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Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host.

Griesenauer B, Tran TM, Fortney KR, Janowicz DM, Johnson P, Gao H, Barnes S, Wilson LS, Liu Y, Spinola SM.

MBio. 2019 Jun 18;10(3). pii: e01193-19. doi: 10.1128/mBio.01193-19.


First-generation structure-activity relationship studies of 2,3,4,9-tetrahydro-1H-carbazol-1-amines as CpxA phosphatase inhibitors.

Li Y, Gardner JJ, Fortney KR, Leus IV, Bonifay V, Zgurskaya HI, Pletnev AA, Zhang S, Zhang ZY, Gribble GW, Spinola SM, Duerfeldt AS.

Bioorg Med Chem Lett. 2019 Jul 15;29(14):1836-1841. doi: 10.1016/j.bmcl.2019.05.003. Epub 2019 May 6.


A Class I Haemophilus ducreyi Strain Containing a Class II hgbA Allele Is Partially Attenuated in Humans: Implications for HgbA Vaccine Efficacy Trials.

Leduc I, Fortney KR, Janowicz DM, Zwickl B, Ellinger S, Katz BP, Lin H, Dong Q, Spinola SM.

Infect Immun. 2019 Jun 20;87(7). pii: e00112-19. doi: 10.1128/IAI.00112-19. Print 2019 Jul.


PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data.

Hsu YH, Churchhouse C, Pers TH, Mercader JM, Metspalu A, Fischer K, Fortney K, Morgen EK, Gonzalez C, Gonzalez ME, Esko T, Hirschhorn JN.

PLoS Comput Biol. 2019 Jan 14;15(1):e1006734. doi: 10.1371/journal.pcbi.1006734. eCollection 2019 Jan.


Drug Repurposing Using Deep Embeddings of Gene Expression Profiles.

Donner Y, Kazmierczak S, Fortney K.

Mol Pharm. 2018 Oct 1;15(10):4314-4325. doi: 10.1021/acs.molpharmaceut.8b00284. Epub 2018 Aug 7.


Multiple Class I and Class II Haemophilus ducreyi Strains Cause Cutaneous Ulcers in Children on an Endemic Island.

Grant JC, González-Beiras C, Amick KM, Fortney KR, Gangaiah D, Humphreys TL, Mitjà O, Abecasis A, Spinola SM.

Clin Infect Dis. 2018 Nov 13;67(11):1768-1774. doi: 10.1093/cid/ciy343.


Evaluation of CpxRA as a Therapeutic Target for Uropathogenic Escherichia coli Infections.

Dbeibo L, van Rensburg JJ, Smith SN, Fortney KR, Gangaiah D, Gao H, Marzoa J, Liu Y, Mobley HLT, Spinola SM.

Infect Immun. 2018 Feb 20;86(3). pii: e00798-17. doi: 10.1128/IAI.00798-17. Print 2018 Mar.

8. a manually-curated database of published biomarkers of human all-cause mortality.

Peto MV, De la Guardia C, Winslow K, Ho A, Fortney K, Morgen E.

Aging (Albany NY). 2017 Aug 31;9(8):1916-1925. doi: 10.18632/aging.101280.


Both MisR (CpxR) and MisS (CpxA) Are Required for Neisseria gonorrhoeae Infection in a Murine Model of Lower Genital Tract Infection.

Gangaiah D, Raterman EL, Wu H, Fortney KR, Gao H, Liu Y, Jerse AE, Spinola SM.

Infect Immun. 2017 Aug 18;85(9). pii: e00307-17. doi: 10.1128/IAI.00307-17. Print 2017 Sep.


Getting Found: Indexing and the Independent Open Access Journal.

Fortney K, Murphy LS.

West J Emerg Med. 2016 Sep;17(5):508-10. doi: 10.5811/westjem.2016.6.30836. Epub 2016 Jul 26. No abstract available.


Optimal multiple testing under a Gaussian prior on the effect sizes.

Dobriban E, Fortney K, Kim SK, Owen AB.

Biometrika. 2015 Dec;102(4):753-766. Epub 2015 Nov 4.


Haemophilus ducreyi Seeks Alternative Carbon Sources and Adapts to Nutrient Stress and Anaerobiosis during Experimental Infection of Human Volunteers.

Gangaiah D, Zhang X, Baker B, Fortney KR, Gao H, Holley CL, Munson RS Jr, Liu Y, Spinola SM.

