Jocelyn Sunseri Selected as Recipient of 2018 Phase-I MolSSI Software Fellowship

Congratulations to Jocelyn Sunseri who was selected as one of only 11 recipients of the 2018 Phase-I MolSSI Software Fellowship. She will receive six months of support in this program funded by the National Science Foundation through Virginia Tech. Jocelyn’s adviser is Dr. David Koes.

For more information, please click here.

Raghav Partha and the Clark and Chikina labs publish in eLife

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

Raghavendran Partha, Bharesh K Chauhan, Zelia Ferreira, Joseph D Robinson, Kira Lathrop, Ken K Nischal, Maria Chikina (corresponding author), Nathan L Clark (corresponding author)

Abstract: The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype–genotype relationships.

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Dr. Robin Lee Lab publish in Cell Systems

Lee Lab publish in Cell Systems


Cell Systems

NF-𝛋B Dynamics Discriminate between TNF Doses in Single Cells

Zhang Q1, Gupta S1, Schipper DL, Kowalczyk GJ, Mancini AE, Faeder JR, Lee REC*

Using an information theory framework and single-cell data, Zhang et al. set out to distinguish between different mechanisms for activation of intracellular signals. They show that heterogeneity between cellular states can lead to underestimates in the capabilities of single cells. In contrast with a switch-like model for pathway activation, they find that single cells can encode multiple levels of response that increase with stimulation strength.

Please click here to view the full article

The Clark and Morehouse Lab research is featured in PNAS and the Atlantic

The group discovered surprising abilities in a seemingly common butterfly, the cabbage whites – their reproductive capabilities are extraordinarily complex and powerful.

Quick highlights about the butterflies from the text:

  • Males create spermatophores that are 13% of their body weight, which he builds inside of the female.
  • Females have reproductive tracts that are more efficiently stomach-like than their own stomachs (including a chewing jaw that helps them break down the nutrients in the spermatophores).
  • Their relationship is a rapidly evolving battle of the sexes.

The article is an interesting read about a seemingly plain jane butterfly. You can read more in the Atlantic: “This Common Butterfly Has an Extraordinary Sex Life” by Ed Yong. The research can be found in PNAS.

Camille Meslin, Tamara S. Cherwin, Melissa S. Plakkec, Brandon S. Small, Breanna J. Goetz, Nathan I. Morehouse, and Nathan L. Clark (2017) Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection PNAS doi: 10.1073/pnas.1707680114.

CSB – Immuno Joint Departmental Retreat

The Department of Computational and Systems Biology and Department of Immunology hosted a joint retreat on June 7, 2017 at The Twentieth Century Club in Pittsburgh, PA.

Speakers included:

  • Keynote – Dr. Steve Kleinstein (Yale)
  • Anne-Ruxandra Carvunis (CSB)
  • Bill Hawse (Immuno)
  • Takis Benos (CSB)
  • Lisa Borghesi (Immuno)
  • Carlos Camacho (CSB)
  • Florian Weisel (Immuno)
  • Chakra Chennubhotla (CSB)
  • Sandra Cascio (Immuno)
  • Jim Faeder (CSB)
  • Dario Vignali (Immuno)

A poster session followed – congratulations to our winners!
1st place: Abigail Overacre-Delgoffe (Immuno)
2nd place: Marta Wells (CSB)
3rd place: Jingyu Zhang (CSB)

1st place: Deepali Sawant (Immuno)
2nd place: Jason Lohmueller (Immuno)
3rd place: Justin Spiriti (CSB)

Later in the evening, the Department of Computational and Systems Biology had a reception with awards at the Carnegie Science Center.

Congratulations to Wynn Meyer (best postdoc), She Zhang (best student), and Marcia Schwab (best staff) on their awards.

More info here: