I am a Bioinformatics researcher and I enjoy exploring the complexities of mammalian gene regulation. I joined the Ecker lab in October 2012. Here I’m focused on four major areas:
- leading the various collaborative projects focused on embryonic stem cell biology, initiated as part of the Center for Excellence in Stem Cell Genomics (CESCG) funded by the California Institute of Regenerative Medicine (CIRM). For more details, please visit Salk CESCG
- building gene regulatory networks [epigenetic and transcription factor mediated regulation] that shape early development in mouse, which is important to understand severe birth defects in humans like orofacial clefts and congenital heart defects, as part of the ENCODE phase 3 project,
- analyzing transcriptomic changes in the brain during development of schizophrenia model of mouse which is relevant to understand long-term effects of neuropsychiatric disorders,
- profiling the small RNA landscape of embryonic stem (ES) cells and their early lineages in order to elucidate their role in cellular differentiation.
Prior to joining the Ecker lab I was a postdoc at Mike Snyder’s lab at Stanford University (and Yale, since Feb 2009) where my focus was mostly on identifying the combinatorial co-association of transcription factors that regulate gene expression, as part of the ENCODE project, phase 2. I was also involved in identifying the role of non-coding regulatory variants – in personal genomes and population wide studies. I did my Ph.D under the guidance of Prof. Samir Brahmachari at the Institute of Genomics and Integrative Biology, Delhi. During this time, I analyzed the role of human intronic microRNAs in gene regulation, using computational approaches.
You can read more about my science and some non-science on my website https://sites.google.com/site/mhmanoj/
Shao-shan Carol Huang
I am a bioinformatician. I joined the Ecker lab in March 2016. In collaboration with wet-lab researchers, I am currently mainly focus on three projects: 1) developing bioinformatics approaches for a project to create next generation interactome maps in model and non-model species; 2) analyzing transcriptome and methylome profiling data generated by collaborators of projects focused on embryonic stem cell biology as part of CESCG (Center of Excellence in Stem Cell Genomics); 3) Profiling the small RNA landscape of human embryonic stem cells.
I got a M.S. in Life Science Informatics at Bonn-Aachen International Center for Information Technology in Germany. My project was to study the relationship between genetic redundancy and correlated expression of duplicated genes in Arabidopsis thaliana and Caenorhabditis elegans. After receiving a M.S. Degree, I worked at the Max-Planck Institute for Plant Breeding Research in Germany to develop bioinformatics tools for identifying candidate genes for tomato genome annotation based on integration of traits and genomic and functional genomics data.