Amenyogbe N, Dimitriu P, Smolen KK, Brown EM, Shannon CP, Tebbutt SJ, Cooper PJ, Marchant A, Goetghebuer T, Esser M, Finlay BB, Kollmann TR, Mohn WW. Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System. American Society for Microbiology, 12 January 2021.  DOI: 10.1128/mBio.03079-20


Kim, YW, Tonti E, Hickey P, Ellis AK, Neighbour H, Larche M, Tebbutt SJ. Immunological changes in peripheral blood following nasal allergen challenge in subjects with allergic rhinitis pre-and post -peptide immunotherapy: An open-label clinical study. 15 December 2020 | https://doi.org/10.1111/all.14710

Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao K, Scheuermann RH, Tebbutt SJ, Hancock REW, Koff WC, Kollmann TR, Sadarangani M, Lee AHY. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front. Immunol., 30 November 2020| https://doi.org/10.3389/fimmu.2020.578801

Ben-Othman, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aeverman B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Shen Lin DT, Gladish N, MacIsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kober MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock. REW, Kollmann TR, Sadarangani M. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis Vaccine in Adults. Front. Immunol., 04 November 2020 |https://doi.org/10.3389/fimmu.2020.580373

Bjerg Bennike T, Fatou B, Angelidou A, Diray-Arce J, Falsafi R, Ford R, Gill EE, van Haren SD, Idoko OT, Lee AH, Ben-Othman R, Pomat WS, Shannon CP, Smolen KK, on half of The EPIC Consortium, Tebbutt SJ, Ozonoff A, Richmond PC, van den Biggelaar AHJ, Hancock REW, Kamp-mann B, Kollmann TR, Levy O, Steen H. Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life. Front. Immunol., 20 Oct 2020| https://doi.org/10.3389/fimmu.2020.578505

Amenyogbe N, Dimitriu P, Cho P, Ruck C, Fortuno III ES, Cai B, Alimenti A, Cote, HCF, Maan EJ, Slogrove AL, Esser M, Marchant A,  Goetghebuer T, Shannon CP, Tebbutt SJ, Kollmann TR, Mohn WW, Smolen KK. Innate Immune Responses and Gut Microbiomes Distinguish HIV-Exposed from HIV-Unexposed Children in a Population-Specific Manner. J Immunol October 16, 2020, ji2000040; DOI: https:/doi.org/10.4049/jimmunol.2000040

Vignolo, S., Diray-Arce, J., McEnaney, K., Rao, S., Shannon, C., Idoko, O., Cole, F, Darboe A, Cessay F, Ben-Othman R, Tebbutt SJ, Kampmann B, Levy O, Ozonoff, A.  A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium. Journal of Clinical and Translational Science, 1-7. doi:10.1017/cts.2020.546

Kim J-YV, Lee B, Koitsopoulos P, Shannon CP, Chen V, Hollander Z, Assadian S, Lam K, Ritchie G, McManus J, McMaster WR, Ng RT, McManus BM, Tebbutt SJ. Analytical Validation of HEARTBiT: A Blood-Based Multiplex Gene Expression of Profiling Assay for Exclusionary Diagnosis of Acute Cellular Rejection in Heart Transplant Patients. Clinical Chemistry, Volume 66, Issue 8, August 2020, DOI: 10.1093/clinchem/hvaa123

Brook B, Harbeson DJ, Shannon CP, Cai B, He D, Ben-Othman R, Francis F, Huang J, Varankovich N, Liu A, Bao W, Bjerregaard-AndersenM, Schaltz-Buchholzer F, Sanca L, Golding CN, Lindberg Larsen K, Levy O, Kampmann B, The EPIC Consortium, Tan R, Charles A, Wynn JL, Shann F, Aaby P, Benn CS, Tebbutt SJ, Kollmann TR, Amenyogbe N. BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis. Sci Transl Med 12, eaax4517 DOI: 10.1126/scitranslmed.aax4517

Idoko OT, Smolen KK, Oghenebrume W, Abdulazeez I, Shannon CP, Dibassey T, Direy-Arce J, Darbor A, Strandmark J, Ben-Otham R, Odumade OA, McEnaney K, Amenyogbe N, Pomat WS, van Haren S, Sanchez-Schmitz G, Brinkman R, Steen H, Hancock REW, Tebbutt SJ, Richmond PC, van den Biggelaar AHJ, Kollmann TR, Levy O, Ozonoff A, Kampmann, B. Clinical Protocol for Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front. Pediatr., 30 April 2020 https://doi.org/10.3389/fped.2020.00197

Aguiar JA, Tremblay B, Mansfield MJ, Woody O, Lobb B, Banerjee A, Chandiramohan A, Tiessen N, Dvorkin-Gheva A, Revill S, Miller MS, Carlsten C, Organ L, Joseph C, John A, Hanson PJ, McManus BM, Jenkins G, Mossman K, Ask K, Doxey AC, Hirota JA. Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue. bioRxiv; doi: https://doi.org/10.1101/2020.04.07.030742.

Zhou Q, Wei X-S, Xiang X, Wang Z, Chen V, Shannon CP, Tebbutt SJ, Kollmann TR, Fish EN. Interferon-a2b treatment for COVID-19. Front. Immunol., 15 May 2020|https://doi.org/10.3389/fimmu.2020.01061

Hensey M, Sellers S, Sathananthan J, Lai A, Landes U, Alkhodair A, McManus BM, Cheung A, Wood D, Blanke P, Leipsic J, Ye J, Webb J. Bioprosthetic Valve Leaflet Displacement During Valve-in-Valve Intervention: An Ex Vivo Bench Study. JACC Cardiovasc Interv. 2020 Mar 23; 13(6):667-678. doi:10.1016/j.jcin.2019.10.021. Epub 2020 Feb 26

Kim AJ, Xu N, Umeyama K, Hulin A, Ponny SR, Vagnozzi RJ, Green EA, Hanson P, McManus BM, Nagashima H, Yutzey KE. Deficiency of Circulating Monocytes Ameliorates the Progression of Myxomatous Valve Degeneration in Marfan Syndrome. Circulation. 2020. Jan 14;141(2):132-146. doi: 10.1161/CIRCULATIONAHA.119.042391. Epub 2020 Jan 13.


