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Items: 20

1.

Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes.

Kent CF, Dey A, Patel H, Tsvetkov N, Tiwari T, MacPhail VJ, Gobeil Y, Harpur BA, Gurtowski J, Schatz MC, Colla SR, Zayed A.

Front Genet. 2018 Aug 10;9:316. doi: 10.3389/fgene.2018.00316. eCollection 2018.

2.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

3.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.

Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

4.

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae.

Simner PJ, Antar AAR, Hao S, Gurtowski J, Tamma PD, Rock C, Opene BNA, Tekle T, Carroll KC, Schatz MC, Timp W.

J Antimicrob Chemother. 2018 Jul 1;73(7):1796-1803. doi: 10.1093/jac/dky121.

5.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

6.

GenomeScope: fast reference-free genome profiling from short reads.

Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC.

Bioinformatics. 2017 Jul 15;33(14):2202-2204. doi: 10.1093/bioinformatics/btx153.

7.

Antibiotic Spacer Arthroplasty for Revision MTP Arthrodesis: A Novel Means to Build the Implant: A Case Report.

Bitterman A, Mathew C, Patel M, Gurtowski JP.

Cureus. 2016 Mar 21;8(3):e537. doi: 10.7759/cureus.537.

8.

The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.

9.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR.

Genome Res. 2015 Nov;25(11):1750-6. doi: 10.1101/gr.191395.115. Epub 2015 Oct 7.

10.

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.

Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12462-7. doi: 10.1073/pnas.1516718112. Epub 2015 Sep 21.

11.

Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano.

Zhou X, Battistoni G, El Demerdash O, Gurtowski J, Wunderer J, Falciatori I, Ladurner P, Schatz MC, Hannon GJ, Wasik KA.

RNA. 2015 Nov;21(11):1885-97. doi: 10.1261/rna.052456.115. Epub 2015 Aug 31.

12.

Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis.

MacColl E, Therkelsen MD, Sherpa T, Ellerbrock H, Johnston LA, Jariwala RH, Chang W, Gurtowski J, Schatz MC, Mozammal Hossain M, Cassidy-Hanley DM, Clark TG, Chang WJ.

Mol Phylogenet Evol. 2015 May;86:1-7. doi: 10.1016/j.ympev.2015.02.017. Epub 2015 Mar 2.

PMID:
25743182
13.

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR.

Genome Biol. 2014;15(11):506.

14.

Genotyping in the cloud with Crossbow.

Gurtowski J, Schatz MC, Langmead B.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.3. doi: 10.1002/0471250953.bi1503s39.

15.

Geoseq: a tool for dissecting deep-sequencing datasets.

Gurtowski J, Cancio A, Shah H, Levovitz C, George A, Homann R, Sachidanandam R.

BMC Bioinformatics. 2010 Oct 12;11:506. doi: 10.1186/1471-2105-11-506.

16.

Normal pelvic strain pattern in vitro.

Ries M, Pugh J, Au JC, Gurtowski J, Dee R.

J Biomed Eng. 1989 Sep;11(5):398-402.

PMID:
2796319
17.

Cortical pelvic strains with varying size hemiarthroplasty in vitro.

Ries M, Pugh J, Au JC, Gurtowski J, Dee R.

J Biomech. 1989;22(8-9):775-80.

PMID:
2613712
18.

The vertical wheeler: a device for ambulation in cerebral palsy.

Manley MT, Gurtowski J.

Arch Phys Med Rehabil. 1985 Oct;66(10):717-20.

PMID:
4051716
19.

The load carrying and fatigue properties of the stem-cement interface with smooth and porous coated femoral components.

Manley MT, Stern LS, Gurtowski J.

J Biomed Mater Res. 1985 May-Jun;19(5):563-75.

PMID:
4066729
20.

Performance characteristics of total hip femoral components as a function of prosthesis modulus.

Manley M, Stern L, Gurtowski J.

Bull Hosp Jt Dis Orthop Inst. 1983 Fall;43(2):130-6.

PMID:
6317096

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