Infect Immun. 2016 Apr 22;84(5):1514-1525. doi: 10.1128/IAI.00048-16. Print 2016 May.


Great Desire for Extended Life and Health amongst the American Public.

Donner Y, Fortney K, Calimport SR, Pfleger K, Shah M, Betts-LaCroix J.

Front Genet. 2016 Jan 20;6:353. doi: 10.3389/fgene.2015.00353. eCollection 2015.


Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity.

Fortney K, Dobriban E, Garagnani P, Pirazzini C, Monti D, Mari D, Atzmon G, Barzilai N, Franceschi C, Owen AB, Kim SK.

PLoS Genet. 2015 Dec 17;11(12):e1005728. doi: 10.1371/journal.pgen.1005728. eCollection 2015 Dec.


The Human Skin Microbiome Associates with the Outcome of and Is Influenced by Bacterial Infection.

van Rensburg JJ, Lin H, Gao X, Toh E, Fortney KR, Ellinger S, Zwickl B, Janowicz DM, Katz BP, Nelson DE, Dong Q, Spinola SM.

MBio. 2015 Sep 15;6(5):e01315-15. doi: 10.1128/mBio.01315-15.


Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells.

Makarev E, Fortney K, Litovchenko M, Braunewell KH, Zhavoronkov A, Atala A.

Oncotarget. 2015 Sep 15;6(27):23204-12.


Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains.

Gangaiah D, Webb KM, Humphreys TL, Fortney KR, Toh E, Tai A, Katz SS, Pillay A, Chen CY, Roberts SA, Munson RS Jr, Spinola SM.

PLoS Negl Trop Dis. 2015 Jul 6;9(7):e0003918. doi: 10.1371/journal.pntd.0003918. eCollection 2015.


DksA and (p)ppGpp have unique and overlapping contributions to Haemophilus ducreyi pathogenesis in humans.

Holley CL, Zhang X, Fortney KR, Ellinger S, Johnson P, Baker B, Liu Y, Janowicz DM, Katz BP, Munson RS Jr, Spinola SM.

Infect Immun. 2015 Aug;83(8):3281-92. doi: 10.1128/IAI.00692-15. Epub 2015 Jun 8.


Phosphoethanolamine Transferase LptA in Haemophilus ducreyi Modifies Lipid A and Contributes to Human Defensin Resistance In Vitro.

Trombley MP, Post DM, Rinker SD, Reinders LM, Fortney KR, Zwickl BW, Janowicz DM, Baye FM, Katz BP, Spinola SM, Bauer ME.

PLoS One. 2015 Apr 22;10(4):e0124373. doi: 10.1371/journal.pone.0124373. eCollection 2015.


Development and validation of a high-throughput cell-based screen to identify activators of a bacterial two-component signal transduction system.

van Rensburg JJ, Fortney KR, Chen L, Krieger AJ, Lima BP, Wolfe AJ, Katz BP, Zhang ZY, Spinola SM.

Antimicrob Agents Chemother. 2015 Jul;59(7):3789-99. doi: 10.1128/AAC.00236-15. Epub 2015 Apr 13.


Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic data.

Fortney K, Griesman J, Kotlyar M, Pastrello C, Angeli M, Sound-Tsao M, Jurisica I.

PLoS Comput Biol. 2015 Mar 18;11(3):e1004068. doi: 10.1371/journal.pcbi.1004068. eCollection 2015 Mar.


Whole-genome sequencing of the world's oldest people.

Gierman HJ, Fortney K, Roach JC, Coles NS, Li H, Glusman G, Markov GJ, Smith JD, Hood L, Coles LS, Kim SK.

PLoS One. 2014 Nov 12;9(11):e112430. doi: 10.1371/journal.pone.0112430. eCollection 2014.


Haemophilus ducreyi RpoE and CpxRA appear to play distinct yet complementary roles in regulation of envelope-related functions.

Gangaiah D, Zhang X, Baker B, Fortney KR, Liu Y, Munson RS Jr, Spinola SM.

J Bacteriol. 2014 Dec;196(23):4012-25. doi: 10.1128/JB.02034-14. Epub 2014 Sep 8.


Outer membrane protein P4 is not required for virulence in the human challenge model of Haemophilus ducreyi infection.

Janowicz DM, Zwickl BW, Fortney KR, Katz BP, Bauer ME.

BMC Microbiol. 2014 Jun 24;14:166. doi: 10.1186/1471-2180-14-166.


