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.


Most DNA- and RNA-binding proteins recognize and bind their targets with remarkable specificity. Moreover, the set of targets of each of these factors can be highly dynamic, and often varies from one cell type to another, and even from one individual to another. We work with several international consortia and interdisciplinary teams of experimental and computational biologists for large-scale characterization of human gene regulatory networks, including identification of in vivo and in vitro binding sites for hundreds of human transcription factors and RNA-binding proteins.

Key collaborators:
Timothy Hughes (University of Toronto)
Guillaume Bourque (McGill University)


Chromatin modifications, transcription factors, RNA-binding proteins, miRNAs and many other factors work together across multiple layers of transcriptional and post-transcriptional programs to regulate the transcriptome of the cell. We combine machine-learning with genomics and transcriptomics data to develop predictive models of gene expression and RNA processing, and work with several international research groups to validate these models and use them to understand the underlying mechanisms of gene regulation in human cells.

Key collaborators:
Hani Goodarzi (UCSF)
Timothy Hughes (University of Toronto)


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. In a highly collaborative research program, we use our regulatory models to uncover factors that contribute to different diseases. A main focus of this program is to identify regulatory factors whose de-regulation drives the development and progression of cancer, by combining our models with large compendiums of genomics, epigenomics and transcriptomics data from cancer patients.

Key collaborators:
Yasser Riazalhosseini (McGill University)
Hani Goodarzi (UCSF)


* Corresponding author
† Equal contribution

– – – – – – 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. 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. 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 *. 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

– – – – – – 2011 – – – – – –

Moshiri H, Acoca S, Kala S, Najafabadi HS, Hogues H, Purisima E, Salavati R (2011). Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. J Biol Chem 286:14178-89. PMID: 21378165

– – – – – – 2010 – – – – – –

Najafabadi HS, Salavati R (2010). Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. PLoS Negl Trop Dis 4:e810. PMID: 20824174

Salavati R, Najafabadi HS (2010). Sequence-based functional annotation: what if most of the genes are unique to a genome? Trends Parasitol 26:225-229. PMID: 20211583

– – – – – – 2009 – – – – – –

Najafabadi HS †, Goodarzi H †, Salavati R (2009). Universal function-specificity of codon usage. Nucleic Acids Res 37:7014-23. PMID: 19773421

Mao Y †, Najafabadi HS †, Salavati R (2009). Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. BMC Genomics 10:355. PMID: 19653906

Azizi H, Hassani K, Taslimi Y, Najafabadi HS, Papadopoulou B, Rafati S (2009). Searching for virulence factors in the non-pathogenic parasite to humans Leishmania tarentolae. Parasitology 136:723-35. PMID: 19416551

– – – – – – 2008 – – – – – –

Najafabadi HS, Salavati R (2008). Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 9:R87. PMID: 18501006

Najafabadi HS, Torabi N, Chamankhah M (2008). Designing multiple degenerate primers via consecutive pairwise alignments. BMC Bioinformatics 9:55. PMID: 18221562

Najafabadi HS, Saberi A, Torabi N, Chamankhah M (2008). MAD-DPD: designing highly degenerate primers with maximum amplification specificity. Biotechniques 44:519-526. PMID: 18476816

– – – – – – 2007 – – – – – –

Goodarzi H, Torabi N, Najafabadi HS, Archetti M (2007). Amino Acid and Codon Usage Profiles: Adaptive Changes in the Frequency of Amino Acids and Codons. Gene 407:30-41. PMID: 17977670

Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS (2007). Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix. J Theor Biol 245:715-725. PMID: 17240399

– – – – – – 2006 – – – – – –

Najafabadi HS *, Lehmann J, Omidi M (2006). Error minimization explains the codon usage of highly expressed genes in Escherichia coli. Gene 387:150-155. PMID: 17097242

Torabi N, Goodarzi H, Najafabadi HS (2006). The case for an error minimizing set of coding amino acids. J Theor Biol 244:737-744. PMID: 17069856

Najafabadi HS *, Goodarzi H, Torabi N (2006). Applying a neural network to predict the thermodynamic parameters for an expanded nearest neighbor model. J Theor Biol 238:657-665. PMID: 16061260

– – – – – – 2005 – – – – – –

Goodarzi H, Najafabadi HS, Torabi N (2005). On the coevolution of genes and genetic code. Gene 362:133-140. PMID: 16213111

Najafabadi HS *, Goodarzi H, Torabi N (2005). Optimality of codon usage in Escherichia coli due to load minimization. J Theor Biol 237:203-209. PMID: 15932760

Goodarzi H, Najafabadi HS, Torabi N (2005). The impact of including tRNA content on the optimality of the genetic code. Bull Math Biol 67:1355-1368. PMID: 16005951

Goodarzi H, Najafabadi HS, Torabi N (2005). On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol 235:318-325. PMID: 15882694

Goodarzi H, Najafabadi HS, Torabi N (2005). Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code. Biosystems 81:91-100. PMID: 15936137


Hamed S. Najafabadi
Principal Investigator

Berat Dogan
Postdoctoral Fellow

Gabrielle Perron
Graduate student
(with Yasser Riazalhosseini)


Rached Alkallas
Graduate student
(with Ian R. Watson)

Colleen Rollins
Undergraduate research assistant



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 University and Génome Québec Innovation 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


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