Function SIG Meetings:

Function-SIG 2016 was held on July 9, 2016 preceding ISMB 2016 in Orlando, FL USA.

Check back for updates on Function-SIG 2017.

Accepting 2017 abstract submissions

Function-SIG 2016 Keynote Speakers

Trey Ideker, University of California, San Diego

Talk Title: Modeling the Cell as a Hierarchy of Subsystems

Speaker Bio: Trey Ideker, Ph.D. is Professor of Genetics in the Department of Medicine at the University of California at San Diego. He serves as Director of the National Resource for Network Biology and Director of the San Diego Center for Systems Biology, as well as being Adjunct Professor of Computer Science and Bioengineering and Member of the Moores UCSD Cancer Center. Ideker received Bachelor’s and Master’s degrees from MIT in Electrical Engineering and Computer Science and his Ph.D. from the University of Washington in Molecular Biology under the supervision of Dr. Leroy Hood. Dr. Ideker’s research is led by the vision that given the right experimentation and analysis, it will be possible to automatically assemble maps of pathways just as we now assemble maps of genomes. During graduate work, he developed a general iterative framework for how biological systems can be systematically perturbed, interrogated and modeled. This framework laid the foundation for many studies in the discipline of Systems Biology. He demonstrated that biological networks could be integrated with gene expression to systematically map pathways and aligned, like sequences, to reveal conserved and divergent functions. He showed that the best biomarkers of disease are typically not single proteins but aggregates of proteins in networks. Dr. Ideker has founded influential bioinformatic tools including Cytoscape, a popular network analysis platform which has been cited >12,000 times. Ideker serves on the Editorial Boards for Cell, Cell Reports, Nature Scientific Data, EMBO Molecular Systems Biology, and PLoS Computational Biology and is a Fellow of AAAS and AIMBE. He was named one of the Top 10 Innovators of 2006 by Technology Review magazine and was the recipient of the 2009 Overton Prize from the International Society for Computational Biology. His work has been featured in news outlets such as The Scientist, the San Diego Union Tribune, Forbes magazine and the New York Times.

Constance Jeffery, University of Illinois, Chicago

Talk title: The Multiple Lives of Moonlighting Proteins

Phosphoglucose isomerase (PGI) catalyzes the second step in glycolysis, the interconversion of glucose-6-phosphate and fructose-6-phosphate. In mammals, PGI is also the same protein as autocrine motility factor (AMF), an extracellular cytokine involved in breast cancer metastasis.  The combination of an enzyme function and a cytokine function in one polypeptide chain makes PGI a great example of a moonlighting protein.  Moonlighting proteins comprise a class of multifunctional proteins in which a single polypeptide chain performs multiple physiologically relevant biochemical or biophysical functions. Over 300 proteins have been found to moonlight, and it is possible that many other proteins also have additional functions that have not yet been found. The known examples of moonlighting proteins include diverse types of proteins, including receptors, enzymes, transcription factors, adhesins and scaffolds, and different combinations of functions are observed. Moonlighting proteins are expressed in many species and cell types and act in many different biochemical pathways. The diverse examples of moonlighting proteins already identified, and the potential benefits moonlighting proteins might provide to an organism, for example, through coordinating cellular activities, suggest that moonlighting proteins are likely to be common.  Further understanding about the structures and functions of moonlighting proteins can aid in many types of research, interpreting results from proteomics experiments, understanding how different biochemical pathways interact in systems biology, studies of protein evolution, and designing proteins with additional functions. The ability of a protein to moonlight can add to the challenge of predicting the functions of proteins and annotating protein structure and sequence databases because, not only can one protein have one, two, three or more different functions, but even close amino acid sequence homologues might share only one and not all functions.

Speaker Bio: Constance (Connie) Jeffery obtained her B.S. degree at the Massachusetts Institute of Technology and her Ph.D. degree at the University of California at Berkeley, where she studied the E. coli aspartate receptor. During her postdoctoral research at Brandeis University, she learned X-ray crystallography and solved the X-ray crystal structure of the moonlighting protein phosphoglucose isomerase/autocrine motility factor/neuroleukin. She joined the faculty of the University of Illinois at Chicago in 1999. In addition to ongoing studies of moonlighting proteins and construction of the MoonProt Database, the Jeffery lab is using biochemistry, X-ray crystallography, and bioinformatics to study the structures and functions of proteins involved in cancer, tuberculosis, and ulcerative colitis.

Important Dates:

  • Wednesday, January 25, 2017: Call for Abstracts Opens
  • Thursday, April 13, 2017: Abstracts Submission Deadline
  • Wednesday, May 10, 2017: Abstracts Acceptance Notification
  • July 24-25, 2017: Function SIG meeting at ISMB 2017

Talks are sought in, but not limited to, the following topics:

  • Sequence, structure, function connection in proteins
  • Prediction of protein function
  • Evolution of function
  • Biocuration
  • Assessment of function prediction methods
  • Research related to the Critical Assessment of Function Annotation, or CAFA challenge

Programs from previous years

2016 Meeting Program

Start Finish Talk Speaker
9:00 AM 9:10 AM Introduction/Welcome Casey Greene/Mark Wass
9:10 AM 9:25 AM Using PSAMM for integrating functional annotations into phenotypic simulations Ying Zhang
9:25 AM 9:40 AM Rule Mining and Selection for Protein Functional Annotation Rabie Saidi
9:40 AM 9:55 AM Hunting Human Mendelian Disease-Associated Genes Using Matrix Completion with Side information Pooya Zakeri
9:55 AM 10:10 AM System-wide automatic extraction of functional features using eADAGE Jie Tan
10:10 AM 10:45 AM Coffee Break
10:45 AM 11:25 AM Keynote: Modeling the Cell as a Hierarchy of Subsystems Trey Ideker
11:25 AM 11:40 AM The search for functional specificity Jesse Gillis
11:40 AM 11:55 AM GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins Asa Ben-Hur
11:55 AM 12:10 PM Explicit Site-specific Function Prediction: automatically inferring function labels for protein regions Richard Bonneau
12:10 PM 12:25 PM Predicting Functional Relationships In Osteoblasts Jacob Luber
12:25 PM 1:40 PM Lunch
1:40 PM 2:20 PM Keynote: The Multiple Lives of Moonlighting Proteins Constance Jeffery
2:20 PM 2:35 PM Utilizing computed chemical properties to characterize the functions of Structural Genomics proteins Caitlyn Mills
2:35 PM 2:50 PM Genome-scale prediction of moonlighting proteins using diverse protein association information Daisuke Kihara
2:50 PM 3:05 PM The Bologna Annotation Resource (BAR 3.0): improving the functional annotation of protein sequences Giuseppe Profiti
3:05 PM 3:20 PM Tribe: a version-control server for user-created gene sets Rene Zelaya
3:20 PM 4:05 PM Coffee and Posters
4:05 PM 4:20 PM Computational prediction of bacterial type III effector proteins Tatyana Goldberg
4:05 PM 4:50 PM CAFA3: The Road Ahead Iddo Friedberg/Casey Greene
4:50 PM 5:00 PM Concluding remarks and awards Casey Greene/Mark Wass
NOTE: 5:30pm opening reception for ISMB

The Function-SIG meeting is funded, in part, by awards DBI-1458359 and DBI-1458477 from the US National Science Foundation.
In the past, the Function-SIG meetings were funded, in part, by R13 HG006079 and R13 HG007807 from the US National Institute of Health, as well as US Department of Energy grant DE-SC0006807TDD.