Shannon CP, Hollander Z, Dai DLY, Chen V, Assadian S, Lam KL, McManus JE, Zarzycki M, Kim Y, Kim J-YV, Balshaw R, Gidlof O, Ohman J, Smith JG, Toma M, Ignaszewski A, Davies RA, Delgado D, Haddad H, Isaac D, Kim D, Mui A, Rajda M, West L, White M, Zieroth S, Tebbutt SJ, Keown PA, McMaster WR, Ng RT, McManus BM. HEARTBiT: A Transcriptomic Signature for Excluding Acute Cellular Rejection in Adult Heart Allograft Patients. Canadian Journal of Cardiology 2019. doi:10.1016/j.cjca.2019.11.017.

He D, Xi Yang C, Sahin B, Singh A, Shannon CP, Oliveria JP, Gauvreau GM, Tebbutt SJ. Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma. Allergy Asthma Clin Immunol 2019; doi: 10.1186/s13223-019-0382-x.

Rajasekaran A, He D, Yue A, Singh A, Shannon CP, Fitzgerald J.M, Boulet L-P, O’Byrne PM, Gauvreau GM, Tebbutt SJ.  Cholinergic synapse pathway gene polymorphisms may play a rold in regulating a type of asthmatic airway response triggered upon allergen challenge. ERJ Open Res 2019; 5:00107-2019. doi: 10.1183/23120541.00107-2019.

Kim JV, Ng RT, Balshaw R, Keown P, McMaster R, McManus B, Tebbutt SJ. Clinical Validation and Biomarker Translation. In: Rahbari R, Van Niewaal J, Bleavins MR. Biomarkers in Drug Discovery and Development: A Handbook of Practice, Application, and Strategy, Second Edition. In Press, Wiley, United States; 2019.

Assadian S, Burgess M, Crouch B, Lam K, McManus B. Ethics of Biomarkers: The Borders of Investigative Research, Informed Consent, and Patient Protection. In: Rahbari R, Van Niewaal J, Bleavins MR. Biomarkers in Drug Discovery and Development: A Handbook of Practice, Application, and Strategy, Second Edition. In Press, Wiley, United States; 2019.

Takiguchi H, Chen V, Obeidat M, Hollander Z, FitzGerald JM, McManus BM, Ng RT, Sin DD. Effect of short-term oral prednisone therapy on blood gene expression: a randomised controlled clinical trial. Respir Res. 2019 Aug 5;20(1):176. doi: 10.1186/s12931-019-1147-2.

Singh A, He M, Chen V, Hollander Z, Tebbutt SJ, Ng RT, McManus BM, Sin DD, Ratjen F, Quon BS. Blood biomarkers to predict short-term pulmonary exacerbation risk in children and adolescents with CF: A pilot study. J Cyst Fibros. 2019 Jun 5. pii: S1569-1993(19)30774-X. doi: 10.1016/j.jcf.2019.05.020. [Epub ahead of print]

Lam K, Zacour M, Kim JY, Hollander Z, Wideman R, Ng R, Tebbutt SJ, McManus BM. Delivering the personalized medicine promise: best practice recommendations for designing biomarker development processes. In: Handbook of Biomarkers and Precision Medicine 1st Edition CRC Press. 2019 May 3.

Singh A, Shannon CP, Lê Cao K-A, Tebbutt SJ. (2017). Can Big Data Analytics Recapitulate Biology? A Survey of Multi-Omics Data Integration Approaches. Claudio Carini. CRC Handbook of Biomarkers & Personalized Medicine. In: Handbook of Biomarkers and Precision Medicine 1st Edition CRC Press. 2019 May 3.

Alotaibi NM, Chen V, Hollander Z, Leipsic JA, Hague CJ, Murphy DT, DeMarco ML, FitzGerald JM, McManus BM, Ng RT, Sin DD. Phenotyping and outcomes of hospitalized COPD patients using rapid molecular diagnostics on sputum samples. Int J Chron Obstruct Pulmon Dis. 2019 Jan 23;14:311-319. doi: 10.2147/COPD.S188186. eCollection 2019.

Pesenacker AM, Chen V, Gillies J, Speake C, Marwaha AK, Sun A, Chow S, Tan R, Elliott T, Dutz JP, Tebbutt SJ, Levings MK. Treg gene signatures predict and measure type 1 diabetes trajectory. JCI Insight. March 21, 2019. doi.org/10.1172/jci.insight.123879

Lee AH, Shannon CP, Amenyogbe N, Bennike TB, Diray-Arce J, Idoko OT, Gill EE, Ben-Othman R, Pomat WS, van Haren SD, Cao K-A L, Cox M, Darboe A, Falsafi R, Ferrari D, Harbeson DJ, He D, Bing C, Hinshaw SJ, Ndure J, Njie-Jobe J, Pettengill MA, Richmond PC, Ford R, Saleu G, Masiria G, Matlam JP, Kirarock W, Roberts E, Malek M, Sanchez-Schmitz G, Singh A, Angelidou A, Smolen KK, Brinkman RR, Ozonoff A, Hancock REW, van den Biggerlaar AHJ, Steen H, Tebbutt SJ, Kampmann B, Levy O, Kollman TR. Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nature Communications. March 2019. DOI: 10.1092

Tigchelaar S., Gupta R, Shannon CP, Streijger F, Sinha S, Flibotte S, Rizzuto M, Street J, Paquette S.J, Ailon T, Charest-Morin R, Dea N, Fisher CG, Dvorak MF, Dhall SS, Mac-Thoing JM, Parent S, Bailey C, Christie S, van Keuren-Jensen K, Nislow C, Kwon BK. MicroRNA biomarkers in cerebrospinal fluid and serum reflect injury severity in human acute traumatic spinal cord injury. J of Neurotrauma. March 2019. DOI:10.1089/neu.2018.6256

Culibrk L, Croft CA, Toor A, Yang SJ, Singera GK, Dorscheid DR, Moore MM, Tebbutt SJ. Phagocytosis of Aspergillus fumigatus by Human Bronchial Epithelial Cells Is Mediated by the ARP2/3 Complex and WIPF2. Frontiers in Cellular and Infection Microbiology. 9:16. February 7, 2019. DOI: 10.3389/fcimb.2019.00016

Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ, Le Cao K-A. DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays. Bioinformatics. In press 2019 January 18. https://doi-org.ezproxy.library.ubc.ca/10.1093/bioinformatics/bty1054

Singh A, Dai DLY, Ioannou K, Chen V, Lam KK, Hollander Z, Wilson-McManus JE, Assadian S, Toma M, Ng R, Virani S, Ignaszewski A, Tebbutt S, Bennett M, McManus BM. Ensembling Electrical and Proteogenomics Biomarkers for Improved Prediction of Cardiac-related 3-month Hospitalizations: A Pilot Study. Can J Cardiol. 2019 Apr;35(4):471-479. doi: 10.1016/j.cjca.2018.12.039. Epub 2019 Jan 4.


Toor A, Culibrk L, Singhera GK, Moon K-M, Prudova A, Foster LJ, Moore MM, Dorscheid DR, Tebbutt SJ. Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium. PLoS ONE. DOI: 10.1371/journal.pone.0209652

Singh A, Shannon CP, Kim YW, Yang CX, Balshaw R, Cohen Freue GV, Gauvreau GM, Fitzgerald JM, Boulet L, O’Byrne PM, Tebbutt SJ. Novel Blood-based Transcriptional Biomarker Panels Predict the Late-Phase Asthmatic Response. Am J Respir Crit Care Med Vol 197. DOI: 10.1164/rccm.201701-0110OC

Manji J, Thamboo A, Sunkaraneni V, Singh A, Tebbutt SJ, Garnis C, Javer A. The association of Leptospermum honey with cytokine expression in the sinonasal epithelium of chronic rhinosinusitis patients. World Journal of Otorhinolaryngology-Head and Neck Surgery (2018). DOI: 10.1016/j.wjorl.2018.07.004

Shannon CP, Yang CX, Tebbutt SJ. A Bloody Primer: Analysis of RNA-Seq from Tissue Admixtures. Springer Science + Business Media, LLC 2018. DOI: 10.1007/978-1-4939-7514-3_12

Wu D, Han JM, Yu X, Lam AJ, Hoeppli RE, Pesenacker AM, Huang Q, Chen V, Speake C, Yorke E, Nguyen N, Sampath S, Harris D, Levings MK. Characterization of regulatory T cells in obese omental adipose tissue in humans. Eur J Immunol. 2018 Dec 19. DOI: 10.1002/eji.201847570. [Epub ahead of print]

Penn AM, Saly V, Trivedi A, Lesperance ML, Votova K, Jackson AM, Croteau NS, Balshaw RF, Bibok MB, Smith DS, Lam KK, Morrison J, Lu L, Coutts SB, Borchers CH. Differential Proteomics for Distinguishing Ischemic Stroke from Controls: a Pilot Study of the SpecTRA Project. Transl Stroke Res 2018;1–10. DOI:10.1007/s12975-018-0609-z

Bennett MT, Hollander Z, Dai DLY, Wilson-McManus JE, Assadian S, Ignaszewski A, Ioannou K, Virani S, Krahn AD, McManus BM, Tebbutt S, Ng RT. Utility of a Novel Biomarker Panel in the Prediction of QT Dynamicity. Car Res Med. 2018 Feb; 2: 1-9

Alotaibi NM, Chen V, Hollander Z, Hague CJ, Murphy DT, Leipsic JA, DeMarco ML, FitzGerald JM, McManus BM, Ng RT, Sin DD. Phenotyping COPD exacerbations using imaging and blood-based biomarkers. International Journal of Chronic Obstructive Pulmonary Disease. 2018 January 8. DOI: 10.2147/COPD.S152484

Brunham L, Lynch K, English A, Sutherland R, Weng J, Cho R, Wong GC, Anis AH, Francis GA, Khan NA, McManus BM, Wood D, Walley KR, Leipsic J, Humphries KH, Hoens A, Krahn AD, Mancini GBJ, Pimstone S. The design and rational of SAVE BC: The Study to Avoid CardioVascular Events in British Columbia. Clinical Cardiology. 2018 April 10. DOI: 10.1002/clc.22959

Jin Z, Collier TS, Dai DLY, Chen V, Hollander Z, Ng RT, McManus BM, Balshaw R, Apostolidou S, Penn MS, Bystrom C. Development and Validation of Apolipoprotein AI-Associated Lipoprotein Proteome Panel for the Prediction of Cholesterol Efflux Capacity and Coronary Artery Disease. Clinical Chemistry. 2018 November 21. pii:clinchem.2018.291922doi: 10.1373/clinchem.2018.291922. [Epub ahead of print].

