The laboratory is always interested in recruiting highly motivated postdoctoral fellows with a strong publication record in signal transduction, cell biology, biochemistry, bioinformatics and/or proteomics. Please forward your CV, references and research interests to Dr. Anne-Claude Gingras.
The Gingras lab is part of the Department of Molecular Genetics at the University of Toronto, which has a central admission committee and a rotation system. Graduate students interested in doing a PhD in the laboratory must first be accepted in the Department of Molecular Genetics.
Summer students are exclusively selected from successful applicants to the Research Training Center (RTC) at the Lunenfeld-Tanenbaum Research Institute. Applications are available online and need to be filled by February 28th.
Four available positions in the lab
Four positions are available immediately in our group: 3 are temporary (currently = one year contract) to assist in our important profiling of the humoral response to SARS-CoV-2; 1 is permanent, to work within our proteomics and molecular biology team. See our job listings for full details. Update February 2022: these positions have been filled.
A new version of ProHits-viz is released
We have just released a new version of our data visualization suite ProHits-viz, including a new interface, more interactive features, a new analysis tool, detailed online help and a number of tutorial videos. Check out our Twitter thread for more details on the changes.
New paper on TurboID-mediated BioID in zebrafish
Our new paper by Shimon Rosenthal (with Ian Scott) describes protocols for TurboID-mediated proximity-dependent biotinylation in zebrafish embryos using either mRNA injections or inducible transgenics.
The human cell map is published at Nature
Our study illuminating the organization of a live human cell through proximity-dependent biotinylation (BioID) profiling of 192 markers is now online at Nature, and the website is live at humancellmap.org.
Welcome new team members
We welcome our new team members: Laurie Seifried, pillar coordinator for CoVaRR-Net, Rod Hardy, CoVaRR-Net research associate, and Monica Dayam, research associate, immunology.
New manuscript at Molecular Cell characterizing J-domain proteins and Hsp70s
Our manuscript (with Mikko Taipale) on the characterization of all J-domain proteins and Hsp70s in human cells by newly minted PhD, Dr. Benjamin Piette, is now out at Molecular Cell.
New CFI funding
New funding from the Canadian Foundation for Innovation (CFI) was awarded for our project (led by AC Gingras and J Wrana) titled “Probing the Molecular State of Rare Cell Phenotypes.”
TV interview with our student research assistant Mahya Fazel-Zarandi
The youngest member of our serology team, Mahya Fazel-Zarandi, has been featured in several media outlets. See her Global News interview here: Student research assistant opting for “gap experience” in the fight against COVID-19.
Welcome new team members
Welcome to new team members, Queenie Hu and Mariam Iskilova, who will join us to support the COVID antibody monitoring efforts, mainly funded through the Canadian Immunity Task Force.
New funding from The Terry Fox Research Institute
Thank you to The Terry Fox Research Institute for funding our program, led by Jeff Wrana, on Hippo signaling in cancer.
New manuscript at Science on the GATOR–Rag GTPase pathway and mTOR
Our manuscript led by postdoctoral fellow Geoff Hesketh on the role of the GATOR–Rag GTPase pathway in the inhibition of mTORC1 activation by lysosome-derived amino acids is out at Science.
New manuscript at Science Immunology on the persistence of antibodies to SARS-CoV-2
Our paper on the persistence of antibodies to SARS-CoV-2 proteins in the blood and saliva is now out at Science Immunology. This was an excellent collaboration with Jen Gommerman and Allison McGeer, led by four co-first authors graduate students, including Kento Abe from our lab.
New preprint on our proximity-dependent map of the SARS-CoV-2 proteins
Our proximity-dependent map of the SARS-CoV-2 proteins is now available as a preprint in bioRχiv. This work was led by postdoctoral fellow Payman Samavarchi-Tehrani, with Hala Abdouni, Zhen Lin, Reuben Samson, Audrey Astori and many others. See the website developed by James Knight here: covid19interactome.org.
Manuscript on SARS-CoV-2 neutralization assay out at JCI Insight
Our SARS-CoV-2 neutralization assay surrogate, developed with Jim Rini’s team, is now out at JCI Insight. Project co-led by Kento Abe and Zhijie Li.
BioID-based map of the mitochondria now out at Cell Metabolism
Our collaborative work with the Shoubridge lab at McGill, led by Hana Antonicka, is now out at Cell Metabolism. In this, we use proximity-dependent biotinylation to explore the spatial organization of the mitochondria.
Human cell map on bioRχiv
Our manuscript describing a proximity map of a human cell by MoGen PhD student Chris Go, bioinformatician James Knight and many colleagues has been submitted for publication and made available as a preprint at bioRχiv. All data is publicly available at humancellmap.org.
Postdoctoral and research associate positions
Postdoctoral positions in computational proteomics (joint with Hannes Roest at UofT) and chemical proteomics are available in the Gingras lab. A Research Associate position is also available in chemical proteomics.
GIX: Gene Information eXtension published
James' new Chrome and Firefox extension to quickly annotate a gene product directly in a web browser is now published a Nature Methods. You can download it from the GIX homepage.
