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Items: 1 to 50 of 114

1.

Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue.

Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A; Accelerating Medicines Partnership RA/SLE Network, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH.

Arthritis Res Ther. 2018 Jul 11;20(1):139. doi: 10.1186/s13075-018-1631-y.

2.

SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.

Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13.

PMID:
29535149
3.

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection.

Weiss ER, Lamers SL, Henderson JL, Melnikov A, Somasundaran M, Garber M, Selin L, Nusbaum C, Luzuriaga K.

J Virol. 2018 Jan 2;92(2). pii: e01466-17. doi: 10.1128/JVI.01466-17. Print 2018 Jan 15.

4.

Acquiring nutrients from tree leaves: effects of leaf maturity and development type on a generalist caterpillar.

Barbehenn RV, Kapila M, Kileen S, Nusbaum CP.

Oecologia. 2017 May;184(1):59-73. doi: 10.1007/s00442-017-3854-z. Epub 2017 Mar 24.

PMID:
28342011
5.

Evolvix BEST Names for semantic reproducibility across code2brain interfaces.

Loewe L, Scheuer KS, Keel SA, Vyas V, Liblit B, Hanlon B, Ferris MC, Yin J, Dutra I, Pietsch A, Javid CG, Moog CL, Meyer J, Dresel J, McLoone B, Loberger S, Movaghar A, Gilchrist-Scott M, Sabri Y, Sescleifer D, Pereda-Zorrilla I, Zietlow A, Smith R, Pietenpol S, Goldfinger J, Atzen SL, Freiberg E, Waters NP, Nusbaum C, Nolan E, Hotz A, Kliman RM, Mentewab A, Fregien N, Loewe M.

Ann N Y Acad Sci. 2017 Jan;1387(1):124-144. doi: 10.1111/nyas.13192. Epub 2016 Dec 5. Review.

6.

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome.

Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS.

Elife. 2016 Nov 28;5. pii: e19090. doi: 10.7554/eLife.19090.

7.

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq.

Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C, Goren A.

Epigenetics Chromatin. 2016 Nov 4;9:49. eCollection 2016.

8.

Genome Sequence of Spizellomyces punctatus.

Russ C, Lang BF, Chen Z, Gujja S, Shea T, Zeng Q, Young S, Cuomo CA, Nusbaum C.

Genome Announc. 2016 Aug 18;4(4). pii: e00849-16. doi: 10.1128/genomeA.00849-16.

9.

Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system".

Haimovich G, Zabezhinsky D, Haas B, Slobodin B, Purushothaman P, Fan L, Levin JZ, Nusbaum C, Gerst JE.

RNA. 2016 May;22(5):660-6. doi: 10.1261/rna.055095.115. Epub 2016 Mar 11.

10.

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA.

Nat Commun. 2016 Feb 22;7:10740. doi: 10.1038/ncomms10740.

11.

Draft Genome Sequence of Cercospora arachidicola, Causal Agent of Early Leaf Spot in Peanuts.

Orner VA, Cantonwine EG, Wang XM, Abouelleil A, Bochicchio J, Nusbaum C, Culbreath AK, Abdo Z, Arias RS.

Genome Announc. 2015 Nov 5;3(6). pii: e01281-15. doi: 10.1128/genomeA.01281-15.

12.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC.

Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.

13.

Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract.

Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, Padavattan N, Ismail N, Moodley A, Sabatini ME, Ghebremichael MS, Nusbaum C, Huttenhower C, Virgin HW, Ndung'u T, Dong KL, Walker BD, Fichorova RN, Kwon DS.

Immunity. 2015 May 19;42(5):965-76. doi: 10.1016/j.immuni.2015.04.019.

14.

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

Lassiter ES, Russ C, Nusbaum C, Zeng Q, Saville AC, Olarte RA, Carbone I, Hu CH, Seguin-Orlando A, Samaniego JA, Thorne JL, Ristaino JB.

Curr Genet. 2015 Nov;61(4):567-77. doi: 10.1007/s00294-015-0480-3. Epub 2015 Mar 10.

15.

Comprehensive variation discovery in single human genomes.

Weisenfeld NI, Yin S, Sharpe T, Lau B, Hegarty R, Holmes L, Sogoloff B, Tabbaa D, Williams L, Russ C, Nusbaum C, Lander ES, MacCallum I, Jaffe DB.

Nat Genet. 2014 Dec;46(12):1350-5. doi: 10.1038/ng.3121. Epub 2014 Oct 19.

16.

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.

Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

17.

Mimicking biological membranes with programmable glycan ligands self-assembled from amphiphilic Janus glycodendrimers.

Zhang S, Moussodia RO, Sun HJ, Leowanawat P, Muncan A, Nusbaum CD, Chelling KM, Heiney PA, Klein ML, André S, Roy R, Gabius HJ, Percec V.

Angew Chem Int Ed Engl. 2014 Oct 6;53(41):10899-903. doi: 10.1002/anie.201403186. Epub 2014 Jun 12.

PMID:
24923471
18.

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

Miranda KC, Bond DT, Levin JZ, Adiconis X, Sivachenko A, Russ C, Brown D, Nusbaum C, Russo LM.

PLoS One. 2014 May 9;9(5):e96094. doi: 10.1371/journal.pone.0096094. eCollection 2014.

19.

Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

Timling I, Walker DA, Nusbaum C, Lennon NJ, Taylor DL.

Mol Ecol. 2014 Jul;23(13):3258-72. doi: 10.1111/mec.12743. Epub 2014 Apr 30.

PMID:
24689939
20.

Regulated aggregative multicellularity in a close unicellular relative of metazoa.

Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I.

Elife. 2013 Dec 24;2:e01287. doi: 10.7554/eLife.01287.

