site templates free download

Computational and Statistical Genomics Lab


The genome serves as a blueprint of the body, with highly detailed regulatory instructions that activate, repress, or modify dynamic programs of gene expression across cell types and tissues. The gene products, in turn, are responsible for reading and executing these regulatory instructions. At the CSG lab, we develop computational methods to characterize these regulatory instructions, understand how proteins and other gene products interpret them, and create models that predict how defects in these instructions can affect the cell function and, eventually, human health.

Our research encompasses the study of transcription factors, RNA-binding proteins, and non-coding RNAs. We combine machine learning and statistical inference with large genomics datasets to characterize gene regulatory networks of these factors, genetic determinants of variation in their regulatory programs, and their association with human diseases.


The human genome encodes more than 1700 transcription factors, representing a massively complex system in which hundreds of proteins work together to affect chromatin organization and gene expression. We combine machine-learning with genomics and transcriptomics data to develop predictive models of DNA-binding by transcription factors, understand how they interact with different components of the chromatin, and reveal their role in regulating the chromatin state and gene expression.

Selected publications:

Najafabadi et al., Nat Biotechnol, 2015
Schmitges et al., Genome Res, 2016
Najafabadi et al., Genome Biol, 2017


The abundance of each mRNA is determined by the balance between its production and decay rates. A large number of factors in the human cell can potentially influence mRNA stability, including more than 390 RNA-binding proteins and 3,600 microRNAs. We develop novel algorithms that enable us to measure mRNA stability from transcriptome profiling data, and use them to uncover the roles of RNA-binding proteins and microRNAs in regulating the stability of various mRNAs across different tissues and cell types.

Selected publications:

Alkallas et al., Nat Commun, 2017
Goodarzi et al., Nature, 2012
Ray et al., Nature, 2013


Various human diseases, from metabolic disorders to developmental disorders and cancer, can be caused by defects in regulatory programs that modulate gene expression at transcriptional or post-transcriptional level. A main focus of our research is to identify factors whose dysregulation drives the development and progression of cancer, by combining novel computational methods with large compendiums of genomics, epigenomics and transcriptomics data from cancer patients.

Selected publications:

Perron et al., Cell Rep, 2018
Goodarzi et al., Nature, 2012
Jandaghi et al., Gastroenterology, 2016


* Corresponding author
† Equal contribution

– – – – – – Preprints – – – – – –

Dogan B †, Kailasam S †, Corchado AH, Naghmeh Nikpoor, Najafabadi HS *. A domain-resolution map of in vivo DNA binding reveals the regulatory consequences of somatic mutations in zinc finger transcription factors. bioRxiv doi:10.1101/630756.

Software: Download the source code.

Lazure F, Blackburn DM, Karam N, Sahinyan K, Sharanek A, Nguyen D, Corchado AH, Lepper C, Najafabadi HS, Perkins TJ, Jahani-Asl A, Soleimani VD. Myf6/Mrf4 is a myogenic niche regulator required for the maintenance of the muscle stem cell pool. bioRxiv doi:10.1101/691386.

Kejiou NS, Ilan L, Aigner S, Luo E, Rabano I, Rajakulendran N, Najafabadi HS, Angers S, Yeo GW, Palazzo AF. Pyruvate kinase M links glucose availability to protein synthesis. bioRxiv doi:10.1101/691386.

– – – – – – 2020 – – – – – –

Farouni R *, Djambazian H, Ferri LE, Ragoussis J,  Najafabadi HS * (2020). Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nat Commun, 11:2704. PMID 32483174.

Supplementary data and code: Visit the web supplement.
Software: Download the source code.

Alkallas R †, Lajoie M †, Moldoveanu D, Hoang K, Lefrançois P, Lingrand M, Ahanfeshar-Adams M, Watters K, Spatz A, Zippin JH, Najafabadi HS, Watson IR (2020). Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma. Nat Cancer, 1:635-652.

Couturier CP, Ayyadhury S, Le PU, Nadaf J, Monlong J, Riva G, Allache R, Baig S, Yan X, Bourgey M, Lee C, Wang YC, Yong VW, Guiot M, Najafabadi HS, Misic B, Antel J, Bourque G, Ragoussis J, Petrecca K (2020). Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun, 11:3406. PMID 32641768.

