* Author affiliated with Donnelly Centre

2019

 

Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization.

Plos Med. 2019 Feb 25.

Eng SWM*, Aeschlimann FA, van Veenendaal M, Berard RA, Rosenberg AM7, Morris Q*, Yeung RSM; ReACCh-Out Research Consortium.

 

Analysis of Mutants Suggests Kamin Blocking in C. elegans is Due to Interference with Memory Recall Rather than Storage.

Sci Rep. 2019 Feb 20.

Merritt DM*, Melkis JG*, Kwok B*, Tran C*, van der Kooy D*.

 

Transplantation of Directly Reprogrammed Human Neural Precursor Cells Following Stroke Promotes Synaptogenesis and Functional Recovery.

Transl Stroke Res. 2019 Feb 12.

Vonderwalde I*, Azimi A*, Rolvink G*, Ahlfors JE*, Shoichet MS*, Morshead CM*.

 

Yeast Two-Hybrid Analysis for Ubiquitin-Variant Inhibitors of Human Deubiquitinases.

J Mol Biol. 2019 Feb 11.

Pascoe N*, Seetharaman A*, Teyra J*, Manczyk N, Satori MA, Tjandra D*, Makhnevych T*, Schwerdtfeger C, Brasher BB, Moffat J*, Costanzo M*, Boone C*, Sicheri F, Sidhu S*.

 

Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates.

Mol Cell. 2019 Jan 31.

Gallo D*, Kim T*, Szakal B, Saayman X, Narula A*, Park Y*, Branzei D, Zhang Z*, Brown GW*.

 

A rapid in vitro methodology for simultaneous target discovery and antibody generation against functional cell subpopulations.

Sci Rep. 2019 Jan 29.

Nixon AML*, Duque A*, Yelle N, McLaughlin M*, Davoudi S*, Pedley NM, Haynes J, Brown KR, Pan J*, Hart T*, Gilbert PM*, Singh SK, O'Brien CA, Sidhu SS*, Moffat J*.

 

Local delivery of stabilized chondroitinase abc degrades chondroitin sulfate proteoglycans in stroke-injured rat brains.

J Control Release. 2019 Jan 25.

Hettiaratchi MH*, O'Meara MJ, Teal CJ*, Payne SL*, Pickering AJ, Shoichet MS*.

 

"Plug-n-Play" Sensing with Digital Microfluidics.

Anal Chem. 2019 Jan 24.

de Campos RPS*, Rackus DG*, Shih R*, Zhao C, Liu X, Wheeler AR*.

 

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.

Nat Protoc. 2019 Jan 21.

Reimand J, Isserlin R*, Voisin V*, Kucera M*, Tannus-Lopes C*, Rostamianfar A*, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD*.

 

Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.

Structure. 2019 Jan 17.

Teyra J*, Singer AU*, Schmitges FW*, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J*, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS*.

 

Digital microfluidics and nuclear magnetic resonance spectroscopy for in situ diffusion measurements and reaction monitoring.

Lab Chip. 2019 Jan 16.

Swyer I*, von der Ecken S, Wu B, Jenne A, Soong R, Vincent F, Schmidig D, Frei T, Busse F, Stronks HJ, Simpson AJ, Wheeler AR*.

 

A web application and service for imputing and visualizing missense variant effect maps.

Bioinformatics. 2019 Jan 14.

Yingzhou W*, Weile J*, Cote A*, Sun S*, Knapp J*, Verby M*, Roth FP*.

 

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Mol Cell Proteomics. 2019 Jan 2.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL*.

 

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens.

PLoS Comput Biol. 2019 Jan 1.

Ostblom J*, Nazareth EJP*, Tewary M*, Zandstra PW*.

 

2018

 

Rationally Designed 3D Hydrogels Model Invasive Lung Diseases Enabling High-Content Drug Screening.

Adv Mater. 2018 Dec 27.

Tam RY*, Yockell-Lelièvre J, Smith LJ*, Julian LM, Baker AEG*, Choey C, Hasim MS, Dimitroulakos J, Stanford WL, Shoichet MS*.

 

Functional genomic characterization of a synthetic anti-HER3 antibody reveals a role for ubiquitination by RNF41 in the anti-proliferative response.

J Biol Chem. 2018 Dec 06.

Turowec JP*, Lau EWT*, Wang X*, Brown KR*, Fellouse FA*, Jawanda KK*, Pan J*, Moffat J*, Sidhu S*.

 

Mapping a diversity of genetic interactions in yeast.

Curr Opin Syst Biol. 2017 Dec 6.

van Leeuwen J, Boone C*, Andrews BJ*.

 

Dual embryonic origin of the mammalian enteric nervous system.

Dev Biol. 2018 Nov 22.

Brokhman I*, Xu J*, Coles BLK*, Razavi R*, Engert S, Lickert H, Babona-Pilipos R, Morshead CM*, Sibley E, Chen C, van der Kooy D*.

 

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

J Mol Biol. 2018 Nov 21.

Ben-David M*, Huang H*, Sun MGF*, Corbi-Verge C*, Petsalaki E, Liu K, Gfeller D*, Garg P*, Tempel W, Sochirca I*, Shifman JM, Davidson A, Min J, Kim PM*, Sidhu SS*.

 

Initial cell maturity changes following transplantation in a hyaluronan-based hydrogel and impacts therapeutic success in the stroke-injured rodent brain.

Biomaterials. 2018 Nov 15.

Payne SL*, Tuladhar A*, Obermeyer JM*, Varga BV, Teal CJ, Morshead CM*, Nagy A, Shoichet MS*.

 

A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the THC/CBD acid synthase locus.

Genome Res. 2018 Nov 08.

Laverty KU*, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR*, Page JE, van Bakel H.

 

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics.

Nat Rev Genet. 2018 Nov 02.

Quesnel-Vallières M*, Weatheritt RJ, Cordes SP, Blencowe BJ*.

 

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons.

Mol Cell. 2018 Nov 01.

Gonatopoulos-Pournatzis T*, Wu M, Braunschweig U*, Roth J*, Han H*, Best AJ, Raj B, Aregger M*, O'Hanlon D, Ellis JD, Calarco JA, Moffat J*, Gingras AC, Blencowe BJ*.

 

Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions.

PLoS Comput Biol. 2018 Oct 30.

Simpkins SW, Nelson J, Deshpande R, Li SC, Piotrowski JS, Wilson EH, Gebre AA, Safizadeh H, Okamoto R, Yoshimura M, Costanzo M*, Yashiroda Y, Ohya Y, Osada H, Yoshida M, Boone C*, Myers CL.

 

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.

Nat Commun. 2018 Oct 22.

MacParland SA, Liu JC*, Ma XZ, Innes BT*, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD*, McGilvray ID.

 

Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop.

Moll Cell 2018 Sep 13.

Sterne-Weiler T*, Weatheritt RJ*, Best AJ*, Ha KCH*, Blencowe BJ*.

 

A feed forward loop enforces YAP/TAZ signaling during tumorigenesis.

Nat Comm 2018 Aug 29.

Gill MK*, Christova T*, Zhang YY, Gregorieff A, Zhang L, Narimatsu M, Song S*, Xiong S, Couzens AL, Tong J, Krieger JR, Moran MF, Zlotta AR, van der Kwast TH, Gingras AC, Sicheri F, Wrana JL & Attisano L*.

 

Stem cell bioengineering: building from stem cell biology.

Nat Rev Genet. 2018 Aug 08.

Tewary M*, Shakiba N*, Zandstra PW*.

 

Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas.

Hum Genet. 2018 Aug 02.

Weile J*, Roth FP*.

 

Acute Effects of Drugs on Caenorhabditis elegans Movement Reveal Complex Responses and Plasticity.

G3 (Bethesda). 2018 Jul 30.

Spensley M*, Del Borrello S*, Pajkic D*, Fraser AG*.

 

Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell.

Curr Opin Microbiol. 2018 Jul 27.

VanderSluis B*, Costanzo M*, Billmann M, Ward HN, Myers CL, Andrews BJ*, Boone C*.

 

Skin-derived precursor cells undergo substrate-dependent galvanotaxis that can be modified by neighbouring cells.

Stem Cell Res. 2018 Jul 19.

Iwasa SN, Popovic MR, Morshead CM*.

 

Two protein/protein interaction assays in one go.

Mol Syst Biol. 2018 Jul 18.

Taipale M*.

 

Biomaterials driving repair after stroke.

Nat Mater. 2018 Jul;17.

Tuladhar A, Shoichet MS*.

 

Mechanics-guided developmental fate patterning.

Nat Mater. 2018 Jul;17.

Tewary M*, Zandstra PW*.

 

New and Prospective Roles for lncRNAs in Organelle Formation and Function.

Trends Genet. 2018 Jul 14.

Krause HM*.

 

Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression.

Trends Genet. 2018 Jun 11.

Hou J*, van Leeuwen J*, Andrews BJ*, Boone C*.

 

The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion.

J Cell Biol. 2018 Jun 06.

Sing TL*, Hung MP*, Ohnuki S, Suzuki G, San Luis BJ*, McClain M, Unruh JR, Yu Z, Ou J*, Marshall-Sheppard J*, Huh WK, Costanzo M*, Boone C*, Ohya Y, Jaspersen SL, Brown GW*.

 

Modulating cell state to enhance suspension expansion of human pluripotent stem cells.

Proc Natl Acad Sci U S A. 2018 Jun 04.

Lipsitz YY*, Woodford C*, Yin T*, Hanna JH, Zandstra PW*.

 

Transfer learning for biomedical named entity recognition with neural networks.

Bioinformatics. 2018 Jun 01.

Giorgi JM*, Bader GD*.

 

Antibody-Antisense Oligonucleotide Conjugate Downregulates a Key Gene in Glioblastoma Stem Cells.

Mol Ther Nucleic Acids. 2018 Jun 01.

Arnold AE*, Malek-Adamian E, Le PU, Meng A, Martínez-Montero S, Petrecca K, Damha MJ, Shoichet MS*.

 

Patient Similarity Networks for Precision Medicine.

J Mol Biol. 2018 May 31.

Pai S*, Bader GD*.

 

Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies.

J Mol Biol. 2018 May 17.

Nelson B*, Adams J*, Kuglstatter A, Li Z*, Harris SF, Liu Y, Bohini S, Ma H, Klumpp K, Gao J, Sidhu SS*.

 

The present and the future of motif-mediated protein-protein interactions.

Curr Opin Struct Biol. 2018 May 03.

Seo MH*, Kim PM*.

 

Calcium influx differentially regulates migration velocity and directedness in response to electric field application.

Exp Cell Res. 2018 May 02.

Babona-Pilipos R*, Liu N*, Pritchard-Oh A,* Mok A,* Badawi D*, Popovic MR, Morshead CM*.

 

Muscle stem cell intramuscular delivery within hyaluronan methylcellulose improves engraftment efficiency and dispersion.

Biomaterials. 2018 Apr 26.

Davoudi S*, Chin CY*, Cooke MJ*, Tam RY*, Shoichet MS*, Gilbert PM*.

 

A digital microfluidic system for serological immunoassays in remote settings.

Sci Transl Med. 2018 Apr 25.

Ng AHC*, Fobel R*, Fobel C*, Lamanna J*, Rackus DG*, Summers A, Dixon C, Dryden MDM, Lam C, Ho M*, Mufti NS*, Lee V*, Asri MAM*, Sykes EA*, Chamberlain MD*, Joseph R, Ope M, Scobie HM, Knipes A, Rota PA, Marano N, Chege PM, Njuguna M, Nzunza R, Kisangau N, Kiogora J, Karuingi M, Burton JW, Borus P, Lam E, Wheeler AR*.

 

Systematic Analysis of Complex Genetic Interactions.

Science. 2018 April 20.

Kuzmin E*, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y*, Usaj M*, Balint A*, Mattiazzi Usaj M*, van Leeuwen J*, Koch EN, Pons C, Dagilis AJ, Pryszlak M*, Wang JZY*, Hanchard J*, Riggi M, Xu K, Heydari H*, San Luis BJ*, Shuteriqi E*, Zhu H*, Van Dyk N, Sharifpoor S*, Costanzo M*, Loewith R, Caudy A*, Bolnick D, Brown GW*, Andrews BJ*, Boone C*, Myers CL.

 

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.

Cell. 2018 April 19.

Espiritu SMG, Liu LY, Rubanova Y*, Bhandari V, Holgersen EM, Szyca LM, Fox NS, Chua MLK, Yamaguchi TN, Heisler LE, Livingstone J, Wintersinger J*, Yousif F, Lalonde E, Rouette A, Salcedo A, Houlahan KE, Li CH, Huang V, Fraser M, van der Kwast T, Morris QD*, Bristow RG, Boutros, PC.

 

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.

Genome Biol. 2018 Mar 28.

Ha KCH*, Blencowe BJ*, Morris Q*.

 

Photo-immobilized EGF chemical gradients differentially impact breast cancer cell invasion and drug response in defined 3D hydrogels.

Biomaterials. 2018 Feb 13.

Fisher SA*, Tam RY*, Fokina A*, Mahmoodi MM, Distefano MD, Shoichet MS*.

 

The human transcription factors.

Cell. 2018 Feb 8.

Lambert SA*, Jolma A*, Campitelli LF*, Das PK, Yin Y, Albu M*, Chen X, Taipale J, Hughes TR*, Weirauch MT8.

 

Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions.

Mol Syst Biol. 2018 Jan 29.

Yachie-Kinoshita A*, Onishi K*, Ostblom J*, Langley MA*, Posfai E, Rossant J, Zandstra PW*.

 

Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB.

Proc Natl Acad Sci U S A. 2018 Jan 29.

Garton M*, Nim S, Stone TA, Wang KE*, Deber CM, Kim PM*.

 

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome.

Cell Syst. 2018 Jan 17.

Ho* B, Baryshnikova A, Brown GW*.

 

Drug development: Allosteric inhibitors hit USP7 hard.

Nat Chem Biol. 2018 Jan 16.

Zhang W*, Sidhu SS*.

 

Cellular Biomechanics in Skeletal Muscle Regeneration.

Curr Top Dev Biol. 2018.

 Li EW, McKee-Muir OC, Gilbert PM*.

 

2017

Effect of removing Kupffer cells on nanoparticle tumor delivery.

Proc Natl Acad Sci U S A. 2017 Dec 05.

Tavares AJ*, Poon W*, Zhang YN*, Dai Q*, Besla R, Ding D*, Ouyang B*, Li A, Chen J, Zheng G, Robbins C, Chan WCW*.

 

Comparison of ChIP-seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins.

G3 (Bethesda). 2017 Nov 16.

Barazandeh M*, Lambert S*, Albu M*, Hughes TR*.

 

The combinatorial control of alternative splicing in C. elegans.

PLoS Genet. 2017 Nov 13.