Leitao Filho FS, Alotaibi NM, Ngan D, Tam S, Yang J, Hollander Z, Chen V, Fitzgerald JM, Nislow C, Leung JM, Man SFP, Sin DD. Sputum Microbiome is Associated with 1-Year Mortality Following COPD Hospitalizations. Am J Respir Crit Care Med. 2018 October 30. DOI: 10.1164/rccm.201806-1135OC. [Epub ahead of print].


Sukma Dewi I, Gidlöf O, Hollander Z, Lam KK, Benson MD, Braun OO, Nilsson J, Tebbutt SJ, Ng RT, Öhman J, McManus BM, Smith JG. Immunological Serum Protein Profiles for Noninvasive Detection of Acute Cellular Rejection After Heart Transplantation. J Am Coll Cardiol. 2017 Dec 12;70(23):2946-2947. DOI: 10.1016/j.jacc.2017.10.012.

Streijger F, Skinnider MA, Rogalski JC, Balshaw R, Shannon CP, Prudova A, Belanger L, Ritchie L, Tsang A, Christie S, Parent S, Mac-Thiong JM, Bailey C, Urquhart J, Ailon T, Paquette S, Boyd M, Street J, Fisher CG, Dvorak MF, Borchers CH, Foster LJ, Kwon BK. A Targeted Proteomics Analysis of Cerebrospinal Fluid after Acute Human Spinal Cord Injury. J Neurotrauma. 2017 Jun 15;34(12):2054-2068. doi: 10.1089/neu.2016.4879. Epub 2017 Apr 7.

Kepplinger D, Takhar M, Sasaki M, Hollander Z, Smith D, McManus B, McMaster WR, Ng RT, Cohen Freue GV. PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data. PLoS One. 2017 May 31;12(5):e0177569. DOI: 10.1371/journal.pone.0177569

Obeidat M, Nie Y, Fishbane N, Li X, Bossé Y, Joubert P, Nickle DC, Hao K, Postma DS, Timens W, Sze MA, Shannon CP, Hollander Z, Ng RT, McManus B, Miller BE, Rennard S, Spira A, Hackett TL, Lam W, Lam S, Faner R, Agusti A, Hogg JC, Sin DD, Paré PD. Integrative Genomics of Emphysema Associated Genes Reveals Potential Disease Biomarkers. Am J Respir Cell Mol Biol. 2017 May 1. DOI: 10.1165/rcmb.2016-0284OC

Yang CX, Singh A, Kim YW, Conway EM, Carlsten C, Tebbutt SJ. Diagnosis of Western Red Cedar Asthma Using a Blood-based Gene Expression Biomarker Panel. Am J Respir Crit Care Med. 2017 May 2. DOI: 10.1164/rccm.201608-1740LE

Obeidat M, Nie Y, Chen V, Shannon CP, Andiappan AK, Lee B, Rotzschke O, Castaldi PJ, Hersh CP, Fishbane N, Ng R, McManus B, Miller BE, Rennard S, Paré PD, Sin DD. Network-Based Analysis Reveals Novel Gene Signatures in Peripheral Blood of Patients with Chronic Obstructive Pulmonary Disease. Respir Res. 2017 Apr 24;18(1):72. DOI: 10.1186/s12931-017-0558-1

Chen RY, Chen V, Hollander Z, Leipsic JA, Hague CJ, DeMarco ML, FitzGerald JM, McManus BM, Ng RT, Sin DDC-reactive Protein and N-Terminal Prohormone Brain Natriuretic Peptide as Biomarkers in Acute Exacerbations of COPD Leading to Hospitalizations. PLoS One. 2017 Mar 22;12(3):e0174063. DOI: 10.1371/journal.pone.0174063

Toma M, Mak GJ, Chen V, Hollander Z, Shannon CP, Lam KKY, Ng RT, Tebbutt SJ, Wilson-McManus JE, Ignaszewski A, Anderson T, Dyck JRB, Howlett J, Ezekowitz J, McManus BM,Oudit GY. Differentiating heart failure phenotypes using sex-specific transcriptomic and proteomic biomarker panels. ESC Heart Failure. 2017 March. DOI: 10.1002/ehf2.12136

Sharma A, Kirkpatrick G, Skolnik K, Chen V, Hollander Z, Wilcox P, Quon BS. Clinical utility of C-reactive protein to predict treatment response during cystic fibrosis pulmonary exacerbations. PLoS One. 2017 Feb 8;12(2):e0171229. DOI: 10.1371/journal.pone.0171229

Hollander Z, DeMarco ML, Sadatsafavi M, McManus BM, Ng RT, Sin DD. Biomarker Development in COPD: Moving from P-Values to Products to Impact Patient Care. Chest. 2017 Feb 1. 151(2):455-467. DOI: 10.1016/j.chest.2016.09.012

Khakban A, Sin DD, FitzGerald JM, McManus B, Ng R, Hollander Z, Sadatsafavi M. The Projected Epidemic of COPD Hospitalizations Over the Next 15 Years: A Population Based Perspective. Am J Respir Crit Care Med. 2017 Feb 1;195(3):287-291. DOI: 10.1164/rccm.201606-1162PP

Sukma Dewi I, Hollander Z, Lam KK, McManus JW, Tebbutt SJ, Ng RT, Keown PA, McMaster RW, McManus BM, Gidlöf O, Öhman J. Association of Serum MiR-142-3p and MiR-101-3p Levels with Acute Cellular Rejection after Heart Transplantation. PLoS One. 2017 Jan 26;12(1):e0170842. DOI: 10.1371/journal.pone.0170842

