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Items: 36

1.

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.

PMID:
29979655
2.

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.

Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC.

Stand Genomic Sci. 2017 Feb 8;12:23. doi: 10.1186/s40793-017-0233-7. eCollection 2017.

3.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW.

Genome Announc. 2015 Mar 12;3(2). pii: e00092-15. doi: 10.1128/genomeA.00092-15.

4.

MetaMicrobesOnline: phylogenomic analysis of microbial communities.

Chivian D, Dehal PS, Keller K, Arkin AP.

Nucleic Acids Res. 2013 Jan;41(Database issue):D648-54. doi: 10.1093/nar/gks1202. Epub 2012 Nov 30.

5.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W604-8. doi: 10.1093/nar/gks562. Epub 2012 Jun 14.

6.

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.

Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A.

Genome Biol. 2011 Oct 12;12(10):R99. doi: 10.1186/gb-2011-12-10-r99.

7.

The generation and evaluation of recombinant human IgA specific for Plasmodium falciparum merozoite surface protein 1-19 (PfMSP1 19).

Shi J, McIntosh RS, Adame-Gallegos J, Dehal PK, van Egmond M, van de Winkel J, Draper SJ, Forbes EK, Corran PH, Holder AA, Woof JM, Pleass RJ.

BMC Biotechnol. 2011 Jul 22;11:77. doi: 10.1186/1472-6750-11-77.

8.

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canché B, Churchill AC, Conde-Ferràez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH.

PLoS Genet. 2011 Jun;7(6):e1002070. doi: 10.1371/journal.pgen.1002070. Epub 2011 Jun 9.

9.

Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.

Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RHY, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JDG, McDowell JM, Beynon J, Tyler BM.

Science. 2010 Dec 10;330(6010):1549-1551. doi: 10.1126/science.1195203.

10.

Magnetizable antibody-like proteins.

Dehal PK, Livingston CF, Dunn CG, Buick R, Luxton R, Pritchard DJ.

Biotechnol J. 2010 Jun;5(6):596-604. doi: 10.1002/biot.200900273.

PMID:
20518063
11.

A universal TagModule collection for parallel genetic analysis of microorganisms.

Oh J, Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin AP, Deutschbauer A.

Nucleic Acids Res. 2010 Aug;38(14):e146. doi: 10.1093/nar/gkq419. Epub 2010 May 21.

12.

FastTree 2--approximately maximum-likelihood trees for large alignments.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490.

13.

MicrobesOnline: an integrated portal for comparative and functional genomics.

Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP.

Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11.

14.

Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.

Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HC, Zhou J, Wall JD, Hazen TC, Arkin AP, Stahl DA.

Environ Microbiol. 2009 Sep;11(9):2244-52. doi: 10.1111/j.1462-2920.2009.01946.x.

PMID:
19737303
15.

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.

Price MN, Dehal PS, Arkin AP.

Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077. Epub 2009 Apr 17.

16.

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.

Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J.

BMC Genomics. 2009 Mar 25;10:131. doi: 10.1186/1471-2164-10-131.

17.

Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism.

Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A, Arkin A, Keasling JD.

Biotechnol Bioeng. 2009 Mar 1;102(4):1161-9. doi: 10.1002/bit.22129.

PMID:
19031428
18.

FastBLAST: homology relationships for millions of proteins.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31.

19.

Environmental genomics reveals a single-species ecosystem deep within Earth.

Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC.

Science. 2008 Oct 10;322(5899):275-8. doi: 10.1126/science.1155495.

20.

Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.

Price MN, Dehal PS, Arkin AP.

Genome Biol. 2008 Jan 7;9(1):R4. doi: 10.1186/gb-2008-9-1-r4.

21.
22.

Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough.

Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, Keasling JD.

J Bacteriol. 2007 Aug;189(16):5996-6010. Epub 2007 Jun 1.

23.

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.

Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM.

Nat Biotechnol. 2007 Mar;25(3):319-26. Epub 2007 Mar 4.

PMID:
17334359
24.

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL.

Science. 2006 Sep 1;313(5791):1261-6.

25.
26.

TreeFam: a curated database of phylogenetic trees of animal gene families.

Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.

27.

Two rounds of whole genome duplication in the ancestral vertebrate.

Dehal P, Boore JL.

PLoS Biol. 2005 Oct;3(10):e314. Epub 2005 Sep 6.

28.

The DNA sequence and biology of human chromosome 19.

Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM.

Nature. 2004 Apr 1;428(6982):529-35.

PMID:
15057824
29.

Pattern recognition molecules and innate immunity to parasites.

McGuinness DH, Dehal PK, Pleass RJ.

Trends Parasitol. 2003 Jul;19(7):312-9. Review.

PMID:
12855382
30.
31.

Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.

Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R.

Genome Res. 2003 Jul;13(7):1580-8. Epub 2003 Jun 12.

32.

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS.

Science. 2002 Dec 13;298(5601):2157-67.

33.

Targeted cytokine delivery to neuroblastoma.

Dehal PK, Embleton MJ, Kemshead JT, Hawkins RE.

Biochem Soc Trans. 2002 Aug;30(4):518-20.

PMID:
12196127
34.

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.

Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S.

Science. 2002 Aug 23;297(5585):1301-10. Epub 2002 Jul 25.

35.

Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.

Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Ecale Zhou CL, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, Richardson P, Rokhsar D, Uberbacher E, Hawkins T, Branscomb E, Stubbs L.

Science. 2001 Jul 6;293(5527):104-11.

36.

Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19.

Kim J, Gordon L, Dehal P, Badri H, Christensen M, Groza M, Ha C, Hammond S, Vargas M, Wehri E, Wagner M, Olsen A, Stubbs L.

Genomics. 2001 Jun 1;74(2):129-41.

PMID:
11386749

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