21.

Semiconductor-based DNA sequencing of histone modification states.

Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I.

Nat Commun. 2013;4:2672. doi: 10.1038/ncomms3672.

22.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I.

Nat Commun. 2013;4:2325. doi: 10.1038/ncomms3325.

23.

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P.

PLoS Genet. 2013 Jun;9(6):e1003272. doi: 10.1371/journal.pgen.1003272. Epub 2013 Jun 13.

24.

Characterizing and measuring bias in sequence data.

Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, Nusbaum C, Jaffe DB.

Genome Biol. 2013 May 29;14(5):R51. doi: 10.1186/gb-2013-14-5-r51.

25.

Modular synthesis of amphiphilic Janus glycodendrimers and their self-assembly into glycodendrimersomes and other complex architectures with bioactivity to biomedically relevant lectins.

Percec V, Leowanawat P, Sun HJ, Kulikov O, Nusbaum CD, Tran TM, Bertin A, Wilson DA, Peterca M, Zhang S, Kamat NP, Vargo K, Moock D, Johnston ED, Hammer DA, Pochan DJ, Chen Y, Chabre YM, Shiao TC, Bergeron-Brlek M, André S, Roy R, Gabius HJ, Heiney PA.

J Am Chem Soc. 2013 Jun 19;135(24):9055-77. doi: 10.1021/ja403323y. Epub 2013 Jun 6.

PMID:
23692629
26.

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):E3629-30. No abstract available.

27.

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta.

Fairclough SR, Chen Z, Kramer E, Zeng Q, Young S, Robertson HM, Begovic E, Richter DJ, Russ C, Westbrook MJ, Manning G, Lang BF, Haas B, Nusbaum C, King N.

Genome Biol. 2013 Feb 18;14(2):R15. doi: 10.1186/gb-2013-14-2-r15.

28.

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hůlková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ.

Nat Genet. 2013 Mar;45(3):299-303. doi: 10.1038/ng.2543. Epub 2013 Feb 10.

29.

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J.

BMC Genomics. 2012 Dec 27;13:734. doi: 10.1186/1471-2164-13-734.

30.

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.

Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.

Mol Cell. 2012 Sep 14;47(5):810-22. doi: 10.1016/j.molcel.2012.07.030. Epub 2012 Aug 30.

31.

Pacific biosciences sequencing technology for genotyping and variation discovery in human data.

Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA.

BMC Genomics. 2012 Aug 5;13:375. doi: 10.1186/1471-2164-13-375.

32.

Finished bacterial genomes from shotgun sequence data.

Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB.

Genome Res. 2012 Nov;22(11):2270-7. doi: 10.1101/gr.141515.112. Epub 2012 Jul 24.

33.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

34.

Genome-wide identification and characterization of replication origins by deep sequencing.

Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N.

Genome Biol. 2012 Apr 24;13(4):R27. doi: 10.1186/gb-2012-13-4-r27.

35.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A.

Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

36.

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3065-70. doi: 10.1073/pnas.1121491109. Epub 2012 Feb 6. Erratum in: Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5547.

37.

Yeast sterol regulatory element-binding protein (SREBP) cleavage requires Cdc48 and Dsc5, a ubiquitin regulatory X domain-containing subunit of the Golgi Dsc E3 ligase.

Stewart EV, Lloyd SJ, Burg JS, Nwosu CC, Lintner RE, Daza R, Russ C, Ponchner K, Nusbaum C, Espenshade PJ.

J Biol Chem. 2012 Jan 2;287(1):672-81. doi: 10.1074/jbc.M111.317370. Epub 2011 Nov 15.

38.

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.

39.

Hybrid selection for sequencing pathogen genomes from clinical samples.

Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D, Sene PD, Wirth DF, Nusbaum C, Volkman SK, Birren BW, Gnirke A, Neafsey DE.

Genome Biol. 2011 Aug 11;12(8):R73. doi: 10.1186/gb-2011-12-8-r73.

40.

High-resolution description of antibody heavy-chain repertoires in humans.

Arnaout R, Lee W, Cahill P, Honan T, Sparrow T, Weiand M, Nusbaum C, Rajewsky K, Koralov SB.

PLoS One. 2011;6(8):e22365. doi: 10.1371/journal.pone.0022365. Epub 2011 Aug 4.

41.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

42.

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.

Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, Amit I, Regev A.

Nat Biotechnol. 2011 May;29(5):436-42. doi: 10.1038/nbt.1861. Epub 2011 Apr 24.

43.

Comparative functional genomics of the fission yeasts.

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

44.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.

Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A.

Genome Biol. 2011;12(2):R18. doi: 10.1186/gb-2011-12-2-r18. Epub 2011 Feb 21.

45.

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.

Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C.

Genome Biol. 2011;12(1):R1. doi: 10.1186/gb-2011-12-1-r1. Epub 2011 Jan 4.

46.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. doi: 10.1073/pnas.1017351108. Epub 2010 Dec 27.

47.

Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate.

Alegado RA, Ferriera S, Nusbaum C, Young SK, Zeng Q, Imamovic A, Fairclough SR, King N.

J Bacteriol. 2011 Mar;193(6):1485-6. doi: 10.1128/JB.01421-10. Epub 2010 Dec 23.

48.

Genome evolution following host jumps in the Irish potato famine pathogen lineage.

Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RH, Zody MC, Kunjeti SG, Donofrio NM, Meyers BC, Nusbaum C, Kamoun S.

Science. 2010 Dec 10;330(6010):1540-3. doi: 10.1126/science.1193070.

49.

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.

Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Genome Biol. 2010;11(8):R87. doi: 10.1186/gb-2010-11-8-r87. Epub 2010 Aug 26.

50.

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.

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