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Items: 43

1.

SLING: a tool to search for linked genes in bacterial datasets.

Horesh G, Harms A, Fino C, Parts L, Gerdes K, Heinz E, Thomson NR.

Nucleic Acids Res. 2018 Aug 16. doi: 10.1093/nar/gky738. [Epub ahead of print]

PMID:
30124998
2.

Admission cardiotocography: A hospital based validation study.

Parts L, Holzmann M, Norman M, Lindqvist PG.

Eur J Obstet Gynecol Reprod Biol. 2018 Oct;229:26-31. doi: 10.1016/j.ejogrb.2018.07.016. Epub 2018 Jul 30.

PMID:
30098449
3.

Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B.

Zyryanova AF, Weis F, Faille A, Alard AA, Crespillo-Casado A, Sekine Y, Harding HP, Allen F, Parts L, Fromont C, Fischer PM, Warren AJ, Ron D.

Science. 2018 Mar 30;359(6383):1533-1536. doi: 10.1126/science.aar5129.

4.

Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes.

Bushell E, Gomes AR, Sanderson T, Anar B, Girling G, Herd C, Metcalf T, Modrzynska K, Schwach F, Martin RE, Mather MW, McFadden GI, Parts L, Rutledge GG, Vaidya AB, Wengelnik K, Rayner JC, Billker O.

Cell. 2017 Jul 13;170(2):260-272.e8. doi: 10.1016/j.cell.2017.06.030.

5.

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

Pärnamaa T, Parts L.

G3 (Bethesda). 2017 May 5;7(5):1385-1392. doi: 10.1534/g3.116.033654.

6.

The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae.

García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM.

BMC Genomics. 2017 Feb 14;18(1):159. doi: 10.1186/s12864-017-3572-2.

7.

Powerful decomposition of complex traits in a diploid model.

Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G.

Nat Commun. 2016 Nov 2;7:13311. doi: 10.1038/ncomms13311.

8.

Deep learning for computational biology.

Angermueller C, Pärnamaa T, Parts L, Stegle O.

Mol Syst Biol. 2016 Jul 29;12(7):878. doi: 10.15252/msb.20156651. Review.

9.

Predicting quantitative traits from genome and phenome with near perfect accuracy.

Märtens K, Hallin J, Warringer J, Liti G, Parts L.

Nat Commun. 2016 May 10;7:11512. doi: 10.1038/ncomms11512.

10.

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP.

Genome Biol. 2016 Mar 8;17:45. doi: 10.1186/s13059-016-0900-9.

11.

Genetic Interaction Scoring Procedure for Bacterial Species.

Wagih O, Parts L.

Adv Exp Med Biol. 2015;883:169-85. doi: 10.1007/978-3-319-23603-2_10. Review.

PMID:
26621468
12.

Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

Anand Brown A, Ding Z, Viñuela A, Glass D, Parts L, Spector T, Winn J, Durbin R.

G3 (Bethesda). 2015 Mar 9;5(5):839-47. doi: 10.1534/g3.114.011411.

13.

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L.

Pac Symp Biocomput. 2015:342-6.

14.

Heritability and genetic basis of protein level variation in an outbred population.

Parts L, Liu YC, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP.

Genome Res. 2014 Aug;24(8):1363-70. doi: 10.1101/gr.170506.113. Epub 2014 May 13.

15.

Genome-wide mapping of cellular traits using yeast.

Parts L.

Yeast. 2014 Jun;31(6):197-205. doi: 10.1002/yea.3010. Epub 2014 May 15.

16.

gitter: a robust and accurate method for quantification of colony sizes from plate images.

Wagih O, Parts L.

G3 (Bethesda). 2014 Mar 20;4(3):547-52. doi: 10.1534/g3.113.009431.

17.

A high-definition view of functional genetic variation from natural yeast genomes.

Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037. Epub 2014 Jan 14.

18.

Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction.

Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L.

Pac Symp Biocomput. 2014;19:224-8. doi: 10.1142/9789814583220_0022. No abstract available.

19.

High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G.

Genetics. 2013 Nov;195(3):1141-55. doi: 10.1534/genetics.113.155515. Epub 2013 Sep 13.

20.

Gene expression changes with age in skin, adipose tissue, blood and brain.

Glass D, Viñuela A, Davies MN, Ramasamy A, Parts L, Knowles D, Brown AA, Hedman AK, Small KS, Buil A, Grundberg E, Nica AC, Di Meglio P, Nestle FO, Ryten M; UK Brain Expression consortium; MuTHER consortium, Durbin R, McCarthy MI, Deloukas P, Dermitzakis ET, Weale ME, Bataille V, Spector TD.

Genome Biol. 2013 Jul 26;14(7):R75. doi: 10.1186/gb-2013-14-7-r75.

21.

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.

Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W591-6. doi: 10.1093/nar/gkt400. Epub 2013 May 15.

22.

Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses.

Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V.

PLoS One. 2013 May 2;8(5):e62266. doi: 10.1371/journal.pone.0062266. Print 2013.

23.

The miRNA profile of human pancreatic islets and beta-cells and relationship to type 2 diabetes pathogenesis.

van de Bunt M, Gaulton KJ, Parts L, Moran I, Johnson PR, Lindgren CM, Ferrer J, Gloyn AL, McCarthy MI.

PLoS One. 2013;8(1):e55272. doi: 10.1371/journal.pone.0055272. Epub 2013 Jan 25.