– – – – – – 2019 – – – – – –

Blackburn DM, Lazure F, Corchado AH, Perkins TJ, Najafabadi HS, Soleimani VD (2019). High resolution genome wide expression analysis of single myofibers using SMART-Seq. J Biol Chem 294:20097-20108. PMID 31753917.

Fish L, Navickas A, Culbertson B, Xu Y, Nguyen HCB, Zhang S, Hochman M, Okimoto R, Dill BD, Molina H, Najafabadi HS, Alarcón C, Ruggero D, Goodarzi H (2019). Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay. Mol Cell 75:967-981. PMID 31300274.

Buckley MA, Woods NT, Tyrer JP, Mendoza-Fandiño G, Lawrenson K, Hazelett DJ, Najafabadi HS, Gjyshi A, Carvalho RS, Lyra PC, Coetzee SG, Shen HC, Yang AW, Earp MA, Yoder S, Risch H, Chenevix-Trench G, Ramus SJ, Phelan CM, Coetzee GA, Noushmehr H, Hughes TR, Sellers TA, Goode EL, Pharoah PDP, Gayther SA, Monteiro AN (2019). Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus. Cancer Res 79:467-481. PMID 30487138.

Feulner L, Najafabadi HS, Tanguay S, Rak J, Riazalhosseini Y (2019). Age-related variations in gene expression patterns of renal cell carcinoma. Urol Oncol 37:166-175. PMID 30478010.

– – – – – – 2018 – – – – – –

Dogan B,  Najafabadi HS * (2018). Computational methods for analysis of the DNA-binding preferences of Cys2His2 zinc-finger proteins. Methods Mol Biol 1867:15-28. PMID 30155812.

Perron G †, Jandaghi P †, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS *, Riazalhosseini Y * (2018). A general framework for interrogation of mRNA stability programs identifies RNA-binding proteins that govern cancer transcriptomes. Cell Rep 23:1639-1650. PMID 29742422.

Supplementary data: Visit the web supplement.

Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y (2018). Aberration hubs in protein interaction networks highlight actionable targets in cancer. Oncotarget 9:25166-25180. PMID  29861861.

– – – – – – 2017 – – – – – –

Alkallas R, Fish L, Goodarzi H, Najafabadi HS * (2017). Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease. Nat Commun 8:909. PMID 29030541

Supplementary data: Visit the web supplement.
Software: Download the source code.

Najafabadi HS *, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR * (2017). Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biol 18:167. PMID 28877740

Related links: See Research Highlight by Alba MM.

– – – – – – 2016 – – – – – –

Schmitges FW †, Radovani E †, Najafabadi HS †, Barazandeh M †, Campitelli LF †, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR (2016). Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Res 26:1742-1752. PMID 27852650

Supplementary data: Visit the web supplement.

Jandaghi P, Najafabadi HS, Bauer AS, Papadakis AI, Fassan M, Hall A, Monast A, von Knebel Doeberitz M, Neoptolemos JP, Costello E, Greenhalf W, Scarpa A, Sipos B, Auld D, Lathrop M, Park M, Büchler MW, Strobel O, Hackert T, Giese NA, Zogopoulos G, Sangwan V, Huang S, Riazalhosseini Y, Hoheisel JD (2016). Expression of DRD2 is Increased in Human Pancreatic Ductal Adenocarcinoma and Inhibitors Slow Tumor Growth in Mice. Gastroenterology 151:1218-1231. PMID 27578530

Lambert SA, Albu M, Hughes TR *, Najafabadi HS * (2016). Motif comparison based on similarity of binding affinity profiles. Bioinformatics 32:3504-3506. PMID 27466627

Software: Download the source code, or use the online web server.

Gazestani VH, Nikpour N, Mehta V, Najafabadi HS, Moshiri H, Jardim A, Salavati R (2016). A Protein Complex Map of Trypanosoma brucei. PLoS Negl Trop Dis 10:e0004533. PMID: 26991453

– – – – – – 2015 – – – – – –

Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM (2015). A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Res 43:9147-9157. PMID: 26384429

Najafabadi HS, Albu M, Hughes TR (2015). Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinformatics 31:2879-81. PMID: 25953800

Software: Download the source code, or use the online web server.

Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR (2015). Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife doi:10.7554/eLife.06967. PMID: 25905672

Najafabadi HS †, Mnaimneh S †, Schmitges FW †, Garton M, Lam K, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR (2015). C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol 33:555-562. PMID: 25690854

Supplementary data: Visit the web supplement.

