Yunshu Song

Yunshu Song, CDB

Yunshu Song, CDB

History

  • B.S, Biochemistry, University of California San Diego, 2012-2016
  • M.S, Chemistry, University of California San Diego, 2016-2017
  • UIUC Cell and Developmental Biology Ph.D. Program 2018-Present

Current Project

Wbscr17 project

Past Projects

Outside the Lab

Publications

 

Email Yunshu Song

yunshus2@illinois.edu

Soumya Negi

Graduate Student, CDB

History

  • Anna University, 2013

Current Project

  • Tbox18 Project- I am working on the NIH funded Tbx18 project. I am looking at the postnatal expression of Tbx18 in the prostate.

Past Projects

  • Undergraduate thesis project: I worked on fluorescent imaging of the bacterium Bacillus megaterium. 

Publications

Coming soon.

Outside the Lab

I really like to travel and visit new places. I have been learning a classical Indian dance form called Bharatnatyam for the last 10 years. I also play the guitar.

Email Soumya

snegi2 [at] illinois [dot] edu

Chris Seward

Chris Seward

Graduate Student, CDB

History

Current Project

Chris is primarily involved in the Simons Project, which is working to identify the molecular and genomic basis of social behavior.  He is focused on using ChIP-Seq to reveal the genetic regulatory mechanisms essential for social behavior in several species.  He is also working on developing bioinformatic pipelines to integrate diverse ChIP-seq and RNASeq data from this project in order to compare cross-species experimental data.

Past Projects

  • Patterns of variation in archaeal genomes from geothermal environments – Whitaker Lab, UIUC
  • Identifying a Role for Vibrio cholerae T3SS Effector VopX – Dziejman Lab, URMC

Outside the Lab

Chris grew up in Boston, MA and went to college in Rochester, NY.  He enjoys travelling, photography, sailing, skiing, weight training, driving, movies, and tinkering with new technology.  Check out his photography on Flickr.

Publications

  1. Shpigler, Hagai; Saul, Michael; Murdoch, Emma; Corona, Frida; Cash-Ahmed, Amy; Seward, Christopher; Chandrasekaran, Sriram; Stubbs, Lisa; Robinson, Gene. Honey bee neurogenomic responses to affiliative and agonistic social interactions, Genes, Brains and Behavior 2018.  doi:10.1111/gbb.12509
  2. Michael Saul*, Charles Blatti, Wei Yang, Syed Abbas Bukhari, Hagai Y. Shpigler, Joseph M. Troy, Chris Seward, Lisa Stubbs, Gene E. Robinson, Sihai Dave Zhao* and Saurabh Sinha*. Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge, Genes, Brains and Behavior 2018. doi:10.1111/gbb.12502
  3. Abbas Bukhari, Michael Saul, Chris Seward, Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell. Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Sticklebacks, PLOS Genetics 2017. doi:10.1371/journal.pgen.1006840
  4. Rika Anderson, Angela Kouris, Chris Seward, Kate Campbell, and Rachel Whitaker. Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements, Genome Biology and Evolution 2017. doi:10.1093/gbe/evx104
  5. Chris Seward*, Michael Saul*, Saurabh Sinha, and Lisa Stubbs, et al. Transcriptional regulatory dynamics set the stage for a coordinated metabolic and neural response to social threat in mice, Genome Research 2017. doi:10.1111/gbb.12379
  6. Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M Troy, Chris Seward, Xiaochen Lu, Lisa Stubbs. ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression, Oncotarget 2017. doi:10.18632/oncotarget.12508
  7. Hagai Shpigler, Michael Saul, Emma Murdoch, Amy Cash‐Ahmed, Chris Seward, Saurabh Sinha, Lisa J Stubbs, Gene E Robinson, et al. Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees, Genes, Brains and Behavior 2017. doi:10.1111/gbb.12379
  8. Chris Seward*, Huimin Zhang*, Zuowei Wu, Huiyan Ye, Youjun Feng. Genomic insights into the ESBL and MCR-1-producing ST648 Escherichia, Science Bulletin 2016. doi:10.1007/s11434-016-1086-y
  9. Kelly Miller, Madeline Sofia, Jacob Weaver, Chris Seward, and Michelle Dziejman.  Regulation by ToxR-like proteins converges on vttRB expression to control T3SS-dependent Caco2-BBE cytotoxicity in V. cholerae, Journal of Bacteriology, 2016. doi:10.1128/JB.00130-16
  10. Christopher H. Seward, Alexander Manzella, Ashfaqul Alam, J. Scott Butler and Michelle Dziejman. Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes, Toxins 2015. doi:10.3390/toxins7104099

Email Chris

seward2 [at] illinois [dot] edu

Joe Troy

Joe Troy, Bioinformatics

Education

  • UIUC Informatics Ph.D. program 2012-Present
  • North Central College, Naperville Computer Science M.S., 2000-2005
  • UIUC Finance B.S., 1977-1981

Work Experience

  • Web Applications Developer and Architect, UIUC Library 2018 to Present
  • Graduate Research Assistant, UIUC 2013 to Present
  • Data Transformation and Database Specialist, UIUC 2017-2018
  • Teaching Assistant, UIUC 2017
  • Visiting Program Manager, UIUC Library 2012-2014
  • Senior Software Development Analyst, The Joint Commission 2005-2013
  • Distribution Systems Team Leader, NAVTEQ 2004-2005
  • Software Engineer, NAVTEQ 1999-2004
  • Adjunct Lecturer, EECS department, University of Illinois at Chicago 1999-1999
  • Software Development Analyst, The Joint Commission 1992-1999
  • Programmer Analyst, Richardson Electronics, LTD. 1985-1992
  • Computer Coordinator, Commercial Law League of America 1984-1985
  • Computer Programmer, Law Data Centre 1983-1984

Projects

As a graduate student pursuing a PhD in informatics I am working in the lab of Dr. Lisa Stubbs, Professor of Cell and Developmental Biology. Presently I am exploring computation methods to identify enhancer / promoter interactions during transcription.  Other projects include searching for new genes by scanning genomes for motifs or by analyzing gene expression data.

Previously I worked on a bioinformatics project to identify interactions between Zinc Finger Protein 558 (ZNF558) and Long Terminal Repeat (LTR) elements in human DNA.  Zinc Finger Protein 558 belongs to the Zinc Finger family of Transcription Factors that bind to DNA thus regulating the expression of DNA.  Through out history many LTRs have been introduced into the human genome via retroviruses.  Of interest is the evolutionary history of Zinc Finger Proteins compared to the evolutionary history of the LTRs they bind to.

Links

Email Joe

Stubbs Lab Bioinformatics Presentations: