Biography

Alper Yilmaz is an Assistant Professor at Yildiz Technical University. His research interest is in various topics in the field of bioinformatics. More specifically, he is interested in genome grammar (text mining in genome), next-generation sequencing analysis and analysis of gene expression via deep learning.

Short Bio: Alper Yilmaz completed his bachelor in 2000 in field of Molecular Biology and Genetics. Then he started his PhD at the Ohio State Universtiy, studied translational control of HIV mRNAs. After completing his PhD in 2007 he studied on DNA words in genomes and next-generation sequencing analysis as a post-doc in same university. He started faculty position in 2012 and is interested in genome grammar, next-generation sequencing analysis and analysis of gene expression via deep learning.

Me in one sentence: Socially awkward, distant and introvert, avid Linux user, commandline guru, fascinated with pipe (| or %>%), plain text enthusiast, excited with (R)Markdown, Docker evangelist, likes coding, Tidyverse fan, amazed with viruses, molecular biologist by training, self-taught bioinformatician, a numberphile and a computerphile.

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Interests
  • Genome Grammar
  • RNA-Seq analysis
  • Deep Learning in gene expression
Education
  • PhD in Molecular Biology, 2007

    The Ohio State University

  • BSc in Molecular Biology and Genetics, 2000

    Bilkent University

Experience

 
 
 
 
 
Faculty
Feb 2012 – Present Turkey
Dept. of Bioengineering
 
 
 
 
 
Post-doctoral Researcher
Jan 2008 – Dec 2011 Ohio
Conducted ChIP-Seq and RNA-Seq analysis.

Projects

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ceRNAnetsim Package

MicroRNAs (miRNAs) are a family of short non-coding RNAs that are key players of post-transciptional regulations. Targets of miRNAs compete against shared miRNAs, hypothesized as competing endogenous RNAs (ceRNAs). We are working on developing network-based computational tools to bring a new perspective to complicated RNA interactions because of the complex interactions of a wide variety of RNA fragments in the cell.

Secondary Metabolite Retrosynthesis

An abstract sample of a research project.

Tissue Specific Gene Expression

Discovery of genes that are expressed specifically in few tissues only.

Deep Learning Gene Expression

Deep Learning Gene Expression

An example of using the in-built project page for deep learning.

External Project

External Project

An example of linking directly to an external project website using external_link.

Internal Project

Internal Project

An example of using the in-built project page.

Metabolic Networks

Metabolic Networks

An example of using the in-built project page.

Word Vectors

Word Vectors

An example of using the in-built project page.

Recent & Upcoming Talks

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