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Items: 24

1.

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.

Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU.

Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4259. [Epub ahead of print]

PMID:
30320766
2.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED.

Gigascience. 2014 Jul 8;3:11. doi: 10.1186/2047-217X-3-11. eCollection 2014.

3.

Genetic comparisons yield insight into the evolution of enamel thickness during human evolution.

Horvath JE, Ramachandran GL, Fedrigo O, Nielsen WJ, Babbitt CC, St Clair EM, Pfefferle LW, Jernvall J, Wray GA, Wall CE.

J Hum Evol. 2014 Aug;73:75-87. doi: 10.1016/j.jhevol.2014.01.005. Epub 2014 May 5.

PMID:
24810709
4.

Genome reference and sequence variation in the large repetitive central exon of human MUC5AC.

Guo X, Zheng S, Dang H, Pace RG, Stonebraker JR, Jones CD, Boellmann F, Yuan G, Haridass P, Fedrigo O, Corcoran DL, Seibold MA, Ranade SS, Knowles MR, O'Neal WK, Voynow JA.

Am J Respir Cell Mol Biol. 2014 Jan;50(1):223-32. doi: 10.1165/rcmb.2013-0235OC.

5.

Reading frame correction by targeted genome editing restores dystrophin expression in cells from Duchenne muscular dystrophy patients.

Ousterout DG, Perez-Pinera P, Thakore PI, Kabadi AM, Brown MT, Qin X, Fedrigo O, Mouly V, Tremblay JP, Gersbach CA.

Mol Ther. 2013 Sep;21(9):1718-26. doi: 10.1038/mt.2013.111. Epub 2013 Jun 4. Erratum in: Mol Ther. 2013 Nov;21(11):2130.

6.

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE.

PLoS Genet. 2012 Jun;8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28.

7.

A potential role for glucose transporters in the evolution of human brain size.

Fedrigo O, Pfefferle AD, Babbitt CC, Haygood R, Wall CE, Wray GA.

Brain Behav Evol. 2011;78(4):315-26. doi: 10.1159/000329852. Epub 2011 Oct 7.

8.

Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution.

Pfefferle AD, Warner LR, Wang CW, Nielsen WJ, Babbitt CC, Fedrigo O, Wray GA.

J Hum Evol. 2011 Feb;60(2):205-212. doi: 10.1016/j.jhevol.2010.10.004. Epub 2010 Dec 28.

9.

Genomic signatures of diet-related shifts during human origins.

Babbitt CC, Warner LR, Fedrigo O, Wall CE, Wray GA.

Proc Biol Sci. 2011 Apr 7;278(1708):961-9. doi: 10.1098/rspb.2010.2433. Epub 2010 Dec 22. Review.

10.

Extensive changes in the expression of the opioid genes between humans and chimpanzees.

Cruz-Gordillo P, Fedrigo O, Wray GA, Babbitt CC.

Brain Behav Evol. 2010;76(2):154-62. doi: 10.1159/000320968. Epub 2010 Nov 15.

PMID:
21079395
11.

A pipeline to determine RT-QPCR control genes for evolutionary studies: application to primate gene expression across multiple tissues.

Fedrigo O, Warner LR, Pfefferle AD, Babbitt CC, Cruz-Gordillo P, Wray GA.

PLoS One. 2010 Sep 2;5(9). pii: e12545. doi: 10.1371/journal.pone.0012545.

12.

Contrasts between adaptive coding and noncoding changes during human evolution.

Haygood R, Babbitt CC, Fedrigo O, Wray GA.

Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7853-7. doi: 10.1073/pnas.0911249107. Epub 2010 Apr 12.

13.

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA.

Genome Biol Evol. 2010 Jan 18;2:67-79. doi: 10.1093/gbe/evq002.

14.

Developmental evolution: how beetles evolved their shields.

Fédrigo O, Wray GA.

Curr Biol. 2010 Jan 26;20(2):R64-6. doi: 10.1016/j.cub.2009.12.012.

15.

Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation.

Tung J, Fédrigo O, Haygood R, Mukherjee S, Wray GA.

Mol Biol Evol. 2009 Sep;26(9):2047-59. doi: 10.1093/molbev/msp113. Epub 2009 Jun 8.

16.

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.

Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA.

Nat Genet. 2007 Sep;39(9):1140-4. Epub 2007 Aug 12.

PMID:
17694055
17.

The genome of the sea urchin Strongylocentrotus purpuratus.

Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 2006 Nov 10;314(5801):941-52. Erratum in: Science. 2007 Feb 9;315(5813):766.

18.

Phylogeny of sharks of the family Triakidae (Carcharhiniformes) and its implications for the evolution of carcharhiniform placental viviparity.

López JA, Ryburn JA, Fedrigo O, Naylor GJ.

Mol Phylogenet Evol. 2006 Jul;40(1):50-60. Epub 2006 Mar 27.

PMID:
16564708
19.

Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics.

Collins TM, Fedrigo O, Naylor GJ.

Syst Biol. 2005 Jun;54(3):493-500. No abstract available.

PMID:
16012114
20.

DRUIDS--detection of regions with unexpected internal deviation from stationarity.

Fedrigo O, Adams DC, Naylor GJ.

J Exp Zool B Mol Dev Evol. 2005 Mar 15;304(2):119-28.

PMID:
15706597
21.

A gene-specific DNA sequencing chip for exploring molecular evolutionary change.

Fedrigo O, Naylor G.

Nucleic Acids Res. 2004 Feb 18;32(3):1208-13. Print 2004.

22.

Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion.

Savolainen V, Chase MW, Salamin N, Soltis DE, Soltis PS, López AJ, Fédrigo O, Naylor GJ.

Syst Biol. 2002 Aug;51(4):638-47. No abstract available.

PMID:
12228005
23.

A model for phylogenetic inference using structural and chemical covariates.

Tavaré S, Adams DC, Fedrigo O, Naylor GJ.

Pac Symp Biocomput. 2001:215-25.

24.

PAQ: Partition Analysis of Quasispecies.

Baccam P, Thompson RJ, Fedrigo O, Carpenter S, Cornette JL.

Bioinformatics. 2001 Jan;17(1):16-22.

PMID:
11222259

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