Rewiring the BET interactome
See our manuscript by Lambert, Picaud et al. that reports the effects of the drug JQ1 on the interactome of the BET family of bromodomains online at Molecular Cell. A great collaboration between the Gingras and Filippakopoulos labs, with help from many colleagues across the world.
Computational postdoc positions available
The Gingras and Rost labs are looking for postdoctoral fellows in Computational Proteomics to lead the development of the next generation of tools for Data Independent Analysis (application).
Become my newest colleague!
The Lunenfeld is recruiting 3 new PIs in the Fall. The Molecular, Cell and Systems Biology position is now open - cross-appointment at the University of Toronto (application). See all open positions.
Lentiviral toolbox: BioID across cell types!
Payman Samavarchi-Tehrani and colleagues report in Molecular and Cellular Proteomics a collection of lentiviral vectors to enable proximity-dependent biotinylation across cell types.
Congrats Boris, recipient of NSERC studentship
PhD student Boris Dyakov recently received an award from the Natural Sciences and Engineering Research Council of Canada for his work aiming at characterizing nuclear bodies using proteomic tools.
Cytosolic RNA granules and bodies out in Mol Cell
Congratulations to all co-authors and to PDF Jiyoung Youn, profiled at Molecular Cell for her paper selected as a Featured Article (free). Also see the nice Preview by Simon Alberti.
We are growing! Welcome to our new students!
The rotation students were great this year: very happy to recruit Kento Abe, Julia Kitaygorodsky, Shimon Rosenthal (co-supervised with Ian Scott) and Francesco Zangari to the lab.
ProHits-Viz paper is out at Nature Methods
Knight et al. publishes web-tool to improve visualization of protein interaction data (read-only version).
Congrats to our students!
Chris Go and Jonathan Roth are each awarded an Ontario Graduate Scholarship while Benjamin Piette receives a FRQNT from the Quebec government.
Papers delineate MOB1 role in Hippo signaling
Amber Couzens, Shawn Xiong and collaborators used proteomics and structural and biophysical studies to uncover the function of MOB1 in the regulation of the Hippo signaling pathway. See both papers at Mol Cell Proteomics.
Fresh off the press: phosphatases in mitosis
St-Denis et al. report in this issue of Cell Reports the identification of phosphatases implicated in mitosis, and the elucidation of their interactomes.
Congratulations to Ben, Boris and Cassandra!
Our new students get departmental awards: a Cecil Yip doctoral award from the Donnelly Centre to Ben, the Norman Bethune Award to Boris and the Hannah Farkas-Himsley and Alexander Himsley Memorial Prize to Cassandra (both from Molecular Genetics). Cassandra and Boris each also received OSOTF funding from the Lunenfeld-Tanenbaum Research Institute.
New TFRI grant to "Team Hippo"
A team composed of Jeff Wrana, Lil Attisano, Frank Sicheri, Helen McNeill, Steve Gallinger and Anne-Claude Gingras receives 2.25M to target the Hippo tumor suppressor pathway in cancer. Thanks to TFRI, donors and volunteers!
Welcome Shen, new PDF in the group
Shen Zhang recently joined from the Dalian Institute of Chemical Physics, Chinese Academy of Sciences and brings new expertise in quantitative proteomics.
ProHits 4.0 released and published
The ProHits 4.0 publication in press at J Proteomics (Liu et al) describes the use of our ProHits LIMS for Data Independent Acquisition through the incorporation of DIA-Umpire, MSPLIT-DIA and mapDIA.
Welcome Bhavisha and Debbie
Bhavisha is now assisting Dushyandi in the essential lab manager position while Debbie is working on our recently funded CCSRI Innovation grant. Amber is back to continue her work on Hippo signaling.
Welcome Stefan, farewell Wade
Welcome to Stefan Maier, PDF who will be developing new proteomics approaches. We are sad to say goodbye to our longtime member Wade Dunham who is starting a new venture outside of the city.
Thank you, Canadian Cancer Society!
Thanks to the donors and volunteers of the Canadian Cancer Society, our lab received a two-year grant to investigate endocytic organelles as sites of cellular growth control.
Happy 2016 and welcome all new members!
Welcome to the lab to our new students Ben, Boris and Cassandra! Dushyandi replaces Marilyn as co-manager of the lab. Good luck to Marilyn and hubby Prof Smith in Montreal!
MSPLIT-DIA paper is out in Nature Methods
In a collaboration with Nuno Bandeira, UCSD, we are reporting in Nature Methods a new spectral matching approach for peptide identification from DIA. This will be incorporated in the next ProHits release.
Thank you, Cancer Research Society!
Our lab receives 2 year grant from the Cancer Research Society. We thank the supporters and volunteers of the CRS for all their efforts!
JP Lambert awarded CRS career transition award
Jean-Philippe is awarded a prestigious Scholarship for the Next Generation of Scientists from the Cancer Research Society!