Tan JH*, Fraser AG*.

 

A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity.

PLoS One. 2017, Nov 6.

Garton M*, Sayadi M*, Kim PM*.

 

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.

Mol Cell. 2017 Oct 19.

Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sibbet GJ, Smith BO, Zhang W*, Sidhu SS*, Huang DT.

 

Emerging and evolving concepts in gene essentiality.

Nat Rev Genet. 2017 Oct 16.

Rancati G, Moffat J*, Typas A, Pavelka N.

 

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

Structure. 2017 Aug 28.

Teyra J*, Huang H*, Jain S*, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM*, Bader GD*, Sidhu SS*.

 

A stepwise model of Reaction-Diffusion and Positional-Information governs self-organized human peri-gastrulation-like patterning.

Development. 2017 Sep 4.

Tewary M*, Ostblom J*, Prochazka L*, Zulueta-Coarasa T, Shakiba N*, Fernandez-Gonzalez R, Zandstra PW*.

 

The New RNA World: Growing Evidence for Long Noncoding RNA Functionality.

Trends Genet. 2017 Sep 1.

Jandura A*, Krause HM*.

 

Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae.

G3 (Bethesda). 2017 Aug 24

 Verster AJ*, Styles EB*, Mateo A, Derry BW, Andrews BJ*, Fraser AG*.

 

Data driven flexible backbone protein design.

PLoS Comput Biol. 2017 Aug 24.

Sun MGF*, Kim PM*.

 

Modular tissue engineering for the vascularization of subcutaneously transplanted pancreatic islets.

Proc Natl Acad Sci U S A. 2017 Aug 16.

Vlahos AE*, Cober N*, Sefton MV*.

 

Quiescent Oct4(+) Neural Stem Cells (NSCs) Repopulate Ablated Glial Fibrillary Acidic Protein(+) NSCs in the Adult Mouse Brain.

Stem Cells. 2017 Jul 21;:

Reeve RL*, Yammine SZ*, Morshead CM*, van der Kooy D*.

 

Functional annotation of chemical libraries across diverse biological processes.

Nat Chem Biol. 2017 Jul 24.

Authors: Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP*, LeBlanc MA, Andrusiak K*, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J*, Shirahige K, Baryshnikova A, Brown GW*, Hirano H, Costanzo M*, Andrews B*, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C*.

 

Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing.

Cell. 2017 Jul 13.

Gueroussov S*, Weatheritt RJ*, O'Hanlon D*, Lin ZY, Narula A*, Gingras AC, Blencowe BJ*.

 

Quantitative analysis of protein interaction network dynamics in yeast.

Mol Syst Biol. 2017 Jul 13.

Celaj A*, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP*, St Onge RP.

 

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens.

G3 (Bethesda). 2017 Jun 27.

Hart T, Tong AHY*, Chan K*, Van Leeuwen J*, Seetharaman A*, Aregger M*, Chandrashekhar M*, Hustedt N, Seth S, Noonan A*, Habsid A*, Sizova O*, Nedyalkova L*, Climie R*, Tworzyanski L*, Lawson K*, Sartori MA*, Alibai S*, Tieu D*, Masud S*, Mero P*, Weiss A*, Brown KR*, Ušaj M*, Billmann M, Rahman M, Costanzo M*, Myers CL, Andrews BJ*, Boone C*, Durocher D, Moffat J*.

 

Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10.

J Mol Biol. 2017 Jun 03.

Zhang W*, Sartori MA*, Makhnevych T*, Federowicz KE, Dong X, Liu L, Nim S, Dong A, Yang J, Li Y, Haddad D, Ernst A, Heerding D, Tong Y, Moffat J*, Sidhu SS*.

 

Mechanisms of suppression: The wiring of genetic resilience.

Bioessays. 2017 Jun 05.

van Leeuwen J*, Pons C*, Boone C*, Andrews BJ*.

 

Engineering cell fitness: lessons for regenerative medicine.

Curr Opin Biotechnol. 2017 May 25.

Shakiba N*, Zandstra PW*.

 

Identifying pathogenicity of human variants via paralog-based yeast complementation.

PLoS Genet. 2017 May 25.

Yang F, Sun S*, Tan G*, Costanzo M*, Hill DE, Vidal M, Andrews BJ*, Boone C*, Roth FP*.

 

Engineering the haemogenic niche mitigates endogenous inhibitory signals and controls pluripotent stem cell-derived blood emergence.

Nat Commun. 2017 May 25.

Rahman N*, Brauer PM, Ho L, Usenko T*, Tewary M*, Zúñiga-Pflücker JC, Zandstra PW*.

 

Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants.

PLoS Pathog. 2017 May 18.

Zhang W*, Bailey-Elkin BA, Knaap RCM, Khare B, Dalebout TJ, Johnson GG, van Kasteren PB, McLeish NJ, Gu J*, He W, Kikkert M, Mark BL, Sidhu SS*.

 

Local delivery of chondroitinase ABC with or without stromal cell-derived factor 1α promotes functional repair in the injured rat spinal cord.

