PUBLICATIONS

LeBlanc Veronique G., Marlo Firme, Jungeun Song, Susanna Y. Chan, Min Hye Lee, Stephen Yip, Suganthi Chittaranjan and Marco M. Marra. (2017) Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade. The Journal of Pathology 242, No. 2: 206-220.

Lee Jessica JY, Wyeth W. Wasserman, Georg F. Hoffmann, Clara DM van Karnebeek, and Nenad Blau. (2018) Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. Genetics in Medicine 20,No.1:151.

Lee Jessica JY, Clara DM van Karnebeek, Britt Drogemoller, Casper Shyr, Maja Tartailo-Graovac, Patice Eydoux, Colin J Ross, Wyeth W. Wasserman, Bruce Bjornson and John K Wu. (2016) Further validation of the SIGMAR1 c.151+1G>Tmutation as cause of distal hereditary motor neuropathy. Child neurology open 3:2329048X16669912.

Bayly Carmen L. and Vikramaditya G. Yadav (2017) Towards precision engineering of canonical polyketide synthase domains: recent advances and future prospects. Molecules 22 , No.2:235.

Bruin Jennifer E, Nelly Saber, Shannon O’Dwyer, Jessica K. Fox, Majid Mojibian, Payal Arora, Alireza Rezania and Timothy J. Kieffer. (2016) Hypothyroidism impairs human stem cell-derived pancreatic progenitor cell maturation in mice. Diabetes: db151439.

Novoa Carolina A., Ang J Sidney and Stirling Peter C. (2018) The A-like Faker assay for measuring yeast chromosome III stability. In Genome Instability, pp. 1-9. Humana Press, New York, NY.

Novoa Carolina A., Yun-Chia Chang Emily, Aristizabal Maria J., Coulombe Yan, Segovia Romulo, Shen Yaoqing, Keong Christelle, et al. (2017) Conserved roles of RECQ-like helicases Sgs1 and BLM in preventing R-loop induced genome instability. bioRxiv:119677.

Chang Emily Yun-Chia, Carolina A. Novoa, Maria J. Aristizabal, Yan Coulombe, Romulo Segovia, Richa Chaturvedi et al. (2017) RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome stability. J Cell Biol: 201703168.

Piret James M, Braam Mitchell, Gordon Catherine, Morales Amarandi H, Wong June, Sherwood Chrstopher, Konorov Stanislav O. et al. (2017) Acoustic cell washing and Raman spectroscopy technologies to address cell therapy bioprocess challenges.

Rangan Shreyas, Kamal Sepehr, Konorov Stanislav O., Schulze Hans George, Blades Michael W., Turner Robin FB and Piret James M. (2018) Types of cell death and apoptotic stages in Chinese hamster ovary cells distinguished by Raman spectroscopy. Biotechnology and bioengineering 115. No. 2:401-412.

Knapp David JHF, Hammond Colin A, Hui Tony, Loenhout Marijin TJ, Wang Fangwu, Aghaeepour Nima, Miller Paul H. et al. (2018) Single cell analysis identifies a CD33+ subset of human cord blood cells with high regenerative potential. Nature cell biology 20, No. 6: 710.

Grants Jennifer, Wegrzyn Joanna, Knapp David, Hui Tony, O’Neill Kieran, Parker Jeremy, Deng Deborah, Eaves Connie, Hirst Martin and Karsan Aly (2017) Roles of microRNA miR-146a in hematopoietic stem cell function. Experimental Hematology 53:S102.

Chan Patrick HW, Lee Lisa, Kim Erin, Hui Tony, Stoynov Nikolay, Nassar, Roy, Moksa Michelle, et al. (2017). The [PSI+] yeast prion does not wildly affect proteome composition whereas selective pressure exerted on [PSI+] cells can promote aneuploidy.  Scientific Reports 7. No. 1:8442.

Lamour Guillaume, Roy Nassar, Patrick HW Chan, Gunes Bozkurt, Jixi Li, Jennifer M Bui et al. (2017) Mapping the broad structural and mechanical properties of amyloid fibrils. Biophysical Journal 112, No. 4: 584-594.

Snieckus Victor, Hurst Timothy, Nerdinger Sven, Kuatsjah Eugene, Eltis Lindsay, Kahlenberg Volker and Schlapp-Hackl Inge. (2018) Bacterial catabolism of biphenyls synthesis and evaluation of analogues. ChenBioChem.

Kuatsjah Eugene, Hong-Ming Chen, Stephen G. Withers and Lindsay D. Eltis. (2017) Characterization of an extradiol dioxygenerase involved in the catabolism of lignin-derived biphenyl. FEBS letters 591, No.7: 1001-1009.

Kuatsjah Eugene, Anson CK Chan, Marek J Kobylarz, Micheal EP Murphy and Lindsay D. Eltis. (2017) The bacterial meta-cleavage hydorlase LigY belongs to the amindohydrolase superfamily, not to the alpha/beta-hydrolase family. Journal of Biological Chemistry:jbc-M117.

Zahir Farah R, Jill C Mwenifumbo, Hye-Jung E. Chun, Emilia L. Lim, Clara DM van Karnebeek, Madeline Couse, Karen L. Mungall et al. (2017) Comprehensive whole genome sequence analyses yields novel genetic and structural insights for intellectual disability. BMC genomics 18., No 1: 403.

Woodsworth Daniel J., Lisa Dreolini, Libin Abraham and Robert A. Holt (2017) Targeted cell-to-cell delivery of protein payloads via the granzyme-perforin pathway. Molecular Therapy-Methods & Clinical Development 7:132-145.

Woodsworth Daniel J., and Robert A. Holt (2017) Cell-based therapeutics: making a faustian pact with biology. Trends in Molecular Medicine 23,No.2: 104-115.

Yeon Ju Hun, Nima Mazinani, Travus S, Schlappi, Karen YT Chan, James R. Baylis, Stephanie A. Smith et al. (2017) Localization of short-chain polyphosphate enhances its ability to clot flowing blood plasma. Scientific Reports 7:42119.

Yeon Ju Hun,  Karen YT Chan, Ting-Chia WOng, Kelvin Chan, Michael R. Sutherland, Rustem F. Ismagilov, Edward LG Pryzdial, and Christian J. Kastrup (2015) A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli. Scientific Reports 5: 10274.

Chan Karen YT, Zhao Chunyi, Siren Erika MJ, Chan Jeanne CY, Boschman Jeffrey and Kastrup Christian J. (2016) Adhesion of blood clots can be enhanced when copolymerized with a macromer that is crosslinkied by coagulation factor XIIIa. (2016) Biomacromolecules 17. No. 6: 2248-2252.

Baylis James R., Karen YT Chan, and Christian J. Kastrup (2016) Halting hemorrhage with self-propelling particles and local drug delivery. Thrombosis Research 141: S36-S39.

Mathew Veena, Tam Annie S., Milbury Karissa L., Hofmann Analise K., Hughes Christopher S., Morin Gregg B., Loewen Christopher JR., and Stirling Peter C. (2017) Selective aggregation of the splicing factor Hsh155 suppresses splicing upon genotoxic stress. J Cell Biol 126, No. 12:4027-4040.

Shalev Tal J, Yuen Macaire MS, Gesell Andreas, Yuen Agnes, Russell John H and Bohlmann Joerg. (2018) An annotated transcriptome of highly inbred Thuja plicata (Cupressaceae) and its utility for gene discovery of terpenoid biosynthesis and conifer defense. Tree Genetics & Genomes 14. No.3: 35.

Skinnider Michael A, Scott Nichollass E, Prudova Anna, Stoynov Nikolay, Stacey R. Greg, Gsponer Joerg, Foster Leonard J. (2018) An atlas of protein-protein interactions across mammalian tissues. bioRxiv: 351247.

Streijgert Femke, Michael A, Skinnider, Jason C. Rogalski, Robert Balshaw, Casey P. Shannon, Anna Prudova, Lise Belanger et al. (2017) A targeted proteomics analysis of cerebrospinal fluid after acute human spinal cord injury. Journal of Neurotrauma 34, No 12.:2054-2068.

Stacey R. Greg, Michael A. Skinnider, Nichollas E. Scott and Leonard J. Foster (2017) A rapid and accurate approach for prediction of interactomes from co-elucidation date (PrinCE). BMC Bioinformatics 18, No 1:457.

Chedgy Edmund CP, Vandekerkhove Gillian, Herberts Cameron, Annala Matti, Donaghue Adam J., Sigouros Michael, Ritch Elie, et al. (2018) Biallelic tumour suppressor loss and DNA repair defects in de novo small cell prostate cancer.  The Journal of Pathology.

Zhang Peter GY, Yeung Joanna, Gupta Ishita, Ramirez Miguel, Ha Thomas, Swanson Douglas J, Nagao-Satro Sayaka, et al. (2018) Discovery of Transcription factors novel to mouse cerebellar granule cell development through laser-capture microdissection.  The Cerebellum 17. No. 3: 308-325.

Heinkel F, Shen L, Richard-Greenblatt M, Gee CL. Gay LM, Okon M, Bui JM, Aber T, Av-Gay Y, Gsponer J and McIntosh LP. (2018) Biophysical characterization of the tandem FHA domain regulatory module from the Mycobacterium tuberculosis ABC transporter Rv1747. Structure (in press).

Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson RA, Radford SE, Ashcroft AE, Henderson PJF (2017). Topological dissection of the membrane transport protein Mhp1 erived from cysteine accessibility and mass spectrometry. Anal. Chem. 89, (17), 8844-8852.

Yeon JH, Heinkel F, Sung M, Na D, and Gsponer J. (2016) Systems-wide identification of cis-regulatory elements in proteins. Cell Systems 2, 89-100.

Heinkel F and Gsponer J. (2016) Determination of protein folding intermediate structures consistent with data from oxidative footprinting mass spectrometry. J. Mol. Biol. 428, 2A, 365-371.

Heinkel F, Cumberworth A and Gsponer J. (2014) Bridging experiments and simulations – structure calculations with dynamical touch. Computational Approaches to Protein Dynamics: From Quantum to Course-Grained Methods. Ed. Monika Fuxreiter.

Meghan  M. Verstraete, Cecilia Perez-Borrajero, Kirstin L. Brown, David E. Heinrichs, Michael E.P. Murphy, (2018). Sbnl is  a free serine kinase that generates O-phospho-L-serine for staphloferrin B synthesis in Staphlococcus aureus.  J. Biol Chem.

Cecilia Perez-Borrajero, Mark Okon and Lawrence P. McIntosh (2016). Structural and dynamics studies of Pax5 reveal asymmetry in stability and DNA binding by the Paired domain. J. Mol. Biol., 428 (11), 2372-91.

Andrew Robert J., Celia G.Fernandez, Molly Stanley, Hong Jiang, Phuong Nguyen, Richard C.Rice et al. (2017) Lack of BACE1 S-palmitolylation reduces amyloid burden and mitigates memory deficits in transgenic mouse models of Alzheimer’s disease. PNAS 114, No. 45:E9665-E9674.

Lund Louise H., Curtis B.Hughesman, Kareem Fakhfkh, Nelly McNeil, Shahira Clemens, Kimberly Hocken, Ryan Pettersson, Aly Karsan, Leonard J. Foster and Charles Haynes (2016) Initial diagnosis of ALK-positive non small-cell lung cancer based on analysis of ALK status utilizing droplet digital PCR. Analytical Chemistry 88,No. 9:4879-4885.

Lund Louise H., Curtis B.Hughesman, Nelly McNeil, Shahira Clemens, Kimberly Hocken, Ryan Pettersson, Aly Karsan, Leonard J. Foster and Charles Haynes (2016) Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Analytical and Bioanalytical Chemistry 408, No. 4:1079-1094.

Li Luolan, Alireza Lorzadeh and Martin Hirst (2014) Regulatory variation: an emerging vantage point for cancer biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 6, No. 1: 37-59.

Li Luolan, Shaban Memon, Yuanchu Fan, Sihai Yand and Shengjun Tan (2012) Recent duplications drive rapid diversification of trypsin genes in 12 Drosophila. Genetica 140, No. 7-9:297-305.

Li L., Lorzadeh A., Hirst M. Regulatory variation: an emerging vantage point for cancer biology. WIREs Syst Biol Med 2013. doi: 10.1002/wsbm.1250.

 

McAfee Alison, Queenie Chan, Jay Evans, and Leonard J. Foster (2017) A Varroa destructor protein atlas reveals molecular underpinnings of developmental transitions and sexual differention. Molecular & Cellualr Proteomics: mcp-000104.

McAfee, Alison, Collins, Troy F. Madilao, Lufiani L. and Foster, Leonard J. (2017) Odorant cues linked to social immunity induce lateralized antenna stimulation in honey bees (Apis mellifera L.) Scientific Reports. (7) 46171; doi: 10.1038/srep46171

McAfee, Alison and Foster, Leonard J. (2016) Proteogenomics: Recycling public data sets to improve genome annotations. Methods in Enzymology. doi:10.1016/bs.mie.2016.09.020

Trapp, Judith*, McAfee, Alison*, and Foster, Leonard J. (2016)  Genomics, transcriptomes and proteomics: Enabling insights into social evolution and disease challenges in managed and wild bees. Molecular ecology. doi:10.1111/mec.13986 (*authors contributed equally).

McAfee, Alison, Harpur, Brock A., Michaud, Sarah, Beavis, Ronald C., Kent, Clement F., Zayed, Amro and Foster, Leonard J. (2016) Toward an upgraded honey bee (Apis mellifera L) genome annotation using proteogenomics. J. Proteome Res. 15 (2), 411-421.

McAfee, Alison, Michaud, Sarah and Foster, Leonard J. (2015) Controlled, cross-species dataset for exploring biases in genome annotation and modification profiles. Data in Brief, vol 5, 829-833.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Borotone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaiser CL, Eddy JA,et al. (2018) The Immune landscape of cancer. Immunity 48(4): 812-830.

Bouquet Jerome, Jennifer L. Gardy, Scott Brown, Jacob Pfeil, Ruth R.Miller, et al. (2017) RNA-seq analysis of gene expression, viral pathogen, and B-cell/T-cell receptor signatures in complex chronic disease.  Clinical Infectious Disease 64, No.4: 476-481.

Brown SD, Hapgood G, Steidl C, Weng AP, Savage KJ and Holt RA. (2017) Defining the clonality of peripheril T Cell lymphomas using RNA-seq. Bioinformatics 33(8);1111-1115.

Brown, SD, Raeburn, LA and Holt RA. (2015) Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Medicine. Nov 30; 7(1):125.

Gibb, EA, Warren, RL, Wilson, GE, Brown, SD, Robertson, G, Morin, GB and Holt, RA. (2015) Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. Genome Medicine. Mar 5; 7(1):22.

Brown SD , Warren RL , Gibb EA , Martin SD , Spinelli JJ , Nelson BH , Holt RA, Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival., Genome research, 24(5), 743-750.

Baier, F., Chen, J., Solomonson, S., Strynadka, N.C.J. and Tokuriki, N. (2015) Distinct metal iso-forms underlie promiscuous activity profiles of metalloenzymes. ACS Chemical Biology. Published online April 16, 2015.

Baier, F., Copp, J.N., Tokuriki, N. (2016): Evolution of enzyme superfamilies: comprehensive exploration of sequence-function relationships. Biochemistry, 55(46), 6375-6388.

Baier F. and Tokuriki N. Connectivity between catalytic landscapes of the Metallo-B-lactamase superfamily. Journal of Molecular Biology, Volume 426, Issue 13, 26 June 2014, Pages 2442–2456.

Purg, M. Pabis, A., Baier, F., Tokuriki, N., Jackson, J.C., Kamerlin, S.C. (2016): Probing the Mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. Phil. Trans. R. Soc. A. 374 (2080), 20160150.

Yang, G., Hong, N., Baier, F., Jackson, J.C., Tokuriki, N. (2016): Conformational tinkering through indirect effects of mutations underlies evolution of a promiscuous enzyme activity. Biochemistry, 55,(32), 4583-4593.

McPherson A., Roth A., Ha G, Chauvre C, Steif A , de Souza CPE, Eirew P, Bouchard-Cote A, Aparicio S, Sahinalp SC, and Shah SP. (2017).  ReMixT:clone-specific genome structure estimation in cancer. Genome Biology 18, 1014.

Smith MA, Nielsen CB, Chan FC, McPherson A, Roth A, Farahani H, Machev D, Steif A, and Shah SP. (2017).  E-scape:interactive visualization of single-cell phylogenetics and cancer evolution. Nature Methods 14; 549-550.

Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Cote A and Shah SP. (2017).   ddClone:joint statistical inference of clonal populations from single cell and bulk tumour sequencing date. Genome Biology 18, 1-18.

Zahn H*, Steif A*, Laks E, Eirew P, VanInsberghe M, Shah SP, Aparicio S and Hansen CL. (2017). Scalable whole-genome single-cell library prparation without preamplification. Nature Methods 14, 167-173.

Campbell Kieran R, Steif Adi, Laks Emma, Zahn Hans, Lai Daniel, McPherson Andrew, Farahani Hossein, et al. (2018) Clonealign: statistical integration of independent single-cell RNA&DNA-seq from human cancers.bioRxiv:344309.

Kaston L, Klaus A, Lin BK, Laks E, Biele J, Lai D, Bashashati A, Huang YF, Aniba R, Moksa M, Steif A, Mes-Masson AM, Hirst M, Shah SP, Aparicio S, and Hansen CL. (2016). Robust high performance nanolitre-volume single-cell multiple displacement amplification. PNAS 113, 8484-8489.

Eirew P*, Steif A*, Khattra J*, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJL, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval J, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall A, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S.  (2015). Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution. Nature 518, 422-426. *joint first authors

Zhu, JY*, Steif A*, Proctor JR, & Meyer IM (2013). Transient RNA structure features are evolutionarily conserved and can be computationally predicted. Nucleic Acids Research, 41(12): 6273-85. *joint first authors

Steif A, & Meyer IM (2012). The hok mRNA family. RNA Biology, 9(12): 1399-404.Steif A, & Meyer IM (2012). The hok mRNA family. RNA Biology, 9(12): 1399-404.