Association of E4orf4 with two major phosphatases
In collaboration with the Branton lab (McGill), MSc student Yiwang Zhou uncovers new mechanisms of signaling regulation by Adenovirus E4orf4: E4orf4 regulates Hippo signaling though PP1 and PP2A.
A Parkinson Society of Canada fellowship to Geoff!
Geoff Hesketh, PDF, receives the prestigious award for his mass spectrometry based characterization of trafficking proteins implicated in Parkinson disease pathogenesis.
Network Biology Collaborative Centre is a GIN node
New Funding from Genome Canada for the SMART and proteomics facilities at LTRI. The NBCC team led by Jeff Wrana and Anne-Claude Gingras becomes a Genomics Innovation network node.
Worm CCM3 regulates excretory canal
Ben Lant publishes new research in Nature Communications; work funded by joint CIHR to Drs. Derry and Gingras.
Non-enzymatic role for myotubularins in cell cycle
Nicole St-Denis et al. report that MTMR3 & 4 control abscission via interactions with PLK1 and CEP55.
DIA-Umpire: a new way to look at SWATH data
A collaboration between the Gingras and Nesvizhskii labs leads to the development of a complete informatics pipeline for the analysis of DIA/SWATH data (publication by Tsou et al. in Nature Methods).
Lap-Chee Tsui Publication award to Amber Couzens
Read again the winning publication on the Hippo interactome.
Improving AP-MS data visualization
James Knight and colleagues publish a web tool for visualization of interaction proteomics data.
How to score true interactions in BioID experiment
JP Lambert et al. thoroughly analyze background subtraction in BioID and compare BioID to standard AP-MS for chromatin proteins.
Cell paper by the Gingras and Lindquist labs
Taipale et al. report a quantitative chaperone interaction network that reveals the architecture of cellular protein homeostasis pathways.
Chris Go receives doctoral award
Congrats to Chris Go on getting a competitive Frederick Banting and Charles Best Canada Graduate Scholarship.
Stopping the Hippos
Hundreds of new connections and mechanisms of phospho-recognition in the Hippo pathway published by Amber Couzens et al. in Science Signaling - also see accompanying perspective by Eric Weiss.
AP-SWATH paper in Nature Methods
In a collaboration with AB SCIEX and the support of Venture Sinai, Lambert et al. present AP-SWATH which rapidly maps differential interactomes.
Congrats Nicole and Chris
Postdoc Nicole St-Denis and grad student Chris Go each obtained competitive CIHR support for their studies of phosphatases.
Publication of the CRAPome
The Nesvizhskii and Gingras teams led an international effort to create a repository to help filter the cra... hmm... contaminants out of AP-MS data. See the paper by Datta Mellacheruvu et al., in Nature Methods.
Funding from Genome Canada
Anne-Claude Gingras and Mike Tyers (IRIC, Montreal) co-lead an international team for the development of ProHits Next Generation, a platform for interaction proteomics. Funding from Genome Canada was awarded in the recent Bioinformatics and Computational Biology competition.
Funding from NSERC awarded
We recently obtained a NSERC Discovery grant and an Accelerator Supplement to study the specificity in RNA storage and degradation associated to p bodies and stress granules.
Special issue of Proteomics
Have a look at the special issue of Proteomics on Protein Complexes and Interaction Networks co-Edited by Alexey Nesvizhskii and Anne-Claude Gingras.
James received Heart and Stroke funding!
Congratulations to James on receiving a prestigious fellowship from the Heart and Stroke Foundation of Canada!
Nicole receives TD Bank scholarship
Postdoctoral fellow Nicole St-Denis is awarded prestigious TD Bank postdoctoral fellowship for her studies of phosphatases in mitosis.
ProHits version 2.0.0
Major new ProHits release - SAINT can be run seamlessly.
Profile of Anne-Claude in ASBMB Today
Zick Zagorski pens the profile of Anne-Claude Gingras in this month's issue of ASBMB Today.
New releases for SAINT and ProHits
We keep updating our software. Check our Resources section for the latest downloads of our interaction proteomics tools.
Publications by two of our students
Graduate students Michelle Kean and Wade Dunham each got their first publication from the Gingras lab. Congrats to both! Access the publications at J Biol Chem and Proteomics.
SAINT paper published
The Gingras and Nesvizhskii labs publish in Nature Methods the new version of the statistical tool SAINT for scoring interaction proteomics data. Download the free software at sourceforge.
ProHits: integrated software for mass spectrometry-based interaction proteomics. The Gingras and Tyers labs publish in Nature Biotechnology their interaction proteomics data management system ProHits. Download the free software at prohitsms.com.
Fresh off the press
A global protein kinase and phosphatase interaction network in yeast. The Tyers, Nesvizhskii and Gingras labs team up to provide a comprehensive interaction map for yeast kinases and phosphatases (Breitkreutz et al., Science, 2010).
New funding announced
Dr. Gingras is part of a research team led by Prof. Pawson that was awarded a $7.7 million GL2 grant from Ontario's Ministry of Research and Innovation, which the team plans to use for understanding the assembly and function of dynamic signaling networks in complex diseases.