Curriculum Vitae

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Christopher John Frederick Cameron, PhD

¹ Simons Electron Microscopy Center, New York Structural Biology Center (NYSBC)

As a computational biologist, I develop novel statistical, machine learning and bioinformatics approaches to emerging molecular biology technologies. At NYSBC, I build new computational methods to improve the center's cryogenic electron microscopy (cryo-EM) and other structural biology pipelines. My postdoctoral research focused on cryo-EM image processing, specifically addressing the modeling and integration of prior information. During my PhD, I implemented analyses of chromosome conformation capture and chromatin immunoprecipitation data that provided insight into the regulation of genomes through the organization of chromatin’s higher-order structures.

Keywords: computational biology, machine learning, cryo-EM, 4D regulatory genomics

Email: ccameron [at] nysbc [dot] org
Website: https://ccameron.github.io/

Education

Positions held

Journal publications

^† co-first or -second authors

1. Leng J, Cameron CJF, Oh S, Khurana E, Noonan JP and Gerstein MB. LESSeq: local event-based analysis of alternative splicing using RNA-Seq data. BioRxiv. DOI:10.1101/841494
2. Prost JA^†, Cameron CJF^† and Blanchette M. SACSANN: identifying sequence-based determinants of chromosomal compartments. BioRxiv. DOI:10.1101/2020.10.06.328039
3. Cameron CJF, Seager SJH, Sigworth FJ, Tagare HD and Gerstein MB. REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers. Commun Biol. DOI:10.1038/s42003-024-07045-0
4. Zhang Y, Cameron CJF, and Blanchette M (2024) Posterior inference of Hi-C contact frequency through sampling. Front Bioinform, (3). DOI: 10.3389/fbinf.2023.1285828
5. Rozowsky J, Gao J, Borsari B, [and 103 others, including Cameron CJF] (2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186(7):1493-1511.e40. DOI:10.1016/j.cell.2023.02.018
6. Tsai P, Cameron CJF, Forni MF, Wasko RR, Naughton BS, Horsley V, Gerstein MB and Schlieker C (2022) Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins. Cell Rep, 41(8):111675. DOI:10.1186/s13104-020-05106-1
7. Amaya C, Cameron CJF^†, Devarkar SC^†, Seager SJH, Gerstein MB, Xiong Y and Schlieker C (2021) Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology. JBC, 297(2):100937. DOI:10.1016/j.jbc.2021.100937
8. Ramilowski J, Yip CW, Agrawal S, [and 115 others, including Cameron CJF] (2020) Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. Genome Res, 30:1060-1072. DOI:10.1101/gr.254219.119
9. Cameron CJF, Wang XQD, Dostie J and Blanchette M (2020) LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads. BMC Res Notes, 13:273. DOI:10.1186/s13104-020-05106-1
10. Bonetti A, Agostini F, Suzuki AM, [and 26 others, including Cameron CJF] (2020) RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun, 11:1018. DOI:10.1038/s41467-020-14337-6
11. Cameron CJF, Dostie J and Blanchette M (2020) HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution. Genome Biol, 21(1):11. DOI:10.1186/s13059-019-1913-y
12. 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
13. 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
14. 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
15. 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. Kirchhof M, Cameron CJF and Kremer SC (2021) End-to-end chromosomal compartment prediction from reference genomes. IEEE BIBM: 50-57. DOI:10.1109/BIBM52615.2021.9669521
2. Cameron CJF, Ma EYT and Kremer SC (2010) Neural Grammar Networks for Toxicology. IEEE CIBCB (Montréal, CAN): 1-8. DOI:10.1109/CIBCB.2010.5510322