A (p)ppGpp-null mutant of Haemophilus ducreyi is partially attenuated in humans due to multiple conflicting phenotypes.

Holley C, Gangaiah D, Li W, Fortney KR, Janowicz DM, Ellinger S, Zwickl B, Katz BP, Spinola SM.

Infect Immun. 2014 Aug;82(8):3492-502. doi: 10.1128/IAI.01994-14. Epub 2014 Jun 9.


Haemophilus ducreyi Hfq contributes to virulence gene regulation as cells enter stationary phase.

Gangaiah D, Labandeira-Rey M, Zhang X, Fortney KR, Ellinger S, Zwickl B, Baker B, Liu Y, Janowicz DM, Katz BP, Brautigam CA, Munson RS Jr, Hansen EJ, Spinola SM.

MBio. 2014 Feb 11;5(1):e01081-13. doi: 10.1128/mBio.01081-13.


The Haemophilus ducreyi Fis protein is involved in controlling expression of the lspB-lspA2 operon and other virulence factors.

Labandeira-Rey M, Dodd DA, Brautigam CA, Fortney KR, Spinola SM, Hansen EJ.

Infect Immun. 2013 Nov;81(11):4160-70. doi: 10.1128/IAI.00714-13. Epub 2013 Aug 26.


Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants.

Gangaiah D, Zhang X, Fortney KR, Baker B, Liu Y, Munson RS Jr, Spinola SM.

J Bacteriol. 2013 Aug;195(15):3486-502. doi: 10.1128/JB.00372-13. Epub 2013 May 31.


Visual data mining of biological networks: one size does not fit all.

Pastrello C, Otasek D, Fortney K, Agapito G, Cannataro M, Shirdel E, Jurisica I.

PLoS Comput Biol. 2013;9(1):e1002833. doi: 10.1371/journal.pcbi.1002833. Epub 2013 Jan 10.


Carbon storage regulator A contributes to the virulence of Haemophilus ducreyi in humans by multiple mechanisms.

Gangaiah D, Li W, Fortney KR, Janowicz DM, Ellinger S, Zwickl B, Katz BP, Spinola SM.

Infect Immun. 2013 Feb;81(2):608-17. doi: 10.1128/IAI.01239-12. Epub 2012 Dec 10.


NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae.

Fortney K, Xie W, Kotlyar M, Griesman J, Kotseruba Y, Jurisica I.

Nucleic Acids Res. 2013 Jan;41(Database issue):D720-7. doi: 10.1093/nar/gks1106. Epub 2012 Nov 29.


Resistance to genotoxic stresses in Arctica islandica, the longest living noncolonial animal: is extreme longevity associated with a multistress resistance phenotype?

Ungvari Z, Sosnowska D, Mason JB, Gruber H, Lee SW, Schwartz TS, Brown MK, Storm NJ, Fortney K, Sowa J, Byrne AB, Kurz T, Levy E, Sonntag WE, Austad SN, Csiszar A, Ridgway I.

J Gerontol A Biol Sci Med Sci. 2013 May;68(5):521-9. doi: 10.1093/gerona/gls193. Epub 2012 Oct 10.


Permeases of the sap transporter are required for cathelicidin resistance and virulence of Haemophilus ducreyi in humans.

Rinker SD, Gu X, Fortney KR, Zwickl BW, Katz BP, Janowicz DM, Spinola SM, Bauer ME.

J Infect Dis. 2012 Nov;206(9):1407-14. doi: 10.1093/infdis/jis525. Epub 2012 Aug 28.


Network-based characterization of drug-regulated genes, drug targets, and toxicity.

Kotlyar M, Fortney K, Jurisica I.

Methods. 2012 Aug;57(4):499-507. doi: 10.1016/j.ymeth.2012.06.003. Epub 2012 Jun 27. Review.


In silico drug screen in mouse liver identifies candidate calorie restriction mimetics.

Fortney K, Morgen EK, Kotlyar M, Jurisica I.

Rejuvenation Res. 2012 Apr;15(2):148-52. doi: 10.1089/rej.2011.1263.


Sialylation of lipooligosaccharides is dispensable for the virulence of Haemophilus ducreyi in humans.

Spinola SM, Li W, Fortney KR, Janowicz DM, Zwickl B, Katz BP, Munson RS Jr.

Infect Immun. 2012 Feb;80(2):679-87. doi: 10.1128/IAI.05826-11. Epub 2011 Dec 5.