Sukma Dewi I, Celik S, Karlsson A, Hollander Z, Lam K, McManus JW, Tebbutt S, Ng R, Keown P, McMaster R, Bruce M. McManus, Öhman J, Gidlöf O. Exosomal miR-142-3p is increased during cardiac allograft rejection and augments vascular permeability through down-regulation of endothelial RAB11FIP2 expression. Cardiovasc Res. 2017 Jan 10. pii: cvw244. DOI: 10.1093/cvr/cvw244

Shannon CP, Balshaw R, Chen V, Hollander Z, Toma M, McManus BM, Fitzgerald JM, Sin DD, Ng RT, Tebbutt SJ. Enumerateblood – an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles. BMC Genomics. 2017 Jan 6;18(1):43. DOI: 10.1186/s12864-016-3460-1


Shannon CP, Chen V, Takhar M, Hollander Z, Balshaw R, McManus BM, Tebbutt SJ, Sin DD, Ng RT. SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations. BMC Bioinformatics. 2016 Nov 14;17(1):460.

Zafari Z, Sin DD, Postma D, Lofdahl, CG, Vonk J, Bryan S, Lam S, Tammemagi M, Khakban R, Man SF, Tashkin D, Wise R, Connett J, McManus B, Ng R, Hollander Z, Sadatsafavi M. Individualised Prediction of Lung Function Decline in COPD. CMAJ. 2016 Oct 4;188(14):1004-1011. DOI: 10.1503/cmaj.151483

Obeidat M, Ding X, Fishbane N, Hollander Z, Ng RT, McManus BM, Miller BE, Rennard S, Paré  PD, Sin DD. The Effect of Different Case Definitions of Current Smoking on the Discovery of Smoking-Related Blood Gene Expression Signatures in Chronic Obstructive Pulmonary Disease. Nicotine Tob Res. 2016 Sep;18(9):1903-9. DOI: 10.1093/ntr/ntw129

Singh A, Gautier B, Shannon CP, Vacher M, Rohart F, Tebutt SJ, Le Cao KA. DIABLO – an integrative, multi-omics, multivariate method for multi-group classification. bioRxiv 067611; DOI: 10.1101/067611 [Preprint]

Leung J, Chen V, Hollander Z, Dai D, Tebbutt S, Aaron SD, Vandemheen KL, Rennard SI, FitzGerald MJ, Woodruff PG, Lazarus SC, Connett JE, Coxson HO, Miller B, Borchers CH, McManus BM, Ng RT, Sin DD. COPD Exacerbation Biomarkers Validated Using Multiple Reaction Monitoring Mass Spectrometry. PLoS One. 2016 Aug 15;11(8):e0161129. DOI: 10.1371/journal.pone.0161129

Meredith AJ, Dai DL, Chen V, Hollander Z, Ng R, Kaan A, Tebbutt S, Ramanathan K, Cheung A, McManus BM. Circulating biomarker responses to medical management vs. mechanical circulatory support in severe inotrope-dependent acute heart failure. ESC Heart Fail. 2016 Jun;3(2):86-96. DOI: 10.1002/ehf2.12076

Pesenacker AM, Wang AY, Singh A, Gillies J, Kim YW, Piccirillo CA, Nguyen C, Haining WN, Tebbutt SJ, Panagiotopoulos C, Levings MK. A Regulatory T-Cell Gene Signature Is a Specific and Sensitive Biomarker to Identify Children With New-Onset Type 1 Diabetes. Diabetes. Apr 2016, 65 (4) 1031-1039; DOI: 10.2337/db15-0572

Croft CA, Culibrk L, Moore MM, Tebbutt SJ (2016) Interactions of Aspergillus fumigatus Conidia with Airway Epithelial Cells: A Critical Review. Front. Microbiol. 7:472. DOI: 10.3389/fmicb.2016.00472

Rider CF, Yamamoto M, Günther OP, Hirota JA, Singh A, Tebbutt SJ, Carlsten C. Diesel exhaust and allergen modulate miRNA and RNA in intact human epithelium. Journal of Allergy and Clinical Immunology (2016), DOI: 10.1016/j.jaci.2016.02.038

Fung G, Luo H, Qiu Y, Yang D, McManus B. Myocarditis. Circulation Research. February 2016; 118: 496-514. DOI: 10.1161/CIRCRESAHA.115.306573

Culibrk L, Croft CA, Tebbutt SJ. Systems Biology Approaches for Host–Fungal Interactions: An Expanding Multi-Omics Frontier. OMICS A Journal of Integrative Biology, 20(3). DOI: 10.1089/omi.2015.0185

Tkacova R, Dai DLY, Vonk JM, Leung JM, Himstra PS, Van den Berge M, Kunz L, Hollander Z, Tashkin, D, Wise R, Connett J, NG RT, McManus BM, Man P, Postma DS, Sin DD. Airway Hyperresponsiveness in COPD: A Marker of Asthma-COPD Overlap Syndrome?. J Allergy Clin Immunol. 2016 Dec;138(6):1571-1579.e10. DOI: 10.1016/j.jaci.2016.04.022


Lane J, van Eeden SF, Obeidat M, Sin DD, Tebbutt SJ, Timens W, et al. (2015) Impact of Statins on Gene Expression in Human Lung Tissues. PLoS ONE 10(11): e0142037. DOI:10.1371/journal. pone.0142037

Obeidat M, Fishbane N, Nie Y, Chen V, Hollander Z, Tebbutt SJ, et al. (2015) The Effect of Statins on Blood Gene Expression in COPD. PLoS ONE 10(10): e0140022. DOI:10.1371/journal.pone.0140022

Straube J, Gorse A-D, PROOF Centre of Excellence Team, Huang BE, Lê Cao K-A (2015) A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data. PLoS ONE 10(8): e0134540. DOI:10.1371/journal.pone.0134540

Sin DD, Hollander Z, DeMarco ML, McManus BM, Ng RT. Biomarker Development for COPD: From Discovery to Clinical Implementation. Am J Respir Crit Care Med. 2015 July 15. DOI: 10.1164/rccm.201505-0871PP

Khakban A, Sin DD, FitzGerald JM, Ng R, Zafari Z, McManus B, Hollander Z, Marra CA, Sadatsafavi M. Ten-Year Trends in Direct Costs of COPD: A Population-Based Study. Chest. 2015 Jun 4. DOI: 10.1378/chest.15-0721.

Quon B, Dai DLY, Hollander Z, Ng RT, Tebbutt S, Wilcox S, Sin DD. Discovery Of Novel Plasma Protein Biomarkers To Predict Imminent Cystic Fibrosis Pulmonary Exacerbations Using Multiple Reaction Monitoring Mass Spectrometry. Thorax. 2015 Mar 16. DOI: 10.1136/thoraxjnl-2014-206710. [Epub ahead of print]

Tremlett H, Dai DLY, Hollander Z, Kapanen A, Aziz T, Wilson-McManus JE; Tebbutt SJ, Borchers CH, Oger J, Cohen Freue GV. Serum Proteomics in Multiple Sclerosis Disease Progression. J Proteomics. 2015 Apr 6;118:2-11. DOI: 10.1016/j.jprot.2015.02.018

Hollander, Z., Dai, D. L.Y., Putko, B. N., Yogasundaram, H., Wilson-McManus, J. E., Thompson, R. B., Khan, A., West, M. L., McManus, B. M. and Oudit, G. Y. (2015), Gender-specific plasma proteomic biomarkers in patients with Anderson–Fabry disease. European Journal of Heart Failure, 17: 291–300. DOI: 10.1002/ejhf.230


Günther Oliver P., Shin Heesun, Ng Raymond T., McMaster W. Robert, McManus Bruce M., Keown Paul A., Tebbutt Scott. J., and Lê Cao Kim-Anh. Novel Multivariate Methods for Integration of Genomics and Proteomics Data: Applications in a Kidney Transplant Rejection Study. OMICS: A Journal of Integrative Biology. November 2014, 18(11): 682-695. DOI:10.1089/omi.2014.0062.

Singh A, Yamamoto M, Ruan J, Choi JY, Gauvreau GM, Olek S, Hoffmueller U, Carlsten C, FitzGerald MJ, Boulet L-P, O’Byrne PM, Tebbutt SJ. Th17/Treg ratio derived using DNA methylation analysis is associated with the late phase asthmatic response. Allergy, Asthma & Clinical Immunology 2014 June; 10(1):32

Hollander Z, Lazarova M, Lam KKY, Ignaszewski A, Oudit GY, Dyck J, Schreiner G, Pauwels J, Chen V, Cohen Freue GV, Ng RT, Wilson-McManus J, Balshaw R, Tebbutt S, McMaster R, Keown PA, McManus BM. Proteomic Biomarkers of Recovered Heart Function. Eur J Heart Fail. 2014 May;16(5):551-9

Shannon CP, Balshaw R, Ng RT, Wilson-McManus JE, Keown P, McMaster R, McManus BM, Landsberg D, Isbel NM, Knoll G, Tebbutt SJ. Two-Stage, In Silico Deconvolution of the Lymphocyte Compartment of the Peripheral Whole Blood Transcriptome in the Context of Acute Kidney Allograft Rejection. PLoS ONE. 2014 April; 9(4):e95224

Shin H, Shannon CP, Fishbane N, Ruan J, Zhou M, Balshaw R, Wilson-McManus JE, Ng RT, McManus BM, and Tebbutt SJ. Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS ONE. 2014 March; 9(3):e91041

Shin H, Günther OP, Hollander Z, Wilson-McManus JE, Ng RT, Balshaw RF, Keown PA, McMaster R, McManus BM, Isbel NM, Knoll G, Tebbutt SJ. Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated With Acute Renal Allograft Rejection. Bioinformatics and Biology Insights. 2014 January; 8:17-33


Meredith AJ, McManus BM. Vitamin D in Heart Failure. J Cardiac Failure. 2013 Oct; 10(19):692-711

Lin D, Cohen Freue G, Hollander Z, Mancini J, Sasaki M, Mui A, Wilson-McManus J, Ignaszewski A, Imai C, Meredith A, Balshaw R, Ng R.T., Keown P.A., McMaster R, Carere R, Webb G, McManus BM. Plasma protein bio-signature for detection of cardiac allograft vasculopathy. J Heart Lung Transplant. 2013 July; 32(7):723-733

Singh A, Yamamoto M, Kam SHY, Ruan J, Gauvreau GM, O’Byrne PM, FitzGerald JM, Schellenberg R, Boulet L-P, Wojewodka G, Kanagaratham C, De Sanctis J, Radzioch D, Tebbutt SJ.  Gene-metabolite expression in blood can discriminate allergen-induced isolated early from dual asthmatic responses. PLOS ONE 2013 July; 8(7):e67907

Scherer A, Günther OP, Balshaw R, Hollander Z, Wilson-McManus J, Ng R, McMaster R, McManus BM, Keown P. Alteration of human gene expression profile in uremia. BMC Med Genomics. 2013 Jun 28;6(1):23

