Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 50

1.

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.

Oliveira FS, Brestelli J, Cade S, Zheng J, Iodice J, Fischer S, Aurrecoechea C, Kissinger JC, Brunk BP, Stoeckert CJ Jr, Fernandes GR, Roos DS, Beiting DP.

Nucleic Acids Res. 2018 Jan 4;46(D1):D684-D691. doi: 10.1093/nar/gkx1027.

2.

EuPathDB: the eukaryotic pathogen genomics database resource.

Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ Jr, Spruill D, Wang H, Warrenfeltz S, Zheng J.

Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591. doi: 10.1093/nar/gkw1105. Epub 2016 Nov 29.

3.

Companion: a web server for annotation and analysis of parasite genomes.

Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD.

Nucleic Acids Res. 2016 Jul 8;44(W1):W29-34. doi: 10.1093/nar/gkw292. Epub 2016 Apr 21.

4.

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.

Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD.

Nat Commun. 2016 Jan 7;7:10147. doi: 10.1038/ncomms10147.

5.

A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum.

Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, Daniel-Naguib G, Ghali F, Brunk BP, Roos DS, Wastling JM, Jones AR.

Proteomics. 2015 Aug;15(15):2618-28. doi: 10.1002/pmic.201400553. Epub 2015 May 15.

6.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B.

Bioinformatics. 2015 May 1;31(9):1496-8. doi: 10.1093/bioinformatics/btv002. Epub 2015 Jan 7.

7.

EuPathDB: the eukaryotic pathogen database.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. doi: 10.1093/nar/gks1113. Epub 2012 Nov 21.

8.

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.

Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A, Wastling JM.

PLoS Pathog. 2012;8(3):e1002567. doi: 10.1371/journal.ppat.1002567. Epub 2012 Mar 22.

9.

GeneDB--an annotation database for pathogens.

Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M.

Nucleic Acids Res. 2012 Jan;40(Database issue):D98-108. doi: 10.1093/nar/gkr1032. Epub 2011 Nov 23.

10.

FungiDB: an integrated functional genomics database for fungi.

Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS.

Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81. doi: 10.1093/nar/gkr918. Epub 2011 Nov 7.

11.

Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.

Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19. doi: 10.1002/0471250953.bi0612s35.

12.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA.

Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.

13.

The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.

Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ.

Database (Oxford). 2011 Jun 23;2011:bar027. doi: 10.1093/database/bar027. Print 2011.

14.

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.

Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Caler EV, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Iodice J, Kissinger JC, Kraemer ET, Li W, Nayak V, Pennington C, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Treatman C, Wang H.

Nucleic Acids Res. 2011 Jan;39(Database issue):D612-9. doi: 10.1093/nar/gkq1006. Epub 2010 Oct 24.

15.

EuPathDB: a portal to eukaryotic pathogen databases.

Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D415-9. doi: 10.1093/nar/gkp941. Epub 2009 Nov 13.

16.

TriTrypDB: a functional genomic resource for the Trypanosomatidae.

Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ Jr, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D457-62. doi: 10.1093/nar/gkp851. Epub 2009 Oct 20.

17.

HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.

Zhang XN, Wu Y, Tobias JW, Brunk BP, Deitzer GF, Liu D.

PLoS One. 2008;3(10):e3563. doi: 10.1371/journal.pone.0003563. Epub 2008 Oct 30.

18.

PlasmoDB: a functional genomic database for malaria parasites.

Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H.

Nucleic Acids Res. 2009 Jan;37(Database issue):D539-43. doi: 10.1093/nar/gkn814. Epub 2008 Oct 28.

19.

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.

Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H.

Nucleic Acids Res. 2009 Jan;37(Database issue):D526-30. doi: 10.1093/nar/gkn631. Epub 2008 Sep 29.

20.

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation.

Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, Roos DS, Wastling JM.

Genome Biol. 2008;9(7):R116. doi: 10.1186/gb-2008-9-7-r116. Epub 2008 Jul 21.

21.

ToxoDB: an integrated Toxoplasma gondii database resource.

Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP.

Nucleic Acids Res. 2008 Jan;36(Database issue):D553-6. Epub 2007 Nov 14.

22.

Identification of candidate maternal-effect genes through comparison of multiple microarray data sets.

Mager J, Schultz RM, Brunk BP, Bartolomei MS.

Mamm Genome. 2006 Sep;17(9):941-9. Epub 2006 Sep 8.

PMID:
16964442
23.
24.

The new mega-users. Seniors are flocking to the Internet faster than other age groups.

Brunk B.

Contemp Longterm Care. 2003 Mar;26(3):40-1. No abstract available.

PMID:
12683161
25.

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.

Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ Jr, Quackenbush J, Richardson J, Bult CJ.

Genome Biol. 2003;4(2):R16. Epub 2003 Feb 3.

26.

Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database.

Li L, Brunk BP, Kissinger JC, Pape D, Tang K, Cole RH, Martin J, Wylie T, Dante M, Fogarty SJ, Howe DK, Liberator P, Diaz C, Anderson J, White M, Jerome ME, Johnson EA, Radke JA, Stoeckert CJ Jr, Waterston RH, Clifton SW, Roos DS, Sibley LD.

Genome Res. 2003 Mar;13(3):443-54.