Biomaterials.  2017 Apr 18.

Pakulska MM*, Tator CH*, Shoichet MS*.

 

Automated analysis of high-content microscopy data with deep learning.

Mol Syst Biol. 2017 Apr 18.

 Kraus OZ*, Grys BT*, Ba J, Chong Y, Frey BJ*, Boone C*, Andrews BJ*.

 

Progenitor T-cell differentiation from hematopoietic stem cells using Delta-like-4 and VCAM-1.

Nat. Methods 2017, April 10.

Shukla S*, Langley MA*, Singh J2, Edgar JM*, Mohtashami M, Zúñiga-Pflücker JC, Zandstra PW*.

 

Systematic protein–protein interaction mapping for clinically relevant human GPCRs.

Mol. Syst. Bio. 2017, March 15.

Kate Sokolina*, Saranya Kittanakom*, Jamie Snider*, Max Kotlyar, Pascal Maurice, Jorge Gandía, Abla Benleulmi‐Chaachoua, Kenjiro Tadagaki, Atsuro Oishi3, Victoria Wong*, Ramy H Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao*, Xavier Morató, David Otasek, Hiroyuki Kobayashi, Javier Menendez*, Daniel Auerbach, Stephane Angers, Natasa Pržulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica and Igor Stagljar*.

 

MARK4 inhibits Hippo signaling to promote proliferation and migration of breast cancer cells.

EMBO Rep.  2017, Feb 09.

Heidary Arash E*, Shiban A*, Song S*, Attisano L*.

 

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors.

Mol Cell. 2017 Feb 02.

Han H*, Braunschweig U*, Gonatopoulos-Pournatzis T*, Weatheritt RJ*, Hirsch CL, Ha KC*, Radovani E*, Nabeel-Shah S*, Sterne-Weiler T*, Wang J*, O'Hanlon D*, Pan Q*, Ray D*, Zheng H*, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR*, Greenblatt JF*, Wrana JL, Moffat J*, Blencowe BJ*.

 

Preclinical evaluation of taxane-binding peptide-modified polymeric micelles loaded with docetaxel in an orthotopic breast cancer mouse model.

Biomaterials. 2017 Jan 26.

Logie J*, Ganesh AN*, Aman AM, Al-Awar RS, Shoichet MS*.

 

Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library.

G3: Genes|Genomes|Genetics. 2017 Jan 25.

Youn JY*, Friesen H*, Nguyen Ba AN, Liang W*, Messier V*, Cox MJ*, Moses AM, Andrews B*.

 

A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome.

Mol Cell.  2017, Jan 19.

Zhong Yao*, Katelyn Darowski, Nicole St-Denis, Victoria Wong, Fabian Offensperger, Annabel Villedieu, Shahreen Amin, Ramy Malty, Hiroyuki Aoki, Hongbo Guo, Yang Xu, Caterina Iorio, Max Kotlyar, Andrew Emili*, Igor Jurisica, Benjamin G. Neel, Mohan Babu, Anne-Claude Gingras, Igor Stagljar*.

 

Achieving Efficient Manufacturing and Quality Assurance through Synthetic Cell Therapy Design.

Cell Stem Cell. 2017 Jan 5.

Lipsitz YY*, Bedford P, Davies AH, Timmins NE, Zandstra PW*.

 

Machine learning and computer vision approaches for phenotypic profiling.

J Cell Biol. 2017 Jan 2.

Grys BT*, Lo DS*, Sahin N*, Kraus OZ*, Morris Q*, Boone C*, Andrews BJ*.

 

2016

 

Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis.

Proc Natl Acad Sci U S A. 2016 Dec 27.

Chen, Silva PN, Syed AM, Sindhwani S, Rocheleau JV, Chan WC*.

 

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

Molecular Cell. 2016 Dec 15.

Mathieu Quesnel-Vallières*, Zahra Dargaei, Manuel Irimia, Thomas Gonatopoulos-Pournatzis*, Joanna Y. Ip, Mingkun Wu*, Timothy Sterne-Weiler, Shinichi Nakagawa, Melanie A. Woodin, Benjamin J. Blencowe*, Sabine P. Cordes.

 

Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis.

Proc Natl Acad Sci U S A. 2016 Dec 12.

Chen YY*, Silva PN, Syed AM, Sindhwani S, Rocheleau JV, Chan WC*.

 

Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level.

PLoS Comput Biol. 2016 Dec;12.

Leung K, Mohammadi A*, Ryu WS*, Nemenman I.

 

Multiparameter functional diversity of human C2H2 zinc finger proteins

Genome Research. 2016 Dec 1.

Frank W. Schmitges*, Ernest Radovani, , Hamed S. Najafabadi*, Marjan Barazandeh*, Laura F. Campitelli, Yimeng Yin, Arttu Jolma*, Guoqing Zhong*, Hongbo Guo*, Tharsan Kanagalingam*, Wei F. Dai*, Jussi Taipale, Andrew Emili*, Jack F. Greenblatt*and Timothy R. Hughes*.