Yamamoto M, Singh A, Tebbutt SJ, Carlsten C.  MicroRNA Expression in Response to Controlled Exposure to Diesel Exhaust: Attenuation by the Antioxidant n-Acetylcysteine in a Randomized Crossover Study. Environmental Health Perspectives 2013 June; 121(6):670-5

Cohen Freue G, Meredith A, Smith D, Bergman A, Sasaki M, Lam K, Hollander Z, Opushneva N, Takhar M, Lin D, Wilson-McManus J, Balshaw R, Keown P, Borchers C, McManus BM, Ng R.T. Computational biomarker pipeline from discovery to clinical implementation; plasma proteomic biomarkers for cardiac transplantation. PLoS Comput biol, 2013 Apr; 9(4):e1002963

Hollander Z, Chen V, Lin D, Ng R.T., Balshaw R, Cohen Freue G, Ignaszewski A, Imai C, Kaan A, Wilson-McManus J, McMaster R, Keown P, McManus BM. Predicting acute cardiac allograft rejection using donor and recipient gene expression. J Heart Lung Transplant. 2013 Feb; 32(2):259-65


Günther OP, Chen V, Cohen Freue G, Balshaw RF, Tebbutt SJ, Hollander Z, Takhar M, McMaster R, McManus BM, Keown PA, Ng R. A computational pipeline for the development of multi marker bio-signature panels and ensemble classifiers. BMC Bioinformatics. 2012 December; 13:326

Yamamoto M, Singh A, Ruan J, Gauvreau GM, O’Byrne PM, Carlsten C, FitzGerald JM, Boulet L-P, Tebbutt SJ.  Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge. BMC Genomics November 2012; 13(1):655

Singh A, Cohen Freue GV, Oosthuizen JL, Kam SHY, Ruan J, Takhar M, Gauvreau GM, O’Byrne PM, FitzGerald JM, Boulet L-P, Borchers CH. Tebbutt SJ. Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge. Proteomics Clinical Applications 2012 October; 6(9-10):476-485

Najafzadeh M, Marra CA, Lynd LD, Sadatsafavi M, FitzGerald JM, et al. (2012) Future Impact of Various Interventions on the Burden of COPD in Canada: A Dynamic Population Model. PLoS ONE. 2012 October; 7(10):e46746

Domanski D, Cohen Freue G, Sojo L, Kuzyk MA, Ratkay L, Parker CE, Goldberg P, Borchers CH. The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation. Journal of Proteomics. 2012 Jun 27;75(12):3514-28

Domanski D, Percy AJ, Yang J, Chambers AG, Hill JS, Cohen Freue G, Borchers, CH. MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Journal of Proteomics. 2012 April; 12(8):1222-1243

Shannon C, Hollander Z, Wilson-McManus J, Balshaw RF, Ng RT, McMaster R, McManus BM, Keown P, Tebbutt SJ. White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection. Bioinform and Biology Insights. 2012 April; 6:49-61

Kam SH, Singh A, He JQ, Ruan J, Gauvreau GM, O’Byrne PM, Fitzgerald JM, Tebbutt SJ. Peripheral blood gene expression changes during allergen inhalation challenge in atopic asthmatic individuals. J Asthma. 2012 Apr;49(3):219-26. doi: 10.3109/02770903.2011.654300

Tebbutt SJ, He JQ, Singh A, Shannon CP, Ruan J, Carlsten C. Transcriptional Changes of Blood Eosinophils After Methacholine Inhalation Challenge in Asthmatics. Genomics Insights. 2012 Jan 30;5:1-12. DOI: 10.4137/GEI.S9125


Lin D, Hollander Z, Meredith A, Stadnick E, Sasaki M, Cohen Freue G, Qasimi P, Mui A, Ng RT, Balshaw RF, Wilson-McManus JE, Wishart D, Hau D, Keown PA, McMaster R, McManus BM. Molecular signatures of end-stage heart failure. Journal of Cardiac Failure. 2011 October; 17(10):867-874

Domanski D, Smith DS, Miller CA, Yang Y, Jackson AM, Cohen Freue G, Hill JS, Parker CE, Borchers CH. High-flow multiplexed MRM-based analysis of proteins in human plasma without depletion or enrichment. Clin Lab Med. 2011 Sep;31(3):371-84

Balshaw RF, Cohen Freue GV. Case study 2: Proteomic biomarkers for disease status. The Canadian Journal of Statistics. 2011 June; 39(2):195-196

Carthy JM, Garmaroudi FS, Luo Z, McManus BM. Wnt3a induces myofibroblast differentiation by upregulating TGF-β signaling through SMAD2 in a β-catenin-dependent manner. PLoS ONE. 2011 May; 6(5):e19809

Stanley R, McManus B, Ng R, Gombocz E, Eshleman J, Rockey C. Case Study: Applied semantic knowledgebase for detection of patients at risk of organ failure through immune rejection. 2011 March; World Wide Web Consortium (W3C), p.1-6

Gunther OP, Lin d, Balshaw RF, Ng RT, Hollander Z, Wilson-McManus J, McMaster WR, McManus B, Keown PA. Effects of sample timing and treatment on gene expression in early acute renal allograft rejection. Transplantation. 2011 Feb; 91(3):323-329

Psychogios N, Hau D, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, Young N, Xia J, Knox C, Dong E, Huang P, Hollander Z, Pedersen T, Bamforth F, Greiner R, McManus B, Newman J, Wishart DS. The human serum metabolome. PLoS ONE. 2011 Feb; 6(2):e16957