Fang, N.N., Chan, G.T., Zhu, M., Comyn, S.A., Persaud, A., Deshaies, R.J., Rotin, D., Gsponer, J., and Mayor, T. (2014). Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress. Nat. Cell Biol. 16, 1227–1237.

Albu, R.F., Chan, G.T., Zhu, M., Wong, E.T.C., Taghizadeh, F., Hu, X., Mehran, A.E., Johnson, J.D., Gsponer, J., and Mayor, T. (2014). A feature analysis of lower solubility proteins in three eukaryotic systems. J. Proteomics.

Comyn, SA, Flibotte, S. Mayor, T. (2016). Recurrent background mutations in WHI2 impair proteostasis and degradation of misfolded cytosolic proteins in Saccharomyces cerevisiae.

Comyn, SA, Young, BP, Loewen, CJ, Mayor, T. (2016). Prefoldin promotes proteasomal degradation of cytosolic proteins with missense mutations by maintaining substrate solubility. PLOS Genet. 12(7): e1006184.

Comyn, S.A., Chan, G.T., and Mayor, T. (2014). False start: cotranslational protein ubiquitination and cytosolic protein quality control. J. Proteomics 100, 92–101.

Hansen L,Comyn S, Mang Y, Lind-Thomsen A, Myhre L, Jean F, Eiberg H, Tommerup N, Rosenberg T, Pilgrim D. (2014). The myosin chaperone UNC45B is involved in lens development and autosomal dominant infantile cataract.  Eur. J Hum Genet, Nov 22(11): 1290-7.

Dorchies OM, Reutenauer-Patte J, Dahmane E, Ismail HM, Petermann O, Patthey-Vuadens O, Comyn SA, Gayi E, Piacenza T, Handa RJ, Décosterd LA, Ruegg TT. The anticancer drug tamoxifen counteracts the pathology in a mouse model of duchenne muscular dystrophy (2013) Am J Pathology 182(2):485-504.

Comyn SA, Pilgrim D. Lack of developmental redundancy between Unc45 proteins in zebrafish muscle development (2012). PLoS One 7(11):e48861.

Fang, NN, Chan, GT, Zhu, M. Comyn, SA, Persaud, A. Deshaies, RJ, Rotin, D, Gsponer, J, Mayor, T. (2014).  Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress. Nat. Cell Biol., 16(12): 1227-37.

Ng, AH, Fang, NN, Comyn, SA, Gsponer, J, Mayor, T. (2013). System-wide analysis reveals intrinsically disordered proteins prone to ubiquitylation after misfolding stress. Mol Cell Proteomics, 12(9): 2456-67.

Khosrow-Khavar, F., Fang, NN, Ng, Ah, Winget, JM, Comyn, SA, Mayor, T. (2012) The yeast ubr1 ubiquitin ligase participates in a prominent pathway that targets cytosolic thermosensitive mutants for degradations, GS (Bethesda) 2(5): 619-28.

Sit Brandon, Crowley Shauna M., Bhullar Kirandeep, Lai Christine Chieh-Lin, Tang Calvin, Hooda Yogesh, Calmettes Charles et al. (2015) Active transport of phosphorylated carbohydrates promotes intestinal colonization and transmission of a bacterial pathogen. PLOS pathogens 11 No. 8:e1005107.

Knodler L.A., Crowley S.M., Sham H.P., Yang H., Wrande M., Ma C., Ernst R.K., Steele-Mortimer O., Celli J. and Vallance B.A. (2014). The non-canonical inflammasome mediates epithelial defenses against enteric bacterial pathogens. Cell. Host. Microbe. 16:249-56.

Stahl M., Ries J., Vermeulen J., Yang H., Sham H.P., Crowley S.M., Badayeva Y., Turvey S.E., Gaynor E.C. and Vallance B.A. (2014). A novel mouse model of Campylobacter jejuni gastroenteritis reveals key pro-inflammatory and tissue protective roles for toll-like receptor signaling during infection. PLoS. Pathog. 10:7, e1004264. doi: 10.1371/journal.ppat.1004264.

Bhinder G., Stahl M., Sham H.P., Crowley S.M., Morampudi V., Dalwadi U., Ma C., Jacobson K., and Vallance B.A. (2014). Intestinal epithelial specific MyD88 signaling impacts host susceptibility to infectious colitis by promoting protective goblet cell and antimicrobial responses. Infect. Immun. 82:3753-63.