 

The profile of adsorbed plasma and serum proteins on methacrylic acid copolymer beads: Effect on complement activation.

Biomaterials. 2016 Nov 25.

Wells LA*, Guo H*, Emili A*, Sefton MV*.

 

Genome-wide CRISPR screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors.

Nat Medicine. 2016 Nov 21.

Steinhart Z, Pavlovic Z*, Chandrashekhar M*, Hart T2* Wang X*, Zhang X*, Robitaille M, Brown KR*, Jaksani S, Overmeer R, Boj SF, Adams J*, Pan J*, Clevers H, Sidhu S*, Moffat J*, Angers S.

 

Engineering cell signaling modulators from native protein-protein interactions.

Curr Opin Struct Biol. 2016 Nov 17.

Zhang W*, Ben-David M*, Sidhu SS*

 

Pan-neuronal screening in Caenorhabditis elegans reveals asymmetric dynamics of AWC neurons is critical for thermal avoidance behavior

Elife. 2016 Nov 16.

Kotera I*, Tran NA*, Fu D*, Kim JH, Byrne Rodgers JD*, Ryu WS*.

 

Controlling DNA-nanoparticle serum interactions

Proc Natl Acad Sci U S A. 2016 Nov 16;:

Zagorovsky K, Chou LY, Chan WC*.

 

Ten Simple Rules for Developing Public Biological Databases

PLoS Comput Biol. 2016 Nov 10.

Helmy M*, Crits-Christoph A, Bader GD*.

 

Exploring genetic suppression interactions on a global scale

Science. 2016 Nov 4.

Jolanda van Leeuwen*, Carles Pons, Joseph C. Mellor*, Takafumi N. Yamaguchi*, Helena Friesen*, John Koschwanez, Mojca Mattiazzi Ušaj*, Maria Pechlaner, Mehmet Takar, Matej Ušaj*, Benjamin VanderSluis, Kerry Andrusiak*, Pritpal Bansal*, Anastasia Baryshnikova, Claire E. Boone*, Jessica Cao*, Atina Cote*, Marinella Gebbia*, Gene Horecka*, Ira Horecka*, Elena Kuzmin*, Nicole Legro*, Wendy Liang*, Natascha van Lieshout*, Margaret McNee*, Bryan-Joseph San Luis1, Fatemeh Shaeri*, Ermira Shuteriqi*, Song Sun*, Lu Yang*, Ji-Young Youn4, Michael Yuen*, Michael Costanzo*, Anne-Claude Gingras, Patrick Aloy, Chris Oostenbrink, Andrew Murray, Todd R. Graham, Chad L. Myers, Brenda J. Andrews*, Frederick P. Roth*, Charles Boone*.

 

Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy.

Proc Natl Acad Sci U S A. 2016 Oct 14.

Kuzmanov U*, Guo H*, Buchsbaum D, Cosme J, Abbasi C, Isserlin R*, Sharma P, Gramolini AO, Emili A*.

 

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery.

Cell Rep. 2016 Oct 11;17(3):904-916

Gagarinova A*, Stewart G, Samanfar B, Phanse S*, White CA*, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M*, Emili A*.

 

A global genetic interaction network maps a wiring diagram of cellular function.

Science. 2016 Sep 23

Michael Costanzo*, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons2, Guihong Tan*, Wen Wang, Matej Usaj*, Julia Hanchard*, Susan D. Lee, Vicent Pelechano, Erin B. Styles*, Maximilian Billmann, Jolanda van Leeuwen*, Nydia van Dyk*, Zhen-Yuan Lin, Elena Kuzmin*, Justin Nelson, Jeff S. Piotrowski*, Tharan Srikumar, Sondra Bahr*, Yiqun Chen*, Raamesh Deshpande, Christoph F. Kurat*, Sheena C. Li*, Zhijian Li*, Mojca Mattiazzi Usaj*, Hiroki Okada, Natasha Pascoe*, Bryan-Joseph San Luis*, Sara Sharifpoor*, Emira Shuteriqi*, Scott W. Simpkins, Jamie Snider*, Harsha Garadi Suresh*, Yizhao Tan*, Hongwei Zhu*, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar*, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy*, Chad L. Myers, Brenda Andrews*, Charles Boone*.

 

Mechanism of hard-nanomaterial clearance by the liver.

Nat. Materials. 2016 Aug 15

Tsoi KM, MacParland SA, Ma XZ, Spetzler VN, Echeverri J, Ouyang B, Fadel SM, Sykes EA, Goldaracena N, Kaths JM, Conneely JB, Alman BA, Selzner M, Ostrowski MA, Adeyi OA, Zilman A, McGilvray ID, Chan WC*.

 

Protein engineering by highly parallel screening of computationally designed variants.

Sci Adv. 2016 Jul 20

Sun MG*, Seo MH*, Nim S*, Corbi-Verge C*, Kim PM*.

 

Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21.

Proc Natl Acad Sci U S A. 2016 Jul 19

Leung I*, Dekel A, Shifman JM, Sidhu SS*.

 

Global Mapping of Human RNA-RNA Interactions.

