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Christopher John Frederick Cameron, PhD

1 Department of Molecular Biophysics and Biochemistry, Yale University

With the advent of the Chromosome Conformation Capture (3C) technologies, the ability to quantify long-range interactions of genomic loci at high-resolution has become possible. My PhD dissertation focuses on applying novel implementations of statistical modeling, machine learning, and bioinformatics approaches to 3C data (in particular, 3C Carbon-Copy [5C] and high-throughput [Hi-C]). The resulting analyses provide insight into the regulation of genomes through the organization of chromatin’s higher-order structures (e.g., Topologically Associating Domains [TAD]).

Keywords: bioinformatics, 4D regulatory genomics, AI specialist

Contact information

christopher [dot] cameron [at] yale [dot] edu
https://ccameron.github.io/

Education

2019-Now Postdoctoral Researcher
Yale University, New Haven, USA
Advisors: Mark Gerstein and Yong Xiong
2013-2019 PhD in Computer Science, concentration in Bioinformatics (Fall 2019)
McGill University, Montréal, Canada
Thesis: High-resolution computational analysis of chromatin architecture and function
Advisors: Mathieu Blanchette and Josée Dostie
2012-2013 MSc in Bioinformatics (February 2014)
University of Guelph, Guelph, Canada
Thesis: Tissue-to-plasma partition coefficient prediction by a multi-channel restricted boltzmann machine
Advisors: Andrea Edginton, Ronald Johnson, and Stefan Kremer
2006-2011 BSc in Biomedical Toxicology, minor in Computer Science (February 2012)
University of Guelph, Guelph, Canada
Thesis: Molecular graph neural networks for toxicology
Advisor: Stefan Kremer

Positions held

2019-Now Postdoctoral Associate
Department of Molecular Biophysics and Biochemistry, Yale University
2013-2019 Research Assistant
School of Computer Science, McGill University
2017 Course Lecturer
School of Computer Science, McGill University
2013-2017 Teaching Assistant
School of Computer Science, McGill University
2012-2013 Graduate Service Assistant
School of Computer Science, University of Guelph
2012-2013 Java Developer
School of Environmental Sciences, University of Guelph
2008-2013 Research Assistant
School of Computer Science, University of Guelph

Journal publications

co-first authors

  1. Prost JA, Cameron CJF., and Blanchette M. Identifying sequence-based determinants of chromosomal compartments. In preparation for submission to Genome Biol.
  2. Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Ross L, Nash A, Ghilotti M, Arner E, Cameron CJF, et al. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. In preparation for submission to Nat Genet.
  3. Cameron CJF, Wang XQD, Dostie J, and Blanchette M. LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads. In submission at Bioinformatics.
  4. Wang XQD, Cameron CJF, Segal D, Paquette D, Blanchette M, and Dostie J. Profiling chromatin landscape at high-throughput and throughput with 2C-ChIP. In submission at Methods Mol Biol.
  5. Cameron CJF, Dostie J, and Blanchette M. Estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution. In review at Genome Biol. doi: 10.1101/377523
  6. Wang XQD, Cameron CJF, Paquette D, Segal D, Warsaba R, Blanchette M, and Dostie J (2019) 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing. BMC Genomics, 20:162. doi:10.1186/s12864-019-5532-5
  7. Roche PJR, Gytz H, Hussain F, Cameron CJF, Paquette D, Blanchette M, Dostie J, Nagar B, and Akavia UD (2018) Double-Stranded Biotinylated Donor Enhances Homology-Directed Repair in Combination with Cas9 Monoavidin in Mammalian Cells. CRISPR J, 1(6). doi:10.1089/crispr.2018.0045
  8. Malina A, Cameron CJF, Robert F, Blanchette M, Dostie J, and Pelletier J (2015) PAM multiplicity marks genomic target sites as inhibitory to CRISPR/Cas9 editing. Nat Commun, 6:10124. doi:10.1038/ncomms10124
  9. Ma EYT, Cameron CJF, and Kremer SC (2010) Classifying and scoring of molecules with the NGN: new data sets, significance tests, and generalization. BMC Bioinformatics, 11(Suppl 8):S4. doi:10.1186/1471-2105-11-S8-S4