Computational advantages of reverberating loops for sensorimotor learning.

Fortney K, Tweed DB.

Neural Comput. 2012 Mar;24(3):611-34. doi: 10.1162/NECO_a_00237. Epub 2011 Nov 17.


Expression of the Flp proteins by Haemophilus ducreyi is necessary for virulence in human volunteers.

Janowicz DM, Cooney SA, Walsh J, Baker B, Katz BP, Fortney KR, Zwickl BW, Ellinger S, Munson RS Jr.

BMC Microbiol. 2011 Sep 22;11:208. doi: 10.1186/1471-2180-11-208.


Integrative computational biology for cancer research.

Fortney K, Jurisica I.

Hum Genet. 2011 Oct;130(4):465-81. doi: 10.1007/s00439-011-0983-z. Epub 2011 Apr 22. Review.


A Haemophilus ducreyi CpxR deletion mutant is virulent in human volunteers.

Labandeira-Rey M, Dodd D, Fortney KR, Zwickl B, Katz BP, Janowicz DM, Spinola SM, Hansen EJ.

J Infect Dis. 2011 Jun 15;203(12):1859-65. doi: 10.1093/infdis/jir190.


Deletion of mtrC in Haemophilus ducreyi increases sensitivity to human antimicrobial peptides and activates the CpxRA regulon.

Rinker SD, Trombley MP, Gu X, Fortney KR, Bauer ME.

Infect Immun. 2011 Jun;79(6):2324-34. doi: 10.1128/IAI.01316-10. Epub 2011 Mar 28.


Activation of the CpxRA system by deletion of cpxA impairs the ability of Haemophilus ducreyi to infect humans.

Spinola SM, Fortney KR, Baker B, Janowicz DM, Zwickl B, Katz BP, Blick RJ, Munson RS Jr.

Infect Immun. 2010 Sep;78(9):3898-904. doi: 10.1128/IAI.00432-10. Epub 2010 Jul 6.


Role played by CD4+FOXP3+ regulatory T Cells in suppression of host responses to Haemophilus ducreyi during experimental infection of human volunteers.

Li W, Tenner-Racz K, Racz P, Janowicz DM, Fortney KR, Katz BP, Spinola SM.

J Infect Dis. 2010 Jun 15;201(12):1839-48. doi: 10.1086/652781.


Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.

Fortney K, Kotlyar M, Jurisica I.

Genome Biol. 2010;11(2):R13. doi: 10.1186/gb-2010-11-2-r13. Epub 2010 Feb 3.


Haemophilus ducreyi SapA contributes to cathelicidin resistance and virulence in humans.

Mount KL, Townsend CA, Rinker SD, Gu X, Fortney KR, Zwickl BW, Janowicz DM, Spinola SM, Katz BP, Bauer ME.

Infect Immun. 2010 Mar;78(3):1176-84. doi: 10.1128/IAI.01014-09. Epub 2010 Jan 19.


Mechanism of human natural killer cell activation by Haemophilus ducreyi.

Li W, Janowicz DM, Fortney KR, Katz BP, Spinola SM.

J Infect Dis. 2009 Aug 15;200(4):590-8. doi: 10.1086/600123.


Inactivation of the Haemophilus ducreyi luxS gene affects the virulence of this pathogen in human subjects.

Labandeira-Rey M, Janowicz DM, Blick RJ, Fortney KR, Zwickl B, Katz BP, Spinola SM, Hansen EJ.

J Infect Dis. 2009 Aug 1;200(3):409-16. doi: 10.1086/600142.


Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED.

Nucleic Acids Res. 2009 Aug;37(14):4707-22. doi: 10.1093/nar/gkp475. Epub 2009 Jun 9.


A fibrinogen-binding lipoprotein contributes to the virulence of Haemophilus ducreyi in humans.

Bauer ME, Townsend CA, Doster RS, Fortney KR, Zwickl BW, Katz BP, Spinola SM, Janowicz DM.

J Infect Dis. 2009 Mar 1;199(5):684-92. doi: 10.1086/596656.


Evaluation of the repertoire of the TonB-dependent receptors of Haemophilus ducreyi for their role in virulence in humans.

Leduc I, Banks KE, Fortney KR, Patterson KB, Billings SD, Katz BP, Spinola SM, Elkins C.

J Infect Dis. 2008 Apr 15;197(8):1103-9. doi: 10.1086/586901.


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