Hollander Z, Lin D, Chen V, Ng R, Wilson-McManus J, Ignaszewski A, Cohen Freue G, Balshaw R, Mui A, McMaster R, Keown PA, McManus BM for the NCE CECR PROOF Centre of Excellence. Whole Blood Biomarkers of Acute Cardiac Allograft Rejection: Double-Crossing the Biopsy. Transplantation. 2010 Dec; 90(12):1388-93

Cohen Freue G,V Sasaki M, Meredith A, Günther OP, Bergman A, Takhar M, Mui A, Balshaw RF, Ng RT, Opushneva N, Hollander Z, Guiyun L, Borchers C, Wilson-McManus J, McManus BM, Keown PA, McMaster WR for the Genome Canada Biomarkers in Transplantation Group. Proteomic signatures in plasma during early acute renal allograft rejection. Mol Cell Proteomics. 2010 Sept; 9:1954-1967

Keown P, McMaster R, McManus B. Tools to identify organ rejection and immune quiescence for biological understanding and personalized medical care. Biomarkers in Medicine. 2010 Feb; 4(1):115-121


Günther O, Balshaw R, Scherer A, Hollander Z, Mui A, Triche T, Cohen Freue G, Li G, Ng R, Wilson-McManus J, McMaster WR, McManus BM, Keown PA for the Biomarkers in Transplantation Team. Functional genomic analysis of peripheral blood during early acute renal allograft rejection. Transplantation. 2009 Oct; 88(7):942-951

Lin D, Hollander Z, Ng RT, Imai C, Ignaszewski A, Balshaw R, Cohen Freue G, Wilson-McManus JE, Qasimi P, Mui A, Triche T, McMaster R, Keown PA, McManus BM for the Biomarkers in Transplantation Team. Whole blood genomic biomarkers of acute heart allograft rejection. The Journal of Heart and Lung Transplantation. 2009 Sept; 28(9): 927-935

McManus B. Trends in genomic biomarkers. Heart and Metabolism. 2009 Aug; 43:19-21

Lin D, Hollander Z, Meredith A, McManus B. Searching for “Omic” biomarkers. The Canadian Journal of Cardiology. 2009 Jun; 25(A):9A-14A

Chailimpamontree W, Dmitrienko S, Li G, Balshaw R, Magil A, Shapiro RJ, Landsberg D, Gill J, Keown PA for the Biomarkers in Transplantation Team. Probability, predictors, and prognosis of posttransplantation glomerulonephritis. Journal of the American Society of Nephrology. 2009 Apr; 20(4):843-851

Barraclough KA, Landsberg DN, Shapiro RJ, Gill JS, Li G, Balshaw RF, Chailimpamontree W, Keown PA for the Biomarkers in Transplantation Team. A matched cohort pharmacoepidemiological analysis of steroid free immunosuppression in renal transplantation. Transplantation. 2009 Mar; 87(5):672-680

Dmitrienko S, Balshaw R, Machnicki G, Shapiro RJ, Keown PA. Probabilistic modeling of cytomegalovirus infection under consensus clinical management guidelines. Transplantation. 2009 Feb; 28(9): 927-935


Fujii H, Cuvelier G, She K, Aslanian S, Shimizu H, Kariminia A, Chen Z, McMaster R, Bergman A, Goldman F, Grupp S, Wall D, Gilman A, Schultz, K. Biomarkers in newly diagnosed pediatric extensive chronic graft-versus-host disease: a report from the children’s oncology group. Blood. 2008 Mar; 111(6):3276-3285

McManus B. Searching for better biomarkers of heart risk and disease. Current Cardiovascular Risk Reports. 2008 Mar; 2(2):79-81


Cohen Freue G, Hollander Z, Shen E, Zamar RH, Balshaw R, Scherer A, McManus B, Keown P, McMaster R, Ng RT. MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics. 2007 Dec; 23(23): 3162-3169

Dmitrienko S, Yu A, Balshaw R, Shapiro RJ, Keown P for the Genome Canada Biomarkers in Transplantation Group. The use of consensus guidelines for management of cytomegalovirus infection in renal transplantation. Kidney International. 2007 Oct; 72(8): 1014–1022

Cohen-Freue G, Holzer G, Forney TR and McMaster WR. Global gene expression in leishmania. International Journal for Parasitology 2007 Aug; 37(10): 1077-1086


Good BM, Kawas EA, Kuo BY, Wilkinson MD. IHOPerator: user-scripting a personalized bioinformatics web, starting with the ihop website. BMC Bioinformatics. 2006 Dec; 7: 534

Kulkarni MM, McMaster WR, Kamysz E, Kamysz W, Engman DM, & McGwire BS. The major surface-metalloprotease of the parasitic protozoan, leishmania, protects against antimicrobial peptide-induced apoptotic killing. Molecular Microbiology. 2006 Dec; 62(5): 1484-97

Rahmani M, Cruz R, Granville D, McManus B. Allograft vasculopathy versus atherosclerosis. Circulation Research. 2006 Oct; 99: 801-815

Wen R, Wu V, Dmitrienko S, Yu A, Balshaw R, Keown PA and the Biomarkers in Transplantation Group. Biomarkers in Transplantation: Prospective, blinded measurement of predictive value for the flow cytometry crossmatch after negative antiglobulin crossmatch in kidney transplantation. Kidney International 2006 Oct; 70(8): 1474-1481

Good B, Wilkinson M. The life science semantic web is full of creeps! Briefings in bioinformatics 2006 Sept; 7(3): 275-286

Rahmani M, Wong BW, Ang L, Cheung CC, Carthy JM, Walinski H, McManus BM. Versican: signaling to transcriptional control pathways. Canadian Journal of Physiology and Pharmacology 2006 Jan; 84: 77-92