Searching for direct causal mechanisms in biological systems | Principles of Bioengineering (Slavov)
Channel: Nikolai Slavov
Date: 2020-04-13

Principles of Bioengineering: http://slavovlab.net/teaching/


Nikolai Slavov
Department of Bioengineering
Northeastern University


Understanding biological systems: In search of direct causal mechanisms

Abstract: The advent of DNA-microarrays spurred a vigorous effort to reverse engineer biological networks. Recently, these efforts have been reinvigorated by the availability of RNA-seq data from perturbed and unperturbed single cells. I will discuss the opportunities and limitations of using such data for inferring networks of direct causal interactions, with emphasis on the distinctions between models based on direct and indirect interactions. This discussion motivates the need to model proteins since most biological interactions involve proteins. Then I will introduce key ideas and technological capabilities of high-throughput single-cell proteomics methods that we have developed and will focus on the opportunities of using such data for inferring direct causal mechanisms in biological systems.


For more information, see

Slavov (2020)
Unpicking the proteome in single cells
Science, Vol. 367, Issue 6477, pp. 512-513
DOI: 10.1126/science.aaz6695 
https://science.sciencemag.org/content/367/6477/512

Slavov (2020)
Single-cells protein analysis by mass-spectrometry
arXiv, arXiv:2004.02069 
https://arxiv.org/abs/2004.02069

Specht H, Emmott E, Petelski A, Huffman RG, Perlman D, Serra M, Kharchenko P, Koller A, Slavov N. (2019)
Single-cell mass-spectrometry quantifies the emergence of macrophage heterogeneity
bioRxiv, DOI: 10.1101/665307 
https://www.biorxiv.org/content/10.1101/665307v3

Slavov N.  (2010)
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks
JMLR, W&CP vol. 9  | arXiv:1406.0193 
http://proceedings.mlr.press/v9/slavov10a.html
https://arxiv.org/abs/1406.0193

Slavov N., Botstein D.  (2011)
Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast
Mol. Biol. Cell, vol. 22
https://www.molbiolcell.org/doi/full/10.1091/mbc.e11-02-0132