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Kinome Analysis of Honeybee (Apis mellifera L.) Dark-Eyed Pupae Identifies Biomarkers and Mechanisms of Tolerance to Varroa Mite Infestation.

Robertson AJ, Scruten E, Mostajeran M, Robertson T, Denomy C, Hogan D, Roesler A, Rutherford C, Kusalik A, Griebel P, Napper S.

Sci Rep. 2020 Feb 7;10(1):2117. doi: 10.1038/s41598-020-58927-2.


Transcriptome Analysis Identifies Plasmodiophora brassicae Secondary Infection Effector Candidates.

Pérez-López E, Hossain MM, Tu J, Waldner M, Todd CD, Kusalik AJ, Wei Y, Bonham-Smith PC.

J Eukaryot Microbiol. 2020 Jan 11. doi: 10.1111/jeu.12784. [Epub ahead of print]


Clinical and associated inflammatory biomarker features predictive of short-term outcomes in non-systemic juvenile idiopathic arthritis.

Rezaei E, Hogan D, Trost B, Kusalik AJ, Boire G, Cabral DA, Campillo S, Chédeville G, Chetaille AL, Dancey P, Duffy C, Watanabe Duffy K, Gordon J, Guzman J, Houghton K, Huber AM, Jurencak R, Lang B, Morishita K, Oen KG, Petty RE, Ramsey SE, Scuccimarri R, Spiegel L, Stringer E, Taylor-Gjevre RM, Tse SML, Tucker LB, Turvey SE, Tupper S, Yeung RSM, Benseler S, Ellsworth J, Guillet C, Karananayake C, Muhajarine N, Roth J, Schneider R, Rosenberg AM.

Rheumatology (Oxford). 2020 Jan 9. pii: kez615. doi: 10.1093/rheumatology/kez615. [Epub ahead of print]


Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection.

Shi J, Yan Y, Links MG, Li L, Dillon JR, Horsch M, Kusalik A.

BMC Bioinformatics. 2019 Dec 24;20(Suppl 15):535. doi: 10.1186/s12859-019-3054-4.


Measuring consistency among gene set analysis methods: A systematic study.

Maleki F, Ovens KL, Hogan DJ, Rezaei E, Rosenberg AM, Kusalik AJ.

J Bioinform Comput Biol. 2019 Oct;17(5):1940010. doi: 10.1142/S0219720019400109.


Size matters: how sample size affects the reproducibility and specificity of gene set analysis.

Maleki F, Ovens K, McQuillan I, Kusalik AJ.

Hum Genomics. 2019 Oct 22;13(Suppl 1):42. doi: 10.1186/s40246-019-0226-2.


Genes responsive to rapamycin and serum deprivation are clustered on chromosomes and undergo re-organization within local chromatin environments.

Belak ZR, Pickering JA, Gillespie ZE, Audette GF, Eramian M, Mitchell JA, Bridger JM, Kusalik A, Eskiw CH.

Biochem Cell Biol. 2019 Sep 3. doi: 10.1139/bcb-2019-0096. [Epub ahead of print]


Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer.

Kirzinger MWB, Vizeacoumar FS, Haave B, Gonzalez-Lopez C, Bonham K, Kusalik A, Vizeacoumar FJ.

BMC Med Genomics. 2019 Jul 27;12(1):112. doi: 10.1186/s12920-019-0554-z.


A β-lactamase-producing plasmid from Neisseria gonorrhoeae carrying a unique 6 bp deletion in blaTEM-1 encoding a truncated 24 kDa TEM-1 penicillinase that hydrolyses ampicillin slowly.

Singh R, Perera SR, Katselis GS, Chumala P, Martin I, Kusalik A, Mitzel KM, Dillon JR.

J Antimicrob Chemother. 2019 Oct 1;74(10):2904-2912. doi: 10.1093/jac/dkz306.


Metformin induces the AP-1 transcription factor network in normal dermal fibroblasts.

Gillespie ZE, Wang C, Vadan F, Yu TY, Ausió J, Kusalik A, Eskiw CH.

Sci Rep. 2019 Mar 29;9(1):5369. doi: 10.1038/s41598-019-41839-1.


Next-generation sequencing-guided identification and reconstruction of antibody CDR combinations from phage selection outputs.

Barreto K, Maruthachalam BV, Hill W, Hogan D, Sutherland AR, Kusalik A, Fonge H, DeCoteau JF, Geyer CR.

Nucleic Acids Res. 2019 May 21;47(9):e50. doi: 10.1093/nar/gkz131.


Identification of Plasmodiophora brassicae effectors - A challenging goal.

Pérez-López E, Waldner M, Hossain M, Kusalik AJ, Wei Y, Bonham-Smith PC, Todd CD.

Virulence. 2018;9(1):1344-1353. doi: 10.1080/21505594.2018.1504560. Review.


Evaluation of a Hydrogel-Based Diagnostic Approach for the Point-of-Care Based Detection of Neisseria gonorrhoeae.

Perera SR, Taheri A, Khan NH, Parti RP, Stefura S, Skiba P, Acker JP, Martin I, Kusalik A, Dillon JR.

Antibiotics (Basel). 2018 Aug 4;7(3). pii: E70. doi: 10.3390/antibiotics7030070.


GrapHi-C: graph-based visualization of Hi-C datasets.

MacKay K, Kusalik A, Eskiw CH.

BMC Res Notes. 2018 Jun 29;11(1):418. doi: 10.1186/s13104-018-3507-2.


EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours.

Toosi BM, El Zawily A, Truitt L, Shannon M, Allonby O, Babu M, DeCoteau J, Mousseau D, Ali M, Freywald T, Gall A, Vizeacoumar FS, Kirzinger MW, Geyer CR, Anderson DH, Kim T, Welm AL, Siegel P, Vizeacoumar FJ, Kusalik A, Freywald A.

Oncogene. 2018 Jul;37(30):4073-4093. doi: 10.1038/s41388-018-0228-x. Epub 2018 Apr 27.


Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root.

Irani S, Trost B, Waldner M, Nayidu N, Tu J, Kusalik AJ, Todd CD, Wei Y, Bonham-Smith PC.

BMC Genomics. 2018 Jan 5;19(1):23. doi: 10.1186/s12864-017-4426-7.


Multiplex Real-Time PCR Assay for Simultaneous Identification of Neisseria gonorrhoeae and Its Ciprofloxacin Susceptibility Status.

Perera SR, Khan NH, Martin I, Taheri A, Parti RP, Levett PN, Horsman GB, Kusalik A, Dillon JR.

J Clin Microbiol. 2017 Nov;55(11):3201-3209. doi: 10.1128/JCM.00855-17. Epub 2017 Aug 16.


NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra.

Yan Y, Kusalik AJ, Wu FX.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):337-344. doi: 10.1109/TCBB.2015.2389813.


Technological advances for interrogating the human kinome.

Baharani A, Trost B, Kusalik A, Napper S.

Biochem Soc Trans. 2017 Feb 8;45(1):65-77. doi: 10.1042/BST20160163. Review.


De novo peptide sequencing using CID and HCD spectra pairs.

Yan Y, Kusalik AJ, Wu FX.

Proteomics. 2016 Oct;16(20):2615-2624. doi: 10.1002/pmic.201500251. Epub 2016 Aug 24.


DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites.

Trost B, Maleki F, Kusalik A, Napper S.

J Proteome Res. 2016 Aug 5;15(8):2760-7. doi: 10.1021/acs.jproteome.6b00304. Epub 2016 Jul 13.


Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites.

Trost B, Kusalik A, Napper S.

PLoS One. 2016 Apr 5;11(4):e0152809. doi: 10.1371/journal.pone.0152809. eCollection 2016.


Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production.

Gillespie ZE, MacKay K, Sander M, Trost B, Dawicki W, Wickramarathna A, Gordon J, Eramian M, Kill IR, Bridger JM, Kusalik A, Mitchell JA, Eskiw CH.

