Select publications

* Author affiliated with Donnelly Centre

2017

 

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