Cameron R. Strachan, Rahul Singh, David VanInsberghe, Kateryna Ievdokymenko, Karen Budwill, William W.Mohn, Lindsay D.Eltis, Steven J. Hallam ” Metagenomic scaffolds enable combinatorial lignin transformation” Proc Natl Acad Sci USA. Jul 15, 2014; 111(28): 10143–10148.

Irmisch Sandra, Jo Seohyun, Roach Christopher R., Jancsik Sharon, Yuen Macaire MS, Madilao Lina, O’Neil-Johnson Mark, Williams Russell, Withers Stephen G. and Bohlmann, Joerg. (2018) Discovery of UDP-glycosyltransferases and BAHD-acyltransferases in the biosynthesis of the anti-diabetic plant metabolite Montbretin A. The Plant Cell:tpv 00406.

Roach, C.R., Hall, D.E., Zerbe, P., and Bohlmann, J. (2014) Plasticity and Evolution of (+)-3-Carene Synthase and (−)-Sabinene Synthase Functions of a Sitka Spruce Monoterpene Synthase Gene Family Associated with Weevil Resistance. J. Biol. Chem. 289.23859-23869.

Chao, J.T., Wong, A.K.O., Tavassoli, S., Young, B.P., Chruscicki, A.,Fang, N.N., Howe, L.J., Mayor, T., Foster, L.J., Loewen, C.J.R. “Polarization of the Endoplasmic Reticulum by ER-Septin Tethering.” Cell, 158 (3), 620-632.

Lahiri, S., Chao, J., Tavassoli, S., Wong, A., Young, B., Loewen, C., Prinz, W. “A conserved ER-membrane complex facilitates phospholipid transport from the ER to mitochondria.” PLOS Biology. In Press.

Zoidl, M., Muller, B., Torvisco, A., Tysoe, C., Benazza, M., Siriwardena, A., Withers, S.G., Wrodnigg, T.A. (2014) Concise synthesis of C-1-cyano-iminosugars via a new Staudinger/aza Wittig/Strecker multicomponent reaction strategy. Bioorganic & Medicinal Chemistry Letters, 24(12), 2777-2780.

Centko, R.M., Ratnaweera, P.B., Tysoe, C., Withers, S.G., Andersen, R.J., de Silva, E.D. (2017) Alpha-glucosidase and alpha-amylase inhibiting thiodiketopiperazines from the endophytic fungus Setosphaeria rostrata isolated from the medicinal plant Costus speciosus in Sri Lanka. Phytochemistry Letters, 22, 76-80.

Jongkees, S.A.K. Caner, S. Tysoe, C., Brayer, G.D., Withers, S.G., Suga, H. (2017) Rapid discovery of potent and selective glycosidase-inhibiting de novo peptides. Cell Chem Biol, 24(3), 381-390.

Schalli, M. Tysoe, C., Fischer, R., Pabst, B.M., Thonhofer, M., Paschke, E. Rappitsch, T. Stutz, A.E., Tschermutter, M., Windischhofer, W., Withers, S.G (2017) N-substituted 5-amino-1-hydroxymethyl-cyclopentanetriols: a new family of activity promotors for the G M1-gangliosidosis related human lysosomal B-galactosidase mutant. Carbohydrate Research, 443, 15-22.

Lebl, R., Thonhofer, M., Tysoe, C., Pabst, B.M., Schalli, M., Weber, P., Paschke, E., Stutz, A.E., Tschemutter, M., Windischhofer, W., Withers, S.G. (2017) A Morita-Baylis-Hillman based route to C-5a-chain-extended 4-epi-isofagomine type glycosidase inhibitors. Carbohydrate Research, 442, 31-40.

Santana, A.G., Tysoe, C., Hu, G., Kronstad, J., Goddard-Border, E.D., Withers, S.G. (2017) Fungal glycolipid hydrolase inhibitors and their effect on Cryptococcus neoformans. ChemBioChem, 18(3), 284-290.

Goddard-Borger, E.D., Tysoe, C., Wither, S.G. (2016) Glycosynthase mediated synthesis of psychosine. Carbohydrate Research, 435, 97-99.

Tysoe, C., Withers, S.G. Fluorinated Mechanism-Based Inhibitors: Common Themes and Recent Developments. Curr. Top. Med. Chem., 2013

Acton Erica, Lee Amy Huei-Yi, Zhao Pei Jun, Flibotte Stephane, Neira Mauricio, Sinha Sunita, Chiang Jennifer, Flaherty Patrick, Nislow Corey and Giaever Guri (2017) Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. Open Biology 7, No. 6:160330.

