Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 20 of 22

1.

More on the Best Evolutionary Rate for Phylogenetic Analysis.

Klopfstein S, Massingham T, Goldman N.

Syst Biol. 2017 Sep 1;66(5):769-785. doi: 10.1093/sysbio/syx051.

2.

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.

Sipos B, Massingham T, Stütz AM, Goldman N.

PLoS One. 2012;7(8):e43359. doi: 10.1371/journal.pone.0043359. Epub 2012 Aug 17.

3.

Error-correcting properties of the SOLiD Exact Call Chemistry.

Massingham T, Goldman N.

BMC Bioinformatics. 2012 Jun 22;13:145. doi: 10.1186/1471-2105-13-145.

4.

All Your Base: a fast and accurate probabilistic approach to base calling.

Massingham T, Goldman N.

Genome Biol. 2012 Feb 29;13(2):R13. doi: 10.1186/gb-2012-13-2-r13.

5.

Experimental design in phylogenetics: testing predictions from expected information.

San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M, Massingham T.

Syst Biol. 2012 Jul;61(4):661-74. doi: 10.1093/sysbio/sys028. Epub 2012 Feb 10.

PMID:
22328568
6.

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.

7.

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.

Sipos B, Massingham T, Jordan GE, Goldman N.

BMC Bioinformatics. 2011 Apr 19;12:104. doi: 10.1186/1471-2105-12-104.

8.

Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1.

San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R, Cotton JA.

Syst Biol. 2009 Aug;58(4):425-38. doi: 10.1093/sysbio/syp043. Epub 2009 Aug 18.

PMID:
20525595
9.

Ensembl's 10th year.

Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM.

Nucleic Acids Res. 2010 Jan;38(Database issue):D557-62. doi: 10.1093/nar/gkp972. Epub 2009 Nov 11.

10.

Genomic DNA k-mer spectra: models and modalities.

Chor B, Horn D, Goldman N, Levy Y, Massingham T.

Genome Biol. 2009;10(10):R108. doi: 10.1186/gb-2009-10-10-r108. Epub 2009 Oct 8.

11.

Rapidly evolving human promoter regions.

Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA.

Nat Genet. 2008 Nov;40(11):1262-3; author reply 1263-4. doi: 10.1038/ng1108-1262. No abstract available.

PMID:
18957975
12.

Detecting the presence and location of selection in proteins.

Massingham T.

Methods Mol Biol. 2008;452:311-29. doi: 10.1007/978-1-60327-159-2_15. Review.

PMID:
18566771
13.

Determination and validation of principal gene products.

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.

Bioinformatics. 2008 Jan 1;24(1):11-7. Epub 2007 Nov 15.

14.

Statistics of the log-det estimator.

Massingham T, Goldman N.

Mol Biol Evol. 2007 Oct;24(10):2277-85. Epub 2007 Aug 16.

PMID:
17703055
15.

Experimental design criteria in phylogenetics: where to add taxa.

Geuten K, Massingham T, Darius P, Smets E, Goldman N.

Syst Biol. 2007 Aug;56(4):609-22.

PMID:
17654365
16.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

17.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

18.

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.

Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM.

Genome Biol. 2006;7(10):R89. Epub 2006 Oct 9.

19.

Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.

Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM.

Genome Biol. 2005;6(7):R56. Epub 2005 Jun 29.

20.

Detecting amino acid sites under positive selection and purifying selection.

Massingham T, Goldman N.

Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.

Supplemental Content

Loading ...
Support Center