I am a Research Scientist, Software Developer and Data Analyst at McGill University’s C3G, probing questions related to human health by building and using bioinformatics tools.

I am an organized modular thinker who breaks problems into their individual, manageable building blocks. I am also an efficient problem solver, with an eye for detail.

Programming Skills:

• Python:
numpy, pandas, matplotlib, seaborn, ggplot2, plotly, sklearn, Keras, jupyter notebooks

• R:
ggplot2, lattice, base R, limma, Genomics Ranges, R markdown notebooks

• Other languages:
Bash, awk , Java
• Markdown & styling:
HTML, CSS, markdown
• Version control using git:
github, bitbucket (user: rdali)
• High Performance Computing: Batch, PBS/Torque, Slurm
• Operating Systems:
Mac, Linux, Windows
• Miscellaneous:
Framework development
Software installation and configuration
Automated testing using Jenkins
Docker, Virtual machines
GSoC Admin for 2018/2019/2020
Season of Docs Admin for 2019
Hackathons: McHacks 2017

Open Source software contributions:
GenPipes
RobusTAD
HiCUP
MultiQC
MultiQC_C3G plugin
mugqic_tools

C3G Technology Development Team - Montreal, QC

July 2017 - current
Software Developer & Data Analyst

I am part of the technology development team at McGill University’s C3G. We are an academic research entity that focuses on writing open source tools for the genomics community, providing data analysis support for academics and training researchers to run bioinformatics analyses.

My role involves several tasks at C3G, under three broad categories:

Technology Development:

• Involved in the development and maintenance of GenPipes, an open source python framework facilitating multi-step analyses on HPC clusters.
• In addition to code contribution to GenPipes, I am heavily involved in documenting GenPipes, creating test datasets for users, user support and user training.
• Set up GenPipes automated testing through Jenkins. Integrated Jenkins with slack, email, and bitbucket.
• Set up scheduled system monitoring of resources across 5 different HPC servers.
• Managing GenPipes data analysis reporting system through interactive plots and customized reports through MultiQc.
• Contributed to several open source tools (HiCUP, MultiQC) to adapt them based on C3G needs.

Data Analysis:

• Involved in several large scale data analysis projects that are aimed at understanding human health and disease. Tasks include data quality control, data parsing/cleaning, script/code development, statistical analysis, data visualization and data reporting/presentation.

Organization logistics:

• involved in C3G grant/manuscript writing and annual performance reporting on computing resources.
• Organization administrator for Google Summer of Code (2018, 2019).
• Organization administrator and mentor for Google Season of Docs (2019).
• Lead and managed bioinformatics workshops with a team of 4-5 people. Handled all logistics, including creating/curating tutorial material, room booking, scheduling, user registration, refunds, catering, feedback collection…

Integrated Program of Neuroscience - McGill University - Montreal, QC

Jan 2014 - Jun 2017
PhD candidate in Neuroscience
Mathieu Blanchette Lab (Computer Science Department)

• Worked on understanding chromatin structure in Brain Cancer through genomics Hi-C analysis.
• developed computational tools to facilitate data analysis.

Montreal Neurological Institute - McGill University - Montreal, QC

Jan 2011 - Jan2014
PhD candidate in Neuroscience

• Worked on identifying molecular mechanisms involved in Brain Cancer development using a combination of molecular biology techniques, bioinformatics tools and statistical approached.

IMBS Department - Massey University - Palmerston North, NZ

Oct 2010 - Dec 2010
Massey University Summer Scholarship
Barry Scott Lab

• Worked on understanding the molecular basis of symbiotic interactions between fungus ,Epichloe festucae, and plants, perennial ryegrass.

BMI Department - University of Ottawa - Ottawa, ON

May 2009 - Oct 2010 NSERC summer student & Honours student Mona Nemer Lab

• Worked on investigating gene networks in cardiac cells, specifically, the effect of cyclinD2 expression on cardiac regeneration.
  

Biology Department - University of Ottawa - Ottawa, ON

May 2008 - May 2009
NSERC summer student & Work-Study Program
Rees Kassen Lab

• Worked on isolating novel antibiotics by applying selective pressure on bacteria that naturally produce bio-active molecules.

Professional Development Certificate in Data Science and Machine Learning McGill University
2018-2019

PhD in NeuroScience & Bioinformatics
McGill University
2011-2017

B.Sc in Biochemistry
University of Ottawa
2006-2010

• An Arf/Rab cascade controls the growth and invasiveness of glioblastoma. BiorXiv 2020.

  Gopinath Kulasekaran, Mathilde Chaineau, Valerio E. Piscopo, Federica Verginelli, Martine Girard, Maryam Fotouhi, Yeman Tang, Rola Dali, Rita Lo, Stefano Stifani, Peter S. McPherson
• Groucho/TLE opposes axial to hypaxial motor neuron development. BiorXiv 2020.