Fletcher M, Whitby L, Whitby A, Richards S, Acton E, Keeney M, Borowitz M, Illingworth A, Sutherland DR, Reilly J, Barnett D, “Standardising Leucocyte PNH Clone Detection: An International Study”. Cytometry B Clin Cytom. 2014 Sep;86(5):311-8. doi: 10.1002/cyto.b.21174. Epub 2014 Apr 9.

Shrestha R., Hodzic E., Yeung J., Wang K., Sauerwald T., Dao P., Anderson S., Beltran H., Rubin MA., Collins C., Haffari G.and S. C. Sahinalp. (2014) HIT’nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time. In Roded Sharan, editor, Research in Computational Molecular Biology – 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings. Volume 8394 of Lecture Notes in Computer Science, pages 293-306, Springer, 2014

Holt R and Sharma G. British Columbia Cancer Agency (BCAA), 2018. T-cell epitope identification. U.S. Patent Application 15/128,923.

Sharma G, Holt RA. T-cell Epitope Discovery Technologies. Hum. Immunol. 2014; 75: 514-519.

Li X, O’Neil NJ, Moshgabadi N, Hieter P. Genetics. (2014). Synthetic cytotoxicity:digenic interactions with TEL1/ATM mutations reveal sensitivity to low doses of camptothecin (2014) Jun;197(2):611-23. doi: 10.1534/genetics.114.161307.

White, A.K., Singhal, A., Hansen, C.L. (2012) Microfluidic single-cell analysis: from promise to practice. Current Opinion in Chemical Biology 16 (3), 381-390.

White, A.K., Heyries, K., Doolin, C., VanInsberghe, M., Hansen C.L. (2013) High throuhput microfluidic single-cell digital polymerase chain reaction. Analytical Chemistry 85 (15), 7182-7190.

White A.K., VanInsberghe M., Petriv O.I., Hamidi M., Sikorski D., Marra M.A., Piret J., Aparicio S., Hansen C.L. (2011) High-throughput microfluidic single-cell RT-qPCR. Proceedings of the National Academy of Science. 108: 13999-14004

Duffy Supipi, Fam Hok Khim, Wang Yi Kan, Styles Erin B., Kim Jung-Hyun, Ang Sidney Ang, Singh Tejomayee, et al. (2016) Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. PNAS 113. No.36:9967.

Bailey Melanie L. Tejomayee Singh, Patricia Mero, Jason Moffat, and Philip Hieter (2015) Dependence of human colorectal cells lacking the FBW7 tumour suppressor on the spindle assembly checkpoint. Genetics 115.

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Goddard-Borger ED, Tropak MB, Yonekawa S, Tysoe C, Mahuran DJ, Withers SG. Rapid assembly of a library of lipophilic imino-sugars via the thiol-ene reaction yields promising pharmacological chaperones for the treatment of Gaucher disease. J Med Chem. 2012 Mar 22;55(6):2737-45.

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Armstrong Zachary, Mewis Keith, Liu Feng, Morgan-Lang Connor, Scofield Melanie, Durno Evan, Chen Hong Ming, Mehr Kevin, Withers Stephen G. and Hallam Steven J. (2018) Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome. The ISME Journal: 1.

Zach Armstrong, Peter Rahfeld, Stephen Withers (2017). Discovery of new glycosidases from metagenomic libraries. Methods in Enzymology 597, 3-23.

Hong-Ming Chen, Zachary Armstrong, Steven Hallam, Stephen Withers (2016). Synthesis and evaluation of a series of 6-cholor-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity. Carbohydrate Research, 421, 33-39.

Zachary Armstrong, Keith Mewis, Cameron Strachan, Steve Hallam (2015). Biocatalysts forbiomass deconstruction from environmental genomics. Current Opinion in Chemical Biology, 29 18-25.

R Singh, JC Grigg, Z Armstrong, MEP Murphy, LD Eltis. Distal Heme Pocket Residues of B-type Dye-decolorizing Peroxidase: arginine but not aspartate is essential for peroxidase activity. Journal of Biological Chemistry 287 (13), 10623-10630

Z Armstrong, SG Withers.(2013) Synthesis of Glycans and Glycopolymers Through Engineered Enzymes. Biopolymers 99 (10), 666-674

Reitinger S, Petriv OI, Mehr K, Hansen CL, Withers SG.  (2012) Purification and quantitation of bacteriophage M13 using desalting spin columns and digital PCR. J Virol Methods. (2012). Oct;185(1):171-4. doi: 10.1016/j.jviromet.2012.06.021. Epub 2012 Jul 2.