Peer-reviewed conference papers

  1. Cameron CJF, Ma EYT, and Kremer SC (2010) Neural Grammar Networks for Toxicology. 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (Montréal, Canada): 1-8. doi:10.1109/CIBCB.2010.5510322

Conferences with abstract submission

  1. Cameron CJF, Dostie J, and Blanchette M (2018) Prediction of complete Hi-C interaction matrices from sequence-based determinants. IRIC 2018 Annual Symposium, Montréal, Canada
  2. Cameron CJF, Dostie J, and Blanchette M (2018) Prediction of complete Hi-C contact maps from genomic sequence. SCS and RegSys COSI at ISMB 2018, Chicago, USA
  3. Cameron CJF, Dostie J, and Blanchette M (2018) Prediction of complete Hi-C contact maps from genomic sequence alone. RECOMB 2018, Paris, France
  4. Cameron CJF, Dostie J, and Blanchette M (2017) High-resolution estimation of true DNA-DNA interaction frequency from Hi-C data. SCS and RegGen COSI at ISMB/ECCB 2017, Prague, Czech Republic
  5. Cameron CJF, Dostie J, and Blanchette M (2016) Improved Hi-C Contact Maps by Adaptive Density Estimation. MRCCT - 1st International Symposium on Immunogenetics of Infectious and Inflammatory Diseases, Montréal, Canada (Ph.D. poster prize)
  6. Cameron CJF, Blanchette M, De Hoon M, and Dostie J (2016) Identifying ncRNA Drivers of Architectural Change in Chromatin. RNA2016, Kyoto, Japan
  7. Cameron CJF, Dostie J, and Blanchette M (2016) Improved Hi-C Contact Maps by Adaptive Density Estimation. GLBIO/CCBC 2016, Toronto, Canada
  8. Cameron CJF, Kaplan M, Drouin A, and Blanchette M (2016) Linking Transposable Elements to Chromatin Architecture in Arabidopsis thaliana. GLBIO/CCBC 2016, Toronto, Canada
  9. Cameron CJF, Fraser J, Dostie J, and Blanchette M (2014) Chromosome conformation capture data improves long-range eQTL prediction. 2014 CSHL Conference on Epigenetics & Chromatin, Huntington, USA

Book chapters, reviews, and non-refereed publications

  1. Cameron CJF, Fraser J, Blanchette M, and Dostie J (2016) Mapping and Visualizing Spatial Genome Organization. In: Bazett-Jones D, Dellaire G (eds) The Functional Nucleus. Springer, Cham. doi:10.1007/978-3-319-38882-3_16
  2. Marhon SA, Cameron CJF, and Kremer SC (2013) Recurrent Neural Networks. In: Bianchini M, Maggini M, Jain L (eds) Handbook on Neural Information Processing. Intelligent Systems Reference Library, vol 49. Springer, Berlin, Heidelberg. doi:10.1007/978-3-642-36657-4_2

Invited talks

  1. (July 2017) The future of Hi-C. Birds of a Feather panel discussion at ISMB/ECCB 2017, Prague, Czech Republic
  2. (April 2017) High-resolution estimation of DNA-DNA contact frequency from Hi-C data. The Physical Basis of Functional Genome Organization: Genome organization as viewed by molecular and visual techniques, Holetown, Barbados
  3. (August 2016) The 3D Genome. Beijing Institute of Genomics (BIG) at the Chinese Academy of Sciences, Beijing, China

Awards and scholarships

2017-2019 Walter Sumner Fellowship, Walter Sumner Foundation
2018 Travel Fellowship Award for ISCB Student Council Symposium, ISCB SCS
2017 Graduate Research Enhancement and Travel Award, McGill University
2017 Graduate Mobility Award, McGill University
2016 Mitacs Globalink Research Award - Japan Society for the Promotion of Science (JSPS), Mitacs/JSPS
2013-2014 Grad Excellence Award in Computer Science, McGill University
2013-2014 Walter Hitschfeld Award - Computer Science, McGill University

Summary of teaching activities

Fall 2017 COMP 364: Computer Tools for Life Sciences, McGill University (with Oliver CG)