Burak Ogan Mancarci

2790 W 33rd Ave V6N 2G1
Vancouver, BC oganm.com
Canada Tel: +1 778 995 1591

Education

2013-2019 (expected)

PhD, Bioinformatics; University of British Columbia (Vancouver, Canada)

Thesis title: Identification/validation of cell type marker genes of the brain and their use in estimating cell type proportions in brain samples.

2009-2013
BSc, Molecular Biology And Genetics; Bilkent University (Ankara, Turkey)

Research Experience

2014 - present

PhD Student at UBC Micheal Smith Laboratories - Supervisor: Dr. Paul Pavlidis

2013

Rotation at BC Children's Hospital - Supervisor: Dr. Wyeth Wasserman

2013

Rotation at Simon Fraser University - Supervisor: Dr. Fiona Brinkman

2012

Summer internship at University of Zurich - Supervisor: Dr. Barbara Tschirren

2011

Summer internship at Harvard Medical School - Supervisor: Dr. George Daley

Teaching Experience

2018
Teaching Assistant for Statistical Methods for High Dimensional Biology course (STAT 540) at UBC - Instructors: Sara Mostafavi, Paul Pavlidis
2016
Teaching Assitant for Exploratory Data Analysis course (STAT 545) at UBC - Instructor: Dr. Jenny Brian
2015
Teaching Assitant for Exploratory Data Analysis course (STAT 545) at UBC - Instructor: Dr. Jenny Brian
2015
Instructional Skills Workshop at UBC - iswnetwork.ca

Awards and Scholarships

2016
1st place in HackSeq hackaton - hackseq.com
2015
3rd place in SportsHack hackaton - sportshackweekend.org/ca/2015
2013-2014
Canadian Institutes of Health Research Training Program Scholarship
2009-2013
Bilkent 50% Scholarship

Publications

Tripathy, S.J., Toker, L., Bomkamp, C., Mancarci, B.O., Belmadani, M., and Pavlidis, P. (2018). Assessing Transcriptome Quality in Patch-Seq Datasets. Front. Mol. Neurosci. 11.

Toker, L., Mancarci, B.O., Tripathy, S., and Pavlidis, P. (2018). Transcriptomic evidence for alterations in astrocytes and parvalbumin interneurons in bipolar disorder and schizophrenia subjects. Biological Psychiatry.

Mancarci, B.O., Toker, L., Tripathy, S.J., Li, B., Rocco, B., Sibille, E., and Pavlidis, P. (2017). Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. ENeuro 4.

Tripathy, S.J., Toker, L., Li, B., Crichlow, C.-L., Tebaykin, D., Mancarci, B.O., and Pavlidis, P. (2017). Transcriptomic correlates of neuron electrophysiological diversity. PLOS Computational Biology 13, e1005814.

Horvath, G.A., Demos, M., Shyr, C., Matthews, A., Zhang, L., Race, S., Stockler-Ipsiroglu, S., Van Allen, M.I., Mancarci, O., Toker, L., et al. (2016). Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target? Mol. Genet. Metab. 117, 42–48.

Onder, T.T., Kara, N., Cherry, A., Sinha, A.U., Zhu, N., Bernt, K.M., Cahan, P., Mancarci, B.O., Unternaehrer, J., Gupta, P.B., et al. (2012). Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598–602.

Software

NeuroExpresso: A web application for visualization of gene expression data in brain cell types. Available at neuroexpresso.org.

markerGeneProfile: An R package for calculation of marker gene profiles as described in Mancarci et al. (2017). Available at github.com/PavlidisLab/markerGeneProfile.

VASCO: A web application for visualization of gene expression data from single cell RNA sequencing experiments. Developed for HackSeq 2016. Available at hackseq.github.io/vasco.

Viral Voyager: A web application for visualization and analysis of metavirome data collected for the Tara Oceans Project. Developed for HackSeq 2018. Available at oganm.com/shiny/taracyc.

Impact Replays: A web application for visualization play-by-play data from football games. Developed for SportsHack hackaton. Available at daattali.com/shiny/cfl.

eggstractor: Software to automate extraction of shape and pigmentation related information from quail eggs. Developed for 2012 summer internship under Barbara Tschirren. Available at github.com/oganm/eggstractor.

Misc. Bioinformatics related R packages: I maintain R packages aimed at making life easier for myslef and other bioinformaticians. See github.com/topics/ogan-bio for a full list.

Misc. D&D related repositories: I maintain R packages and web applications to be used while playing Dungeon's and Dragons, a popular tabletop roleplaying game. See github.com/topics/ogan-dnd for a full list.

Presentations

Society for Neuroscience Annual Meeting 2017: Mancarci, B.O., Toker, L., Li, B., Rocco, B., Tripathy, S., Sibille, E., and Pavlidis, P. NeuroExpresso: A brain cell type specific gene expression database composed of pooled microarray and single cell RNA sequencing data.

25th Annual International Conference on Intelligent Systems for Molecular Biology: Mancarci, B.O., Toker, L., Li, B., Rocco, B., Tripathy, S., Sibille, E., and Pavlidis, P. (2017). NeuroExpresso: Cross laboratory database of brain cell type specific gene expression.

Society for Neuroscience Annual Meeting 2016: Toker, L., Mancarci, B.O., Tripathy, S., and Pavlidis, P. (2016). Deciphering the cell-type specific component in the pathophysiology of brain-related disorders.

Society for Neuroscience Annual Meeting 2016: Tripathy, S., Tebaykin, D., Mancarci, O., Toker, L., and Pavlidis, P. (2016). Transcriptomic correlates of brain-wide electrophysiological diversity.

Society for Neuroscience Annual Meeting 2016: Mancarci, O., Toker, L., and Pavlidis, P. (2016). Comparison of single cell and pooled cell expression data from mouse and human brain.

24th Annual International Conference on Intelligent Systems for Molecular Biology: Mancarci, O., Toker, L., Li, B., Tripathy, S., and Pavlidis, P. (2016). Identification of novel markers for mammalian brain cell types.

Organization of Computational Neurosciences Conference 2015: Tripathy, S.J., Tebaykin, D., Li, B., Mancarci, O., Toker, L., and Pavlidis, P. (2015). Large-scale analysis of brain-wide electrophysiological diversity reveals novel characterization of mammalian neuron types. BMC Neurosci 16, O4.

23rd Annual International Conference on Intelligent Systems for Molecular Biology: Mancarcı, O., Toker, L., Tripathy, S., Pavlidis, P., Mancarcı, O., Toker, L., Tripathy, S., and Pavlidis, P. (2015). A comprehensive database of cell-type specific marker genes for the mammalian brain. F1000Research 4.

23rd Annual International Conference on Intelligent Systems for Molecular Biology: Toker, L., Mancarci, O., Tripathy, S., and Pavlidis, P. (2015). A transcriptomics approach for revealing cell-type proportion changes in psychiatric disorders.