Mol Cell. 2016 May 11.

Sharma E*, Sterne-Weiler T*, O'Hanlon D*, Blencowe BJ*.

 

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.

Genome Med. 2016 May 12.

Narayan S*, Bader GD*, Reimand J*.

 

Encapsulation-free controlled release: Electrostatic adsorption eliminates the need for protein encapsulation in PLGA nanoparticles.

Sci Adv. 2016 May 2.

Pakulska MM*, Elliott Donaghue I*, Obermeyer JM*, Tuladhar A, McLaughlin CK, Shendruk TN, Shoichet MS*.

 

A Multi-Lineage Screen Reveals mTORC1 Inhibition Enhances Human Pluripotent Stem Cell Mesendoderm and Blood Progenitor Production.

Stem Cell Reports. 2016 Apr 27.

Nazareth EJ*, Rahman N*, Yin T, Zandstra PW*.

 

The MADD-3 LAMMER Kinase Interacts with a p38 MAP Kinase Pathway to Regulate the Display of the EVA-1 Guidance Receptor in Caenorhabditis elegans.

PLoS Genet. 2016 Apr.

D'Souza SA*, Rajendran L*, Bagg R*, Barbier L*, van Pel DM*, Moshiri H*, Roy PJ*.

 

Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.

Proc Natl Acad Sci U S A. 2016 Mar 14.

Gorelik M*, Orlicky S, Sartori MA*, Tang X, Marcon E*, Kurinov I, Greenblatt JF*, Tyers M, Moffat J, Sicheri F, Sidhu SS*.

 

An extended set of yeast-based functional assays accurately identifies human disease mutations.

Genome Res. 2016 Mar 14.

Sun S*, Yang F*, Tan G*, Costanzo M*, Oughtred R, Hirschman J, Theesfeld C, Bansal P*, Sahni N, Yi S, Yu A*, Tyagi T*, Tie C*, Hill DE, Vidal M, Andrews BJ*, Boone C*, Dolinski K, Roth FP*.

 

Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs.

Genes Dev. 2016 Mar 1.

Wilk R*, Hu J*, Blotsky D, Krause HM*.

 

System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.

Mol Cell. 2016 Mar 2.

Zhang W*, Wu KP, Sartori MA*, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J, Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KR*, Lemichez E, Chen J, Tong Y, Harper JW, Moffat J*, Rotin D, Schulman BA, Sidhu SS*.

 

MTE1 Functions with MPH1 in Double-Strand Break Repair.

Genetics. 2016 Feb 26.

Yimit A*, Kim T*, Anand R, Meister S*, Ou J*, Haber JE, Zhang Z*, Brown GW*.

 

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction.

Science. 2016 Feb 19.

Ohta S*, Glancy D*, Chan WC*.

 

Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Nat Chem Biol. 2016 Feb 22.

Nim S*, Jeon J*, Corbi-Verge C*, Seo MH*, Ivarsson Y, Moffat J*, Tarasova N, Kim PM*.

 

Tailoring nanoparticle designs to target cancer based on tumor pathophysiology.

Proc Natl Acad Sci U S A. 2016 Feb 16;

Sykes EA, Dai Q, Sarsons CD, Chen J, Rocheleau JV, Hwang DM, Zheng G, Cramb DT, Rinker KD, Chan WC*.

 

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination.

Nature. 2016 Jan 07;

Dorothy Yanling Zhao*, Gerald Gish, Ulrich Braunschweig*, Yue Li*, Zuyao Ni*, Frank W. Schmitges*, Guoqing Zhong*, Ke Liu, Weiguo Li, Jason Moffat*, Masoud Vedadi, Jinrong Min, Tony J. Pawson, Benjamin J. Blencowe* & Jack F. Greenblatt*.

 

2015

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

Cell. 2015 Dec 3.

Traver Hart*, Megha Chandrashekhar*, Michael Aregger*, Zachary Steinhart, Kevin R. Brown*, Graham MacLeod, Monika Mis, Michal Zimmermann, Amelie Fradet-Turcotte, Song Sun*, Patricia Mero*, Peter Dirks, Sachdev Sidhu*, Frederick P. Roth*, Olivia S. Rissland, Daniel Durocher, Stephane Angers, Jason Moffat*.

 

Adult Neural Stem Cells from the Subventricular Zone Give Rise to Reactive Astrocytes in the Cortex after Stroke.

Cell Stem Cell. 2015 Oct 6;

Faiz M, Sachewsky N*, Gascón S, Bang KW, Morshead CM*, Nagy A.

 

Panorama of ancient metazoan macromolecular complexes.

Nature. 2015 Sep 17;

Cuihong Wan*, Blake Borgeson, Sadhna Phanse*, Fan Tu, Kevin Drew, Greg Clark, Xuejian Xiong, Olga Kagan*, Julian Kwan*, Alexandr Bezginov, Kyle Chessman, Swati Pal, Graham Cromar, Ophelia Papoulas, Zuyao Ni*, Daniel R. Boutz, Snejana Stoilova*, Pierre C. Havugimana*, Xinghua Guo*, Ramy H. Malty, Mihail Sarov, Jack Greenblatt*, Mohan Babu, W. Brent Derry, Elisabeth R. Tillier, John B. Wallingford, John Parkinson, Edward M. Marcotte & Andrew Emili*.

 

RNA SPLICING. An alternative splicing event amplifies evolutionary differences between vertebrates.

Science. 2015 Aug 21;349(6250):868-73.

Gueroussov S*, Gonatopoulos-Pournatzis T*, Irimia M*, Raj B*, Lin ZY, Gingras AC, Blencowe BJ*.

 

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.

Nat Methods. 2015 Aug;12(8):725-31.

Marcon E*, Jain H, Bhattacharya A, Guo H*, Phanse S*, Pu S*, Byram G, Collins BC, Dowdell E, Fenner M, Guo X*, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S1*, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G*, Zhong N, Zhao L, Aebersold R, Arrowsmith CH2, Emili A*, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS*, Wodak SJ, Gräslund S, Greenblatt JF*, Edwards AM.

 

Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes.

Cell. 2015 Jul 16;162(2):391-402.

Vu V*, Verster AJ*, Schertzberg M*, Chuluunbaatar T*, Spensley M*, Pajkic D*, Hart GT*, Moffat J*, Fraser AG*.

 

Digital microfluidic immunocytochemistry in single cells.

Nat Commun. 2015 Jun 24;6:7513.

Ng AH*, Dean Chamberlain M*, Situ H*, Lee V*, Wheeler AR*.

 

CD24 tracks divergent pluripotent states in mouse and human cells 

Nat Commun. 2015 Jun 16;6:7329.

Shakiba N, White CA*, Lipsitz YY, Yachie-Kinoshita A*, Tonge PD, Hussein SM, Puri MC, Elbaz J, Morrissey-Scoot J, Li M, Munoz J, Benevento M, Rogers IM, Hanna JH, Heck AJ, Wollscheid B, Nagy A, Zandstra PW*.

 

INNATE IMMUNITY. Cytosolic detection of the bacterial metabolite HBP activates TIFA-dependent innate immunity. 

Science. 2015 Jun 12;348(6240):1251-5.

Gaudet RG1, Sintsova A, Buckwalter CM, Leung N, Cochrane A, Li J, Cox AD, Moffat J*, Gray-Owen SD..

 

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis.

Cell. 2015 Jun 4;161(6):1413-24.

Chong YT*, Koh JL*, Friesen H*, Duffy K*, Cox MJ*, Moses A, Moffat J*, Boone C*, Andrews BJ*.

 

A Hyaluronan-Based Injectable Hydrogel Improves the Survival and Integration of Stem Cell Progeny following Transplantation.

Stem Cell Reports. 2015 Jun 9;4(6):1031-45.

Ballios BG*, Cooke MJ*, Donaldson L, Coles BL, Morshead CM*, van der Kooy D*, Shoichet MS*.

 

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nat Methods. 2015 Jun;12(6):531-3.

Wagih O*, Reimand J*, Bader GD*.

 

Widespread macromolecular interaction perturbations in human genetic disorders.

Cell. 2015 Apr 23;161(3):647-60. Co-first author: Mikko Taipale.

Sahni N, Yi S, Taipale M*, Fuxman Bass JI, Coulombe-Huntington J, Yang F*, Peng J, Weile J*, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH*, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N*, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP*, Xia Y, Walhout AJ, Lindquist S, Vidal M.

 

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development.

Genes Dev. 2015 Apr 1;29(7):746-59.

Quesnel-Vallières M*, Irimia M*, Cordes SP, Blencowe BJ*.

 

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Nat Biotechnol. 2015 May;33(5):555-62.

Najafabadi HS*, Mnaimneh S*, Schmitges FW*, Garton M*, Lam KN, Yang A*, Albu M*, Weirauch MT, Radovani E, Kim PM*, Greenblatt J*, Frey BJ*, Hughes TR*.

 

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. 

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):851-6.

Meyer M, Reimand J*, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, Bader GD*, Dirks PB.

 

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.

Nat Methods. 2015 Feb;12(2):154-9.

Taşan M*, Musso G, Hao T, Vidal M, MacRae CA, Roth FP*.

 

A highly conserved program of neuronal microexons is misregulated in autistic brains.

Cell. 2014 Dec 18;159(7):1511-23.

Irimia M*, Weatheritt RJ*, Ellis JD*, Parikshak NN, Gonatopoulos-Pournatzis T*, Babor M*, Quesnel-Vallières M*, Tapial J, Raj B*, O'Hanlon D*, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP*, Wrana JL, Geschwind DH, Blencowe BJ*.

 

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science. 2015 Jan 9;347(6218):1254806.

Xiong HY*, Alipanahi B*, Lee LJ*, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S*, Najafabadi HS*, Hughes TR*, Morris Q*, Barash Y*, Krainer AR, Jojic N, Scherer SW, Blencowe BJ*, Frey BJ*.

 

* Author affiliated with the Donnelly Centre