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 (2015). The human splicing code reveals new insights into the genetic determinants of disease. Science 347:1254806. PMID: 25525159

Razavi R, Najafabadi HS, Abdullah S, Smukler S, Arntfield M, van der Kooy D (2015). Diabetes enhances the proliferation of adult pancreatic multipotent progenitor cells and biases their differentiation to more β-cell production. Diabetes 64:1311-23. PMID: 25392245

– – – – – – 2014 – – – – – –

Weirauch MT, Yang A, Albu M, Cote A, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey M, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget F, Ratsch G, Larrondo LF, Ecker JR, and Hughes TR (2014). Determination and inference of Eukaryotic transcription factor sequence specificity. Cell 158:1431-1443. PMID: 25215497

– – – – – – 2013 – – – – – –

Najafabadi HS †, Lu Z †, MacPherson C, Mehta V, Adoue V, Pastinen T, Salavati R (2013). Global identification of conserved post-transcriptional regulatory programs in trypanosomatids. Nucleic Acids Res 41:8591-8600. PMID: 23877242

Ray D †, Kazan H †, Cook K †, Weirauch M †, Najafabadi HS †, Li X, Albu M, Zheng H, Yang A, Na H, Guerrousov S, Irimia M, Matzat L, Dale R, Smith S, Yarosh C, Kelly S, Nabet B, Mecenas D, Li W, Laishram R, Qiao M, Lipshitz H, Piano F, Corbett A, Carstens R, Frey B, Anderson R, Lynch K, Penalva L, Lei E, Blencowe B, Fraser A, Morris Q, Hughes T (2013). A compendium of RNA binding motifs for decoding gene regulation. Nature 499:172–177. PMID: 23846655

– – – – – – 2012 – – – – – –

Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485:264-8. PMID: 22495308

For older publications, click here.


Hamed S. Najafabadi
Principal Investigator

Rick Farouni
Postdoctoral Researcher

Ali Nehme
Postdoctoral Researcher
(with Yasser Riazalhosseini)

Rached Alkallas
Ph.D. Student
(with Ian R. Watson)

Wenmin Zhang
PhD Student
(with Yue Li)

Ariel Madrigal
M.Sc. Student

Larisa Morales Soto
M.Sc. Student

Tianyuan Lu
Graduate Research Assistant

Juan Pablo Bernal Tamayo
PhD student (QLS rotation)



Pubudu Nawarathna
- Position in the CSG lab: M.Sc. Student
- Current position: Bioinformatics Consultant, Canadian Centre for Computational Genomics, Canada

Larry Dong
- Position in the CSG lab: Undergraduate Research Assistant
- Current position: Graduate student, McGill University, Canada

Senthil Kailasam
- Position in the CSG lab: Postdoctoral Researcher
- Current position: Bioinformatics Consultant, Canadian Centre for Computational Genomics, Canada

Mehryar Keshavarz
- Position in the CSG lab: Research Intern
- Current position: Software Developer, Montrium, Canada

Nathalie Neriec
- Position in the CSG lab: Visiting Research Scholar
- Current position: Business Development Specialist, Mitacs, Canada

Jose Enrique Leon Burguete
- Position in the CSG lab: Mitacs Globalink Research Intern
- Current position: Undergraduate student, Universidad Nacional Autónoma de México, Mexico

Berat Dogan
- Position in the CSG lab: Postdoctoral Fellow
- Current position: Assistant Professor, İnönü University, Turkey

Colleen Rollins
- Position in the CSG lab: Undergraduate Research Assistant
- Current position: Graduate student, University of Cambridge, UK


August 21, 2020

Congratulations to Ariel Madrigal and Zohreh Mehrjoo on receiving the Faculty of Medicine studentship award!

The awards that Zohreh and Ariel received will support their research on the cellular heterogeneity of cancer.

June 9, 2020

Our paper on estimation and remediation of sample index hopping is out!

In this paper, we show that when multiple droplet-based scRNA-seq samples are multiplexed on the same sequencing lane, incorrect sample assignment of reads can greatly compromise downstream analysis of data by creating a substantial number of "phantom molecules". We present a method to identify and remove such index hopping artifacts.

July 23, 2019

Congratulations to Ali Nehme on receiving a Peter Quinlan Postdoctoral Fellowship from Faculty of Medicine!