  Adèle Salin-Cantegrel, Rola Dali, Jae Woong Wang, Marielle Beaulieu, Mira Deshmukh, Ye Man Tang, Stefano Stifani
• Avoidance Learning Using Observational Reinforcement Learning. ArXiv 2019.

  David Venuto, Léonard Boussioux, Junhao Wang, Rola Dali, Jhelum Chakravorty, Yoshua Bengio, Doina Precup
• Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene. Genome Biol. 2019.

  S. Lalonde, V. A. Codina-Fauteux, S. M. de Bellefon, F. Leblanc, M. Beaudoin, M. M. Simon, R. Dali, T. Kwan, K. S. Lo, T. Pastinen, G. Lettre
• GenPipes: an open-source framework for distributed and scalable genomic analyses. Gigascience 2019.

  M. Bourgey, R. Dali, R. Eveleigh, K. C. Chen, L. Letourneau, J. Fillon, M. Michaud, M. Caron, J. Sandoval, F. Lefebvre, G. Leveque, E. Mercier, D. Bujold, P. Marquis, P. T. Van, D. Anderson de Lima Morais, J. Tremblay, X. Shao, E. Henrion, E. Gonzalez, P. O. Quirion, B. Caron, G. Bourque
• Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome. Nat. Genet. 2018.

  T. Gayden, F. E. Sepulveda, D. A. Khuong-Quang, J. Pratt, E. T. Valera, A. Garrigue, S. Kelso, F. Sicheri, L. G. Mikael, N. Hamel, A. Bajic, R. Dali, S. Deshmukh, D. Dervovic, D. Schramek, F. Guerin, M. Taipale, H. Nikbakht, J. Majewski, D. Moshous, J. Charlebois, S. Abish, C. Bole-Feysot, P. Nitschke, B. Bader-Meunier, D. Mitchell, C. Thieblemont, M. Battistella, S. Gravel, V. H. Nguyen, R. Conyers, J. S. Diana, C. McCormack, H. M. Prince, M. Besnard, S. Blanche, P. G. Ekert, S. Fraitag, W. D. Foulkes, A. Fischer, B. Neven, D. Michonneau, G. de Saint Basile, N. Jabado
• RobusTAD: A Tool for Robust Annotation of Topologically Associating Domain Boundaries. BiorXiv 2018.

  Rola Dali, Guillaume Bourque, Mathieu Blanchette
• Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma-initiating cells. Molecular Oncology 2018.

  Rola Dali, Federica Verginelli, Albena Pramatarova, Robert Sladek, Stefano Stifani
• A critical assessment of topologically associating domain prediction tools. Nucleic Acids Research 2017.

  Rola Dali, Mathieu Blanchette
• Transcriptional regulation of mouse hypoglossal motor neuron somatotopic map formation. Brain Structure and Function 2015.

  Xin Chen, Jae Woong Wang, Adele Salin-Cantegrel, Rola Dali, Stefano Stifani
• Cyclin D2 is a GATA4 cofactor in cardiogenesis. Proceedings of the National Academy of Sciences 2014.

  A. Yamak, B. V. Latinkic, R. Dali, R. Temsah, M. Nemer
• Transcription factors FOXG1 and Groucho/TLE promote glioblastoma growth. Nature Communications 2013.

  Federica Verginelli, Alessandro Perin, Rola Dali, Karen H. Fung, Rita Lo, Pierluigi Longatti, Marie-Christine Guiot, Rolando F. Del Maestro, Sabrina Rossi, Umberto di Porzio, Owen Stechishin, Samuel Weiss, Stefano Stifani
• Prolyl isomerase Pin1 and protein kinase HIPK2 cooperate to promote cortical neurogenesis by suppressing Groucho/TLE:Hes1-mediated inhibition of neuronal differentiation. Cell Death & Differentiation 2013.

  R Ciarapica, L Methot, Y Tang, R Lo, R Dali, M Buscarlet, F Locatelli, G del Sal, R Rota, S Stifani
• Multivariate Phenotypic Divergence Due to the Fixation of Beneficial Mutations in Experimentally Evolved Lineages of a Filamentous Fungus. PLoS ONE 2012.

  Sijmen E. Schoustra, David Punzalan, Rola Dali, Howard D. Rundle, Rees Kassen
• Antagonistic interactions peak at intermediate genetic distance in clinical and laboratory strains of Pseudomonas aeruginosa. BMC Microbiology 2012.

  Sijmen E Schoustra, Jonathan Dench, Rola Dali, Shawn D Aaron, Rees Kassen
• Fitness-Associated Sexual Reproduction in a Filamentous Fungus. Current Biology 2010.

  Sijmen Schoustra, Howard D. Rundle, Rola Dali, Rees Kassen

I keep notes and tutorials in Computer Science, Data Science and various topics. Check it out at:

Food4Thought: Journals of a meandering mind

• roladali@gmail.com
• roladali
• Room 4200, 740 Docteur Penfield Av., H3A 1A5, Montreal, Canada