Nucleus. 2015;6(6):490-506. doi: 10.1080/19491034.2015.1128610.


Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.

Trost B, Moir CA, Gillespie ZE, Kusalik A, Mitchell JA, Eskiw CH.

R Soc Open Sci. 2015 Sep 30;2(9):150402. doi: 10.1098/rsos.150402. eCollection 2015 Sep.


A Framework of De Novo Peptide Sequencing for Multiple Tandem Mass Spectra.

Yan Yan, Kusalik AJ, Fang-Xiang Wu.

IEEE Trans Nanobioscience. 2015 Jun;14(4):478-484. doi: 10.1109/TNB.2015.2419194. Epub 2015 Apr 29.


Induction of tissue- and stressor-specific kinomic responses in chickens exposed to hot and cold stresses.

Napper S, Dadgar S, Arsenault RJ, Trost B, Scruten E, Kusalik A, Shand P.

Poult Sci. 2015 Jun;94(6):1333-45. doi: 10.3382/ps/pev046. Epub 2015 Apr 1.


Characterization of the host response to pichinde virus infection in the Syrian golden hamster by species-specific kinome analysis.

Falcinelli S, Gowen BB, Trost B, Napper S, Kusalik A, Johnson RF, Safronetz D, Prescott J, Wahl-Jensen V, Jahrling PB, Kindrachuk J.

Mol Cell Proteomics. 2015 Mar;14(3):646-57. doi: 10.1074/mcp.M114.045443. Epub 2015 Jan 8.


A Synthetic Kinome Microarray Data Generator.

Maleki F, Kusalik A.

Microarrays (Basel). 2015 Oct 16;4(4):432-53. doi: 10.3390/microarrays4040432.


Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee).

Trost B, Napper S, Kusalik A.

Brief Bioinform. 2015 Sep;16(5):820-9. doi: 10.1093/bib/bbu040. Epub 2014 Nov 6.


A better sequence-read simulator program for metagenomics.

Johnson S, Trost B, Long JR, Pittet V, Kusalik A.

BMC Bioinformatics. 2014;15 Suppl 9:S14. doi: 10.1186/1471-2105-15-S9-S14. Epub 2014 Sep 10.


Equivalent input produces different output in the UniFrac significance test.

Long JR, Pittet V, Trost B, Yan Q, Vickers D, Haakensen M, Kusalik A.

BMC Bioinformatics. 2014 Aug 13;15:278. doi: 10.1186/1471-2105-15-278.


Using crude whole-genome assemblies of Neisseria gonorrhoeae as a platform for strain analysis: clonal spread of gonorrhea infection in Saskatchewan, Canada.

Vidovic S, Caron C, Taheri A, Thakur SD, Read TD, Kusalik A, Dillon JA.

J Clin Microbiol. 2014 Oct;52(10):3772-6. doi: 10.1128/JCM.01502-14. Epub 2014 Jul 23.


Ebola virus modulates transforming growth factor β signaling and cellular markers of mesenchyme-like transition in hepatocytes.

Kindrachuk J, Wahl-Jensen V, Safronetz D, Trost B, Hoenen T, Arsenault R, Feldmann F, Traynor D, Postnikova E, Kusalik A, Napper S, Blaney JE, Feldmann H, Jahrling PB.

J Virol. 2014 Sep 1;88(17):9877-92. doi: 10.1128/JVI.01410-14. Epub 2014 Jun 18.


Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee.

Robertson AJ, Trost B, Scruten E, Robertson T, Mostajeran M, Connor W, Kusalik A, Griebel P, Napper S.

Front Genet. 2014 May 21;5:139. doi: 10.3389/fgene.2014.00139. eCollection 2014.


NovoHCD: de novo peptide sequencing from HCD spectra.

Yan Y, Kusalik AJ, Wu FX.

IEEE Trans Nanobioscience. 2014 Jun;13(2):65-72. doi: 10.1109/TNB.2014.2316424. Epub 2014 Apr 22.


