EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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Publications

Total: 29 publication(s)

2014

Parts L. (2014)

Genome-wide mapping of cellular traits using yeast

Yeast 31(6):197-205. doi:10.1002/yea.3010
Europe PMC | doi

Parts L, Liu YC, Tekkedil M, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP. (2014)

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

Genome Res. 24(8):1363-1370. doi:10.1101/gr.170506.113
Europe PMC | doi

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. (2014)

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

Mol. Biol. Evol. 31(4):872-888. doi:10.1093/molbev/msu037
Europe PMC | doi

Wagih O, Parts L. (2014)

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

G3 (Bethesda) 4(3):547-552. doi:10.1534/g3.113.009431
Europe PMC | doi


2013

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. (2013)

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

Genetics 195(3):1141-1155. doi:10.1534/genetics.113.155515
Europe PMC | doi

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. (2013)

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

Genome Biol. 14(7) doi:10.1186/gb-2013-14-7-r75
Europe PMC | doi

Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L. (2013)

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

Nucleic Acids Res. 41(Web Server issue):W591-6. doi:10.1093/nar/gkt400
Europe PMC | doi

Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V. (2013)

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

PLoS ONE 8(5):e62266. doi:10.1371/journal.pone.0062266
Europe PMC | doi

van de Bunt M, Gaulton KJ, Parts L, Moran I, Johnson PR, Lindgren CM, Ferrer J, Gloyn AL, McCarthy MI. (2013)

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

PLoS ONE 8(1):e55272. doi:10.1371/journal.pone.0055272
Europe PMC | doi


2012

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. (2012)

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

Nat. Genet. 44(10):1084-1089. doi:10.1038/ng.2394
Europe PMC | doi

Tullus A, Kupper P, Sellin A, Parts L, Sõber J, Tullus T, Lõhmus K, Sõber A, Tullus H. (2012)

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

PLoS ONE 7(8):e42648. doi:10.1371/journal.pone.0042648
Europe PMC | doi

Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V. (2012)

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

Mol. Biol. Evol. 29(4):1187-1197. doi:10.1093/molbev/msr289
Europe PMC | doi

Stegle O, Parts L, Piipari M, Winn J, Durbin R. (2012)

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

Nat Protoc 7(3):500-507. doi:10.1038/nprot.2011.457
Europe PMC | doi

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. (2012)

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

PLoS Genet. 8(5):e1002704. doi:10.1371/journal.pgen.1002704
Europe PMC | doi

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. (2012)

Patterns of cis regulatory variation in diverse human populations

PLoS Genet. 8(4):e1002639. doi:10.1371/journal.pgen.1002639
Europe PMC | doi


2011

Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ, Liti G. (2011)

Assessing the complex architecture of polygenic traits in diverged yeast populations

Mol. Ecol. 20(7):1401-1413. doi:10.1111/j.1365-294x.2011.05005.x
Europe PMC | doi

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. (2011)

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

Genome Res. 21(7):1131-1138. doi:10.1101/gr.116731.110
Europe PMC | doi

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. (2011)

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

PLoS Genet. 7(2):e1002003. doi:10.1371/journal.pgen.1002003
Europe PMC | doi

Parts L, Stegle O, Winn J, Durbin R. (2011)

Joint genetic analysis of gene expression data with inferred cellular phenotypes

PLoS Genet. 7(1):e1001276. doi:10.1371/journal.pgen.1001276
Europe PMC | doi


2010

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. (2010)

A map of human genome variation from population-scale sequencing

Nature 467(7319):1061-1073. doi:10.1038/nature09534
Europe PMC | doi

Glass D, Parts L, Knowles D, Aviv A, Spector TD. (2010)

No correlation between childhood maltreatment and telomere length

Biol. Psychiatry 68(6):e21-2; author reply e23-4. doi:10.1016/j.biopsych.2010.02.026
Europe PMC | doi

Parts L. (2010)

Genetic mapping of cellular traits


Europe PMC

Stegle O, Parts L, Durbin R, Winn J. (2010)

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

PLoS Comput. Biol. 6(5):e1000770. doi:10.1371/journal.pcbi.1000770
Europe PMC | doi


2009

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. (2009)

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

Genome Res. 19(12):2308-2316. doi:10.1101/gr.097097.109
Europe PMC | doi

Liti G, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ. (2009)

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

PLoS Genet. 5(9):e1000659. doi:10.1371/journal.pgen.1000659
Europe PMC | doi

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. (2009)

Population genomics of domestic and wild yeasts

Nature 458(7236):337-341. doi:10.1038/nature07743
Europe PMC | doi


2007

Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. (2007)

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Genome Res. 17(12):1865-1879. doi:10.1101/gr.6593807
Europe PMC | doi

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. (2007)

Evolution of genes and genomes on the Drosophila phylogeny

Nature 450(7167):203-218. doi:10.1038/nature06341
Europe PMC | doi

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. (2007)

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Nature 450(7167):219-232. doi:10.1038/nature06340
Europe PMC | doi