 Apr;33(4):266-282. doi: 10.1016/j.tig.2017.01.008. Epub 2017 Feb 22. Review.

PMID:
28236503
17.

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.

18.

Streamlined analysis of duplex sequencing data with Du Novo.

Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A.

Genome Biol. 2016 Aug 26;17(1):180. doi: 10.1186/s13059-016-1039-4.

19.

Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.

Arbeithuber B, Makova KD, Tiemann-Boege I.

DNA Res. 2016 Dec;23(6):547-559. Epub 2016 Jul 31.

20.

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

Fungtammasan A, Tomaszkiewicz M, Campos-Sánchez R, Eckert KA, DeGiorgio M, Makova KD.

Mol Biol Evol. 2016 Oct;33(10):2744-58. doi: 10.1093/molbev/msw139. Epub 2016 Jul 12.

21.

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.

22.

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.

Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD.

Genome Res. 2016 Apr;26(4):530-40. doi: 10.1101/gr.199448.115. Epub 2016 Mar 2.

23.

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD.

Genome Res. 2015 May;25(5):736-49. doi: 10.1101/gr.185892.114. Epub 2015 Mar 30.

24.

The effects of chromatin organization on variation in mutation rates in the genome.

Makova KD, Hardison RC.

Nat Rev Genet. 2015 Apr;16(4):213-23. doi: 10.1038/nrg3890. Epub 2015 Mar 3. Review.

25.

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.

26.

Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq.

McElhoe JA, Holland MM, Makova KD, Su MS, Paul IM, Baker CH, Faith SA, Young B.

Forensic Sci Int Genet. 2014 Nov;13:20-9. doi: 10.1016/j.fsigen.2014.05.007. Epub 2014 May 20.

27.

The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study.

Paul IM, Williams JS, Anzman-Frasca S, Beiler JS, Makova KD, Marini ME, Hess LB, Rzucidlo SE, Verdiglione N, Mindell JA, Birch LL.

BMC Pediatr. 2014 Jul 18;14:184. doi: 10.1186/1471-2431-14-184.

28.

Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes.

Ananda G, Hile SE, Breski A, Wang Y, Kelkar Y, Makova KD, Eckert KA.

PLoS Genet. 2014 Jul 17;10(7):e1004498. doi: 10.1371/journal.pgen.1004498. eCollection 2014 Jul.

29.

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.

30.

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach.

Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A.

Biotechniques. 2014 Mar 1;56(3):134-141. doi: 10.2144/000114146. eCollection 2014.

31.

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.

32.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

33.

Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells.

Baptiste BA, Ananda G, Strubczewski N, Lutzkanin A, Khoo SJ, Srikanth A, Kim N, Makova KD, Krasilnikova MM, Eckert KA.

G3 (Bethesda). 2013 Mar;3(3):451-63. doi: 10.1534/g3.112.005173. Epub 2013 Mar 1.

34.

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.

35.

Gene survival and death on the human Y chromosome.

Wilson Sayres MA, Makova KD.

Mol Biol Evol. 2013 Apr;30(4):781-7. doi: 10.1093/molbev/mss267. Epub 2012 Dec 4.

36.

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.

37.

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.

38.

SMBE proposal to the government of Japan.

Wolfe K, Wayne ML, Makova K, Steen TY, Uyenoyama M, Takahata N.

Mol Biol Evol. 2012 Jan;29(1):441. doi: 10.1093/molbev/msr209. Epub 2011 Nov 10. No abstract available.

PMID:
22080475
39.

Harnessing cloud computing with Galaxy Cloud.

Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J.

Nat Biotechnol. 2011 Nov 8;29(11):972-4. doi: 10.1038/nbt.2028. No abstract available.

40.

Genome analyses substantiate male mutation bias in many species.

Wilson Sayres MA, Makova KD.

Bioessays. 2011 Dec;33(12):938-45. doi: 10.1002/bies.201100091. Epub 2011 Oct 18. Review.

41.

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.

42.

Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes.

Wilson Sayres MA, Venditti C, Pagel M, Makova KD.

Evolution. 2011 Oct;65(10):2800-15. doi: 10.1111/j.1558-5646.2011.01337.x. Epub 2011 Jun 20.

PMID:
21967423
43.

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD.

Genome Biol Evol. 2011;3:1096-106. doi: 10.1093/gbe/evr067. Epub 2011 Jul 29.

44.

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.

Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A.

Genome Biol. 2011;12(6):R59. doi: 10.1186/gb-2011-12-6-r59. Epub 2011 Jun 23.

46.

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.

47.

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.

48.

Strong purifying selection at genes escaping X chromosome inactivation.

Park C, Carrel L, Makova KD.

Mol Biol Evol. 2010 Nov;27(11):2446-50. doi: 10.1093/molbev/msq143. Epub 2010 Jun 9.

49.

The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.

Kvikstad EM, Makova KD.

Genome Res. 2010 May;20(5):600-13. doi: 10.1101/gr.099044.109. Epub 2010 Mar 10.

50.

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.

Supplemental Content

Loading ...
Support Center