Conferences with abstract submission

1. Cameron CJF, Seager SJH, Sigworth FJ, Tagare HD and Gerstein MB (2023) REPIC — an ensemble learning methodology for cryo-EM particle picking. MLCSB COSI at ISMB/ECCB, Lyon, FRA
2. Cameron CJF, Seager SJH, Sigworth FJ, Tagare HD and Gerstein MB (2023) REPIC — an ensemble learning methodology for cryo-EM particle picking. 3DEM GRC/GRS, Newry, USA
3. Cameron CJF, Seager SJH, Sigworth FJ, Tagare HD and Gerstein MB (2023) REPIC — an ensemble learning methodology for cryo-EM particle picking. BPS, San Diego, USA. DOI:10.1016/j.bpj.2022.11.914
4. Cameron CJF, Sigworth FJ, Gerstein MB, and Tagare HD (2023) MIDLS — membrane detection in cryo-EM using deep level sets. BPS, San Diego, USA. DOI:10.1016/j.bpj.2022.11.913
5. Cameron CJF, Seager SJH, Tagare HD and Gerstein MB (2022) Reliably expanding SPA cryo-EM particle sets by machine-learning consensus. 3DEM GRC/GRS, Castelldefels, ESP (GRS-selected talk)
6. Cameron CJF, Tagare HD, Gerstein MB and Xiong Y (2020) Improving agreement between structural models and cryo-EM maps in reciprocal space. 5th NE Cryo-EM Symp, Boston, USA
7. Cameron CJF, Dostie J and Blanchette M (2018) Prediction of complete Hi-C interaction matrices from sequence-based determinants. IRIC Annual Symp, Montréal, CAN
8. Cameron CJF, Dostie J and Blanchette M (2018) Prediction of complete Hi-C contact maps from genomic sequence. SCS and RegSys COSI at ISMB, Chicago, USA
9. Cameron CJF, Dostie J and Blanchette M (2018) Prediction of complete Hi-C contact maps from genomic sequence alone. RECOMB, Paris, FRA
10. 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, Prague, CZE
11. Cameron CJF, Dostie J and Blanchette M (2016) Improved Hi-C Contact Maps by Adaptive Density Estimation. MRCCT - 1st International Symp on Immunogenetics of Infectious and Inflammatory Diseases, Montréal, CAN (PhD poster prize)
12. Cameron CJF, Blanchette M, De Hoon M and Dostie J (2016) Identifying ncRNA Drivers of Architectural Change in Chromatin. RNA, Kyoto, JPN
13. Cameron CJF, Dostie J and Blanchette M (2016) Improved Hi-C Contact Maps by Adaptive Density Estimation. GLBIO/CCBC, Toronto, CAN
14. Cameron CJF, Kaplan M, Drouin A and Blanchette M (2016) Linking Transposable Elements to Chromatin Architecture in Arabidopsis thaliana. GLBIO/CCBC, Toronto, CAN
15. Cameron CJF, Fraser J, Dostie J and Blanchette M (2014) Chromosome conformation capture data improves long-range eQTL prediction. Epigenetics & Chromatin CSHL, Huntington, USA

Book chapters, reviews and non-refereed publications

1. Wang XQD, Cameron CJF, Segal D, Paquette D, Blanchette M and Dostie J (2021) Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP. In: Bodega B., Lanzuolo C. (eds) Capturing Chromosome Conformation. Methods in Molecular Biology, vol 2157. Humana, New York, NY. DOI:10.1007/978-1-0716-0664-3_8
2. 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
3. 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. (Aug 2023) Reliable protein identification in cryo-EM images by machine-learning consensus. New York Structural Biology Center, NYC, USA
2. (Aug 2023) Reliable protein identification in cryo-EM images by machine-learning consensus. Spanish National Research Council, Madrid, ESP
3. (Jul 2017) The future of Hi-C. Birds of a Feather panel discussion at ISMB/ECCB, Prague, CZE
4. (Apr 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, BRB
5. (Aug 2016) The 3D genome. Beijing Institute of Genomics (BIG) at the Chinese Academy of Sciences, Beijing, CHN

Awards and scholarships

Training and workshops

Academic service