TFPI1 mediates resistance to doxorubicin in breast cancer cells by inducing a hypoxic-like response.

Davies GF, Berg A, Postnikoff SD, Wilson HL, Arnason TG, Kusalik A, Harkness TA.

PLoS One. 2014 Jan 28;9(1):e84611. doi: 10.1371/journal.pone.0084611. eCollection 2014.


Peptide Arrays for Kinome Analysis of Livestock Species.

Daigle J, Van Wyk B, Trost B, Scruten E, Arsenault R, Kusalik A, Griebel PJ, Napper S.

Front Vet Sci. 2014 Oct 14;1:4. doi: 10.3389/fvets.2014.00004. eCollection 2014. Review.


Kinotypes: stable species- and individual-specific profiles of cellular kinase activity.

Trost B, Kindrachuk J, Scruten E, Griebel P, Kusalik A, Napper S.

BMC Genomics. 2013 Dec 5;14:854. doi: 10.1186/1471-2164-14-854.


PIIKA 2: an expanded, web-based platform for analysis of kinome microarray data.

Trost B, Kindrachuk J, Määttänen P, Napper S, Kusalik A.

PLoS One. 2013 Nov 29;8(11):e80837. doi: 10.1371/journal.pone.0080837. eCollection 2013.


Divergent immune responses to Mycobacterium avium subsp. paratuberculosis infection correlate with kinome responses at the site of intestinal infection.

Määttänen P, Trost B, Scruten E, Potter A, Kusalik A, Griebel P, Napper S.

Infect Immun. 2013 Aug;81(8):2861-72. doi: 10.1128/IAI.00339-13. Epub 2013 May 28.


DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.

Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.

Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.


Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights.

Trost B, Kusalik A.

Bioinformatics. 2013 Mar 15;29(6):686-94. doi: 10.1093/bioinformatics/btt031. Epub 2013 Jan 22.


Altered Toll-like receptor 9 signaling in Mycobacterium avium subsp. paratuberculosis-infected bovine monocytes reveals potential therapeutic targets.

Arsenault RJ, Li Y, Maattanen P, Scruten E, Doig K, Potter A, Griebel P, Kusalik A, Napper S.

Infect Immun. 2013 Jan;81(1):226-37. doi: 10.1128/IAI.00785-12. Epub 2012 Oct 31.


Pentamers not found in the universal proteome can enhance antigen specific immune responses and adjuvant vaccines.

Patel A, Dong JC, Trost B, Richardson JS, Tohme S, Babiuk S, Kusalik A, Kung SK, Kobinger GP.

PLoS One. 2012;7(8):e43802. doi: 10.1371/journal.pone.0043802. Epub 2012 Aug 24.


Induction of ligand-specific PrP (C) signaling in human neuronal cells.

Arsenault RJ, Li Y, Potter A, Griebel PJ, Kusalik A, Napper S.

Prion. 2012 Nov-Dec;6(5):477-88. doi: 10.4161/pri.21914. Epub 2012 Aug 23.


Mycobacterium avium subsp. paratuberculosis inhibits gamma interferon-induced signaling in bovine monocytes: insights into the cellular mechanisms of Johne's disease.

Arsenault RJ, Li Y, Bell K, Doig K, Potter A, Griebel PJ, Kusalik A, Napper S.

Infect Immun. 2012 Sep;80(9):3039-48. doi: 10.1128/IAI.00406-12. Epub 2012 Jun 11.


Comparing the similarity of different groups of bacteria to the human proteome.

Trost B, Pajon R, Jayaprakash T, Kusalik A.

PLoS One. 2012;7(4):e34007. doi: 10.1371/journal.pone.0034007. Epub 2012 Apr 25.


A systematic approach for analysis of peptide array kinome data.

Li Y, Arsenault RJ, Trost B, Slind J, Griebel PJ, Napper S, Kusalik A.

Sci Signal. 2012 Apr 17;5(220):pl2. doi: 10.1126/scisignal.2002429.


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