This internal fellowship will support Ali's research on examining the role of RNA-binding proteins in regulating microRNAs.

April 30, 2019

Congratulations to Rached Alkallas and Gabrielle Perron on receiving the FRQS doctoral award!

Gabrielle and Rached received their FRQS doctoral awards for their research on gene regulatory programs of cancer.

April 16, 2019

Congratulations to Gabrielle Perron on receiving the Frederick Banting and Charles Best Canada Graduate Scholarship!

This prestigous CIHR doctoral award supports Gabrielle's research on modeling the regulatory networks that govern mRNA stability and their implication in cancer.

February 4, 2019

Congratulations to Gabrielle Perron on receiving the Human Genetics Excellence Award!

Gabrielle is among the six PhD candidates that received the Excellence Award from the Department of Human Genetics.

July 11, 2018

Congratulations to Rached Alkallas on receiving the Canderel Graduate Studentship!

This award supports Rached's research on integrative analysis of gene expression patterns in cutaneous melanoma.

May 23, 2018

Congratulations to Rached Alkallas on receiving the best poster award at the Human Genetics Research Day!

For the second year in a row, Rached's presentation was selected for the best M.Sc. poster award at the Human Genetics Research Day.

May 8, 2018

Our paper on modeling the mRNA stability programs of clear cell renal cell carcinoma is now published in Cell Reports!

In this paper, we show that RNA-binding proteins play a cruicial role in shaping the transcriptome of renal cell carcinoma by modulating the stability of mRNAs, and identify key RNA-binding proteins that affect pathways such as cell cycle and hypoxia signaling.

February 15, 2018

The CSG lab joins the research groups recognized by the Alfred P. Sloan Research Fellowship!

Read more about our 2018 Sloan Fellowship here.

January 23, 2018

The CSG lab has been awarded a CIHR Project Grant to map the cellular mechanisms that can be exploited to modulate miRNAs!

We will analyze thousands of genomics datasets to uncover the genetic and chemical perturbations that can modulate microRNAs, and will elucidate the significance of the associated cellular mechanisms in development of cancer.

October 13, 2017

Our paper on the inference of mRNA stability from RNA-seq data is now published in Nature Communications!

In this paper, we introduce a new method for inferring differential mRNA stability based on intronic and exonic reads in RNA-seq data, and use it to investigate the post-transcriptional regulatory programs of human brain and Alzheimer's disease.

May 18, 2017

Congratulations to Rached Alkallas on receiving the best poster award at the Human Genetics Research Day!

Rached's presentation on our new method for estimating mRNA stability from RNA-seq data was selected for the best M.Sc. poster award at the Human Genetics Research Day.

May 15, 2017

Congratulations to Gabrielle Perron on receiving the FRQS training award!

Gabrielle has been awarded a two-year M.Sc. FRQS training scholarship for her work on "modeling the role of RNA-binding proteins in regulation of the stability of messenger RNAs".

April 4, 2017

Congratulations to Colleen Rollins on receiving the Gates Cambridge Scholarship!

Colleen has received the prestigous Gates Cambridge Scholarship, and will join the University of Cambridge in September to pursue a Ph.D. degree in psychiatry.

November 14, 2016

Congratulations to Dr. Berat Dogan on receiving the TUBITAK Postdoctoral Fellowship!

Berat has received the prestiguous TUBITAK Postdoctoral Fellowship from the Scientific and Technological Research Council of Turkey, and will join us in in 2017 to work on predictive models of DNA binding by Cys2His2 zinc finger proteins.

May 22, 2016

Congratulations to Pubudu Nawarathna on receiving the Queen Elizabeth II Diamond Jubilee Scholarship!

Pubudu will join us in September as a graduate student of Human Genetics.



We are looking for motivated graduate students at the M.Sc. or Ph.D. level. Interested applicants should send their CV, a statement of research interests, a copy of their academic transcripts, and the contact information of at least two references to


We are recruiting postdoctoral fellows with expertise in developing and applying innovative computational methods for solving problems related to functional genomics and epigenomics. Interested applicants should send a cover letter, CV, and the contact information of at least three references to


McGill Genome Centre
740 Dr. Penfield Avenue, Room 7202
Montréal, Québec, H3A 0G1, Canada


Hamed S. Najafabadi, Ph.D.

Assistant Professor, Department of Human Genetics, McGill University

Office: (514) 398-5308


Your message was sent to the CSG lab.