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Hamidi Mani, Ricicova Marketa, Quiring Adam, Niemisto, Antti, Falconnet Didier, Emberly eldon and Hansen Carl. Sources o fnon-genetic variability and heritability in pheromone signaling observed on a microfluidic device.

Chan QW, Chan MY, Logan M, Fang Y, Higo H, Foster LJ.  (2013). Honey bee protein atlas at organ-level resolution. Genome Res. 2013 Nov;23(11):1951-60. doi: 10.1101/gr.155994.113. Epub 2013 Jul 22.

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H. Zahn, A. Steif, E Laks, P. Eirew, M. VanInsberghe, S.P. Shah, S. Aparicio and C.L. Hansen. (2017). Scalable whole-genome single-cell library preparation without preamplification. Nat. Methods, 14, no. 2, pp 167-173.

C.L. Hansen, H. Zahn, J. Huft, M. Van Loenhout, K. Leung, N. Lin, A. Klaus, S. Aparicio and S.P. Shah (2016). Methods and devices for analyzing particles. PCT/CA2016/000031. (PATENT)

M. Ricicova, K. Heyries, H. Zahn, O. Petriv, V. Lecault, A. Singhal, D. Costa, C.L. Hansen, B. Nelson, J. Nielsen, and K. Lisaingo (2014). Microfluidic devices and methods for use thereof in multicellular assays of secretion. PCT/CA2014/000304. (PATENT)

C.L. Hansen, K. Leung, T. Leaver, and H. Zahn. (2014). Methods and apparatus for flow-controlled wetting. US20140208832A1. (PATENT)

Leung K., Zahn H, Leaver T , Konwar KM , Hanson NW , Pagé AP , Lo CC , Chain PS , Hallam SJ , Hansen CL (2012).  A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc Natl Acad Sci U S A.  May 15;109(20):7665-70. doi: 10.1073/pnas.1106752109. Epub 2012 Apr 30.

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D. J. Sikorski, N.J. Caron, M. VanInsberghe, H. Zahn, C.J. Eaves, J.M. Piret and C.L. Hansen. (2015).  Clonal analysis of individual human embryonic stem cell differentiating patterns in microfluidic cultures. Biotechnol. J. 10, no. 10 pp. 1546-1554.

Carl L. Hansen, Michael VanInsberghe, Georgia E. Mewis, Kevin A. Heyries, Daniel Da Costa, Marketa Ricicova. Methods for determining lymphocyte receptor chain pairs  (2015)(PATENT APPLICATION)

Petriv, O.I., Heyries, K.A., VanInsberghe, M., Walker, D., Hansen, C.L. (2014) Methods for Multiplex Template Sampling in Digital PCR Assays. PLoS One. 9 (5), e98341

VanInsberghe M., Heyries K.A., Hansen C.L. (2012) Should genetic testing go digital? Expert Review of Molecular Diagnostics. 12: 111:114

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Carl L. Hansen, Michael VanInsberghe, Adam K. White, Oleh I. Petriv, Timothy Leaver, Anupam Singhal, William Bowden, Veronique Lecault, Daniel Da Costa, Leo Wo, Georgia E. Russell, Derek Sikorski. (2011) Microfluidic cell trap and assay apparatus for high-throughput analysis. PCT/CA2011/000612.2011 (PATENT)

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Keith Mewis, Nicolas Lenfant, Vincent Lombard, Bernard Henrissant. (2016). Dividing the large glycoside hydrolase family 43 into subfamilies: a motivation for detailed enzyme characterization. Appl Env. Microbi.

Wright JJ, Mewis K, Hanson NW, Konwar KM, Maas KR, Hallam SJ. (2013).  Genomic properties of Marine group A bacteria indicate a role in the marine sulfur cycle. ISME Journal, September. doi:10.1038/ismej.2013.152

Mewis K, Armstrong Z, Song YC, Baldwin SA, Withers SG, Hallam SJ. Biomining Active Cellulases from a mining bioremediation system. (2013) Journal of Biotechnol.  Sep 20;167(4):462-71. doi: 10.1016/j.jbiotec.2013.07.015. Epub 2013 Jul 29.

Mewis, K. The world of metagenomics: studying microbes as a community. Ideas, Numbers, Knowledge, March 2012.

Taupp, M., Mewis, K., Hallam, S.J. (2011). The Art and Design of Functional Metagenomic Screening. Current Opinion in Biotechnology 22 (3), 465-472.

Mewis, K., Taupp, M., Hallam, SJ. (2011). A high throughput screen for biomining cellulase activity form metagenomic libraries.  Journal of Visualized Experimentation 48.