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Items: 1 to 20 of 79

1.

Corrigendum: Direct determination of diploid genome sequences.

Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB.

Genome Res. 2018 Apr;28(4):606.1. doi: 10.1101/gr.235812.118. No abstract available.

2.

A computational model for how the fast afterhyperpolarization paradoxically increases gain in regularly firing neurons.

Jaffe DB, Brenner R.

J Neurophysiol. 2018 Apr 1;119(4):1506-1520. doi: 10.1152/jn.00385.2017. Epub 2018 Jan 10.

PMID:
29357445
3.

Downregulation of KCNMB4 expression and changes in BK channel subtype in hippocampal granule neurons following seizure activity.

Whitmire LE, Ling L, Bugay V, Carver CM, Timilsina S, Chuang HH, Jaffe DB, Shapiro MS, Cavazos JE, Brenner R.

PLoS One. 2017 Nov 16;12(11):e0188064. doi: 10.1371/journal.pone.0188064. eCollection 2017.

4.

Direct determination of diploid genome sequences.

Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB.

Genome Res. 2017 May;27(5):757-767. doi: 10.1101/gr.214874.116. Epub 2017 Apr 5. Erratum in: Genome Res. 2018 Apr;28(4):606.1.

5.

Local GABAergic signaling within sensory ganglia controls peripheral nociceptive transmission.

Du X, Hao H, Yang Y, Huang S, Wang C, Gigout S, Ramli R, Li X, Jaworska E, Edwards I, Deuchars J, Yanagawa Y, Qi J, Guan B, Jaffe DB, Zhang H, Gamper N.

J Clin Invest. 2017 May 1;127(5):1741-1756. doi: 10.1172/JCI86812. Epub 2017 Apr 4.

6.

Knockout of the BK β4-subunit promotes a functional coupling of BK channels and ryanodine receptors that mediate a fAHP-induced increase in excitability.

Wang B, Bugay V, Ling L, Chuang HH, Jaffe DB, Brenner R.

J Neurophysiol. 2016 Aug 1;116(2):456-65. doi: 10.1152/jn.00857.2015. Epub 2016 May 4.

7.

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly.

Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE.

BMC Genomics. 2016 Mar 5;17:187. doi: 10.1186/s12864-016-2531-7.

8.

Spike propagation through the dorsal root ganglia in an unmyelinated sensory neuron: a modeling study.

Sundt D, Gamper N, Jaffe DB.

J Neurophysiol. 2015 Dec;114(6):3140-53. doi: 10.1152/jn.00226.2015. Epub 2015 Sep 2.

9.

Current understanding of iberiotoxin-resistant BK channels in the nervous system.

Wang B, Jaffe DB, Brenner R.

Front Physiol. 2014 Oct 9;5:382. doi: 10.3389/fphys.2014.00382. eCollection 2014. Review.

10.

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.

11.

The genomic substrate for adaptive radiation in African cichlid fish.

Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F.

Nature. 2014 Sep 18;513(7518):375-381. doi: 10.1038/nature13726. Epub 2014 Sep 3.

12.

Control of somatic membrane potential in nociceptive neurons and its implications for peripheral nociceptive transmission.

Du X, Hao H, Gigout S, Huang D, Yang Y, Li L, Wang C, Sundt D, Jaffe DB, Zhang H, Gamper N.

Pain. 2014 Nov;155(11):2306-22. doi: 10.1016/j.pain.2014.08.025. Epub 2014 Aug 26.

13.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

14.

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.

15.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

16.

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.

17.

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.

18.

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.

19.

The genomic basis of adaptive evolution in threespine sticklebacks.

Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C; Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM.

Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944.

20.

Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing.

Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK.

Sci Transl Med. 2012 Jan 25;4(118):118ra10. doi: 10.1126/scitranslmed.3003310.

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