24.

Mapping cis- and trans-regulatory effects across multiple tissues in twins.

Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett J, Sekowska M, Wilk A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M, Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni L, Tsoka S, Bataille V, Durbin R, Nestle FO, O'Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KR, Schadt EE, Stefansson K, Smith GD, McCarthy MI, Deloukas P, Dermitzakis ET, Spector TD; Multiple Tissue Human Expression Resource (MuTHER) Consortium.

Nat Genet. 2012 Oct;44(10):1084-9. doi: 10.1038/ng.2394. Epub 2012 Sep 2.

25.

Climate change at northern latitudes: rising atmospheric humidity decreases transpiration, N-uptake and growth rate of hybrid aspen.

Tullus A, Kupper P, Sellin A, Parts L, Sõber J, Tullus T, Lõhmus K, Sõber A, Tullus H.

PLoS One. 2012;7(8):e42648. doi: 10.1371/journal.pone.0042648. Epub 2012 Aug 6.

26.

Extent, causes, and consequences of small RNA expression variation in human adipose tissue.

Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J; MuTHER Consortium, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM.

PLoS Genet. 2012;8(5):e1002704. doi: 10.1371/journal.pgen.1002704. Epub 2012 May 10.

27.

Patterns of cis regulatory variation in diverse human populations.

Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.

PLoS Genet. 2012;8(4):e1002639. doi: 10.1371/journal.pgen.1002639. Epub 2012 Apr 19.

28.

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.

Stegle O, Parts L, Piipari M, Winn J, Durbin R.

Nat Protoc. 2012 Feb 16;7(3):500-7. doi: 10.1038/nprot.2011.457.

29.

Quantifying selection acting on a complex trait using allele frequency time series data.

Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V.

Mol Biol Evol. 2012 Apr;29(4):1187-97. doi: 10.1093/molbev/msr289. Epub 2011 Nov 23.

30.

Revealing the genetic structure of a trait by sequencing a population under selection.

Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead SJ, Molin M, Zia A, Simpson JT, Quail MA, Moses A, Louis EJ, Durbin R, Liti G.

Genome Res. 2011 Jul;21(7):1131-8. doi: 10.1101/gr.116731.110. Epub 2011 Mar 21.

31.

The architecture of gene regulatory variation across multiple human tissues: the MuTHER study.

Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M, Travers M, Potter S, Grundberg E, Small K, Hedman AK, Bataille V, Tzenova Bell J, Surdulescu G, Dimas AS, Ingle C, Nestle FO, di Meglio P, Min JL, Wilk A, Hammond CJ, Hassanali N, Yang TP, Montgomery SB, O'Rahilly S, Lindgren CM, Zondervan KT, Soranzo N, Barroso I, Durbin R, Ahmadi K, Deloukas P, McCarthy MI, Dermitzakis ET, Spector TD; MuTHER Consortium.

PLoS Genet. 2011 Feb 3;7(2):e1002003. doi: 10.1371/journal.pgen.1002003.

32.

Joint genetic analysis of gene expression data with inferred cellular phenotypes.

Parts L, Stegle O, Winn J, Durbin R.

PLoS Genet. 2011 Jan 20;7(1):e1001276. doi: 10.1371/journal.pgen.1001276.

33.

Assessing the complex architecture of polygenic traits in diverged yeast populations.

Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ, Liti G.

Mol Ecol. 2011 Apr;20(7):1401-13. doi: 10.1111/j.1365-294X.2011.05005.x. Epub 2011 Jan 25.

PMID:
21261765
34.

No correlation between childhood maltreatment and telomere length.

Glass D, Parts L, Knowles D, Aviv A, Spector TD.

Biol Psychiatry. 2010 Sep 15;68(6):e21-2; author reply e23-4. doi: 10.1016/j.biopsych.2010.02.026. Epub 2010 Aug 3. No abstract available.

35.

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.

Stegle O, Parts L, Durbin R, Winn J.

PLoS Comput Biol. 2010 May 6;6(5):e1000770. doi: 10.1371/journal.pcbi.1000770.

36.

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants.

Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK.

Genome Res. 2009 Dec;19(12):2308-16. doi: 10.1101/gr.097097.109. Epub 2009 Oct 13.

37.

Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.

Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ.

PLoS Genet. 2009 Sep;5(9):e1000659. doi: 10.1371/journal.pgen.1000659. Epub 2009 Sep 18.

38.

Population genomics of domestic and wild yeasts.

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.

39.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.

40.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
41.

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.

Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M.

Genome Res. 2007 Dec;17(12):1865-79. Epub 2007 Nov 7.

42.

Polymorphic glutathione S-transferase M1 is a risk factor of primary open-angle glaucoma among Estonians.

Juronen E, Tasa G, Veromann S, Parts L, Tiidla A, Pulges R, Panov A, Soovere L, Koka K, Mikelsaar AV.

Exp Eye Res. 2000 Nov;71(5):447-52.

PMID:
11040079
43.

Polymorphic glutathione S-transferases as genetic risk factors for senile cortical cataract in Estonians.

Juronen E, Tasa G, Veromann S, Parts L, Tiidla A, Pulges R, Panov A, Soovere L, Koka K, Mikelsaar AV.

Invest Ophthalmol Vis Sci. 2000 Jul;41(8):2262-7.

PMID:
10892871

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