27.

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.

Bahl A, Brunk B, Crabtree J, Fraunholz MJ, Gajria B, Grant GR, Ginsburg H, Gupta D, Kissinger JC, Labo P, Li L, Mailman MD, Milgram AJ, Pearson DS, Roos DS, Schug J, Stoeckert CJ Jr, Whetzel P.

Nucleic Acids Res. 2003 Jan 1;31(1):212-5.

28.

The Plasmodium genome database.

Kissinger JC, Brunk BP, Crabtree J, Fraunholz MJ, Gajria B, Milgram AJ, Pearson DS, Schug J, Bahl A, Diskin SJ, Ginsburg H, Grant GR, Gupta D, Labo P, Li L, Mailman MD, McWeeney SK, Whetzel P, Stoeckert CJ, Roos DS.

Nature. 2002 Oct 3;419(6906):490-2. No abstract available.

PMID:
12368860
29.

A molecular profile of a hematopoietic stem cell niche.

Hackney JA, Charbord P, Brunk BP, Stoeckert CJ, Lemischka IR, Moore KA.

Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):13061-6. Epub 2002 Sep 11.

30.

Gene expression profile for schizophrenia: discrete neuron transcription patterns in the entorhinal cortex.

Hemby SE, Ginsberg SD, Brunk B, Arnold SE, Trojanowski JQ, Eberwine JH.

Arch Gen Psychiatry. 2002 Jul;59(7):631-40.

PMID:
12090816
31.

Predicting gene ontology functions from ProDom and CDD protein domains.

Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ Jr.

Genome Res. 2002 Apr;12(4):648-55.

32.

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).

Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, Schug J, Stoeckert CJ Jr.

Nucleic Acids Res. 2002 Jan 1;30(1):87-90.

33.

High-resolution BAC-based map of the central portion of mouse chromosome 5.

Crabtree J, Wiltshire T, Brunk B, Zhao S, Schug J, Stoeckert CJ Jr, Bucan M.

Genome Res. 2001 Oct;11(10):1746-57.

34.

A relational schema for both array-based and SAGE gene expression experiments.

Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J, Shen-Orr S, Overton GC.

Bioinformatics. 2001 Apr;17(4):300-8.

PMID:
11301298
35.

The genetic program of hematopoietic stem cells.

Phillips RL, Ernst RE, Brunk B, Ivanova N, Mahan MA, Deanehan JK, Moore KA, Overton GC, Lemischka IR.

Science. 2000 Jun 2;288(5471):1635-40.

36.

bioWidgets: data interaction components for genomics.

Fischer S, Crabtree J, Brunk B, Gibson M, Overton GC.

Bioinformatics. 1999 Oct;15(10):837-46. Erratum in: Bioinformatics 1999 Oct;15(10):864.

PMID:
10705436
37.

Sonic hedgehog controls epaxial muscle determination through Myf5 activation.

Borycki AG, Brunk B, Tajbakhsh S, Buckingham M, Chiang C, Emerson CP Jr.

Development. 1999 Sep;126(18):4053-63.

38.

EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis.

Stoeckert CJ Jr, Salas F, Brunk B, Overton GC.

Nucleic Acids Res. 1999 Jan 1;27(1):200-3.

39.

Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa.

Ajioka JW, Boothroyd JC, Brunk BP, Hehl A, Hillier L, Manger ID, Marra M, Overton GC, Roos DS, Wan KL, Waterston R, Sibley LD.

Genome Res. 1998 Jan;8(1):18-28.

40.

EpoDB: a database of genes expressed during vertebrate erythropoiesis.

Salas F, Haas J, Brunk B, Stoeckert CJ Jr, Overton GC.

Nucleic Acids Res. 1998 Jan 1;26(1):288-9.

41.

Regulated demethylation of the myoD distal enhancer during skeletal myogenesis.

Brunk BP, Goldhamer DJ, Emerson CP Jr.

Dev Biol. 1996 Aug 1;177(2):490-503.

42.

Embryonic activation of the myoD gene is regulated by a highly conserved distal control element.

Goldhamer DJ, Brunk BP, Faerman A, King A, Shani M, Emerson CP Jr.

Development. 1995 Mar;121(3):637-49.

43.
44.

The sequence of the Drosophila regulatory gene Suppressor two of zeste.

Brunk BP, Adler PN.

Nucleic Acids Res. 1991 Jun 11;19(11):3149. No abstract available.

46.

The Canada-Alaska Health Agreement--a practical approach to developing cross border links.

Wheatley B, Brunk B, Chase Y, Lalley E.

Arctic Med Res. 1991;Suppl:114-6. No abstract available.

PMID:
1365072
47.

Keeping children on top of the states' policy agendas.

Scales P, Brunk B.

Child Welfare. 1990 Jan-Feb;69(1):23-32.

PMID:
2295267
48.
49.

[Fibrin glue].

Brunk B.

Dtsch Med Wochenschr. 1989 Dec 22;114(51-52):2028-9. German. No abstract available.

PMID:
2598799
50.

Genetic interactions of the suppressor 2 of zeste region genes.

Adler PN, Charlton J, Brunk B.

Dev Genet. 1989;10(3):249-60.

PMID:
2500288

Supplemental Content

Support Center