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Items: 1 to 20 of 46

1.

Random forest based similarity learning for single cell RNA sequencing data.

Pouyan MB, Kostka D.

Bioinformatics. 2018 Jul 1;34(13):i79-i88. doi: 10.1093/bioinformatics/bty260.

2.

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages.

Kostka D, Holloway AK, Pollard KS.

Mol Biol Evol. 2018 Aug 1;35(8):2034-2045. doi: 10.1093/molbev/msy109.

3.

The complex genetics of hypoplastic left heart syndrome.

Liu X, Yagi H, Saeed S, Bais AS, Gabriel GC, Chen Z, Peterson KA, Li Y, Schwartz MC, Reynolds WT, Saydmohammed M, Gibbs B, Wu Y, Devine W, Chatterjee B, Klena NT, Kostka D, de Mesy Bentley KL, Ganapathiraju MK, Dexheimer P, Leatherbury L, Khalifa O, Bhagat A, Zahid M, Pu W, Watkins S, Grossfeld P, Murray SA, Porter GA Jr, Tsang M, Martin LJ, Benson DW, Aronow BJ, Lo CW.

Nat Genet. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870. Epub 2017 May 22.

4.

Correction: DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans.

Amrit FR, Steenkiste EM, Ratnappan R, Chen SW, McClendon TB, Kostka D, Yanowitz J, Olsen CP, Ghazi A.

PLoS Genet. 2016 Oct 7;12(10):e1006381. doi: 10.1371/journal.pgen.1006381. eCollection 2016 Oct.

5.

DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans.

Amrit FR, Steenkiste EM, Ratnappan R, Chen SW, McClendon TB, Kostka D, Yanowitz J, Olsen CP, Ghazi A.

PLoS Genet. 2016 Feb 10;12(2):e1005788. doi: 10.1371/journal.pgen.1005788. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 Oct 7;12 (10 ):e1006381.

6.
7.

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

8.

Modeling DNA methylation dynamics with approaches from phylogenetics.

Capra JA, Kostka D.

Bioinformatics. 2014 Sep 1;30(17):i408-14. doi: 10.1093/bioinformatics/btu445.

9.

Integrating diverse datasets improves developmental enhancer prediction.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677. eCollection 2014 Jun.

10.

MicroRNA-17~92 is required for nephrogenesis and renal function.

Marrone AK, Stolz DB, Bastacky SI, Kostka D, Bodnar AJ, Ho J.

J Am Soc Nephrol. 2014 Jul;25(7):1440-52. doi: 10.1681/ASN.2013040390. Epub 2014 Feb 7.

11.

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A.

PLoS Genet. 2013;9(8):e1003684. doi: 10.1371/journal.pgen.1003684. Epub 2013 Aug 15.

12.

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Kostka D, Hubisz MJ, Siepel A, Pollard KS.

Mol Biol Evol. 2012 Mar;29(3):1047-57. doi: 10.1093/molbev/msr279. Epub 2011 Nov 10.

13.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

14.

Noncoding sequences near duplicated genes evolve rapidly.

Kostka D, Hahn MW, Pollard KS.

Genome Biol Evol. 2010;2:518-33. doi: 10.1093/gbe/evq037. Epub 2010 Jun 29.

15.

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH.

Mol Biol Evol. 2010 Oct;27(10):2322-32. doi: 10.1093/molbev/msq128. Epub 2010 May 21.

16.

Regulatory networks define phenotypic classes of human stem cell lines.

Müller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF.

Nature. 2008 Sep 18;455(7211):401-5. doi: 10.1038/nature07213. Epub 2008 Aug 24.

17.

Analyzing gene perturbation screens with nested effects models in R and bioconductor.

Fröhlich H, Beissbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F.

Bioinformatics. 2008 Nov 1;24(21):2549-50. doi: 10.1093/bioinformatics/btn446. Epub 2008 Aug 21.

18.

Computational diagnostics with gene expression profiles.

Lottaz C, Kostka D, Markowetz F, Spang R.

Methods Mol Biol. 2008;453:281-96. doi: 10.1007/978-1-60327-429-6_15.

PMID:
18712310
19.

Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs.

Jacob J, Jentsch M, Kostka D, Bentink S, Spang R.

Bioinformatics. 2008 Apr 1;24(7):995-1001. doi: 10.1093/bioinformatics/btn056. Epub 2008 Feb 19.

PMID:
18285370
20.

Microarray based diagnosis profits from better documentation of gene expression signatures.

Kostka D, Spang R.

PLoS Comput Biol. 2008 Feb;4(2):e22. doi: 10.1371/journal.pcbi.0040022.

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