Join us at the Great Lakes Bioinformatics Conference 2013 in Pittsburgh, PA!

SAVE THE DATE! GLBIO 2014 May 16 - 18, 2014 Cincinnati Children’s Hospital Medical Center Cincinnati, Ohio.
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Connect with us!
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Program Book (pdf) >> Click Here <<

The conference is organized by the Great Lakes Bioinformatics Consortium to provide an interdisciplinary forum for the discussion of research findings and methods. An important goal for the conference is to foster long term collaborative relationships and networking opportunities within the domain of computational approaches to biology. GLBIO 2013 is co-hosted by Carnegie Mellon University and the University of Pittsburgh, with the conference taking place on the Carnegie Mellon campus. The program will include oral presentations, poster presentations, invited keynote speakers and tutorials.

Mark your calendar today and join us at GLBIO 2013, May 14-16, 2013.

ONSITE REGISTRATION
Registration will be in the Wean Commons (1st Floor) of University Center on Monday, May 13 from 4pm to 6pm and again Tuesday, May 14 at 8:00am. The registration desk will be open throughout the conference hours.

NEW IN 2013, THE GLBIO CAREER FAIR! Connecting employers with job seekers in computational biology and bioinformatics.

• Employers/Recruiters
• Post jobs
• online at the GLBIO website (link is forthcoming) prior to and during the conference
• onsite at conference jobs board
• on the ISCB Careers site for 90 days after the conference.

Sign up now! (Click here)

• Job Seekers
• Search job postings freely
• Network and schedule interviews
• Resume/CV review and one-on-one career advice available throughout the conference
• Attend a career development session

The CV, the Resume, and the Scientist's Job Search: What to Use, When and Why
Presenter: Joe Tringali
Session Sponsor: FASEB MARC Program

Any job search is, at its very core, a self marketing campaign. The best strategy is one that targets your message to the specific audience in order to help them move your candidacy forward. In this session, we will discuss who the audience may be, the message you might wish to convey, the vehicle in which it is conveyed, and the concept of message consistency. Our objective is to maximize the return you get on your efforts

Sponsors and Exhibitors will get the benefit of complimentary posting(s) with their booths or sponsorship. The packages are listed below.

CLICK HERE to download the promotional flyer (pdf).

KEYNOTES

	Ivet Bahar University of Pittsburgh www.ccbb.pitt.edu/Faculty/bahar/ Title: Protein Dynamics: Relevance to Sequence Evolution and Drug Discovery > Click here for presentation details <
	Ziv Bar-Joseph Carnegie Mellon University www.cs.cmu.edu/~zivbj/ Title: Reconstructing Dynamic Networks in Development and Disease > Click here for presentation details <
	Jing Li Case Western Reserve University http://engr.case.edu/li_jing/ Title: Haplotype Reconstruction in Large Pedigrees: Recent Development and Applications > Click here for presentation details <
	Isidore Rigoutsos Thomas Jefferson University http://cm.jefferson.edu/people/rigoutsos.html Title: Unraveling the Rules of MicroRNA Targeting: Towards an "Expanded" Model > Click here for presentation details <

EDUCATION SESSION - Wednesday, May 15, 2013
3:45pm – 5:30pm, Location: Connan

Educating Biologists and Bioinformatics Professionals for the Future - Are We Getting It Right?
Panel Co-Chairs: Guenter Tusch, Grand Valley State U, and Sarah Elgin,Washington U in St. Louis

TUTORIAL SESSIONS - Tuesday, May 14, 2013, Location: McConomy

TUTORIAL 1
9:00 am - 11:00 am
Spatial Rule-based Modeling of Cellular Biochemistry with MCell/BioNetGen/CellBlender
James Faeder, University of Pittsburgh School of Medicine
Markus Dittrich, Pittsburgh Supercomputing Center
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
TUTORIAL 2
12:00 pm - 2:00 pm
Exploring and Enabling Biomedical Data Analysis with Galaxy
Chair: Anton Nekrutenko, Penn State University
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
TUTORIAL 3
2:30 pm - 4:30 pm
Machine Learning in High Dimension for Genomic Data Analysis
Chairs: Seyoung Kim, Machine Learning in Biology

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Great Lakes Bioinformatics Conference 2013

News

Connect with us!
*********
Program Book (pdf) >> Click Here <<

NEW IN 2013, THE GLBIO CAREER FAIR! Connecting employers with job seekers in computational biology and bioinformatics.

• Employers/Recruiters
• Post jobs
• online at the GLBIO website (link is forthcoming) prior to and during the conference
• onsite at conference jobs board
• on the ISCB Careers site for 90 days after the conference.

Sign up now! (Click here)

• Job Seekers
• Search job postings freely
• Network and schedule interviews
• Resume/CV review and one-on-one career advice available throughout the conference
• Attend a career development session

The CV, the Resume, and the Scientist's Job Search: What to Use, When and Why
Presenter: Joe Tringali
Session Sponsor: FASEB MARC Program

Any job search is, at its very core, a self marketing campaign. The best strategy is one that targets your message to the specific audience in order to help them move your candidacy forward. In this session, we will discuss who the audience may be, the message you might wish to convey, the vehicle in which it is conveyed, and the concept of message consistency. Our objective is to maximize the return you get on your efforts

Sponsors and Exhibitors will get the benefit of complimentary posting(s) with their booths or sponsorship. The packages are listed below.

CLICK HERE to download the promotional flyer (pdf).

KEYNOTES

	Ivet Bahar University of Pittsburgh www.ccbb.pitt.edu/Faculty/bahar/ Title: Protein Dynamics: Relevance to Sequence Evolution and Drug Discovery > Click here for presentation details <
	Ziv Bar-Joseph Carnegie Mellon University www.cs.cmu.edu/~zivbj/ Title: Reconstructing Dynamic Networks in Development and Disease > Click here for presentation details <
	Jing Li Case Western Reserve University http://engr.case.edu/li_jing/ Title: Haplotype Reconstruction in Large Pedigrees: Recent Development and Applications > Click here for presentation details <
	Isidore Rigoutsos Thomas Jefferson University http://cm.jefferson.edu/people/rigoutsos.html Title: Unraveling the Rules of MicroRNA Targeting: Towards an "Expanded" Model > Click here for presentation details <

EDUCATION SESSION - Wednesday, May 15, 2013
3:45pm – 5:30pm, Location: Connan

Educating Biologists and Bioinformatics Professionals for the Future - Are We Getting It Right?
Panel Co-Chairs: Guenter Tusch, Grand Valley State U, and Sarah Elgin,Washington U in St. Louis

TUTORIAL SESSIONS - Tuesday, May 14, 2013, Location: McConomy

TUTORIAL 1
9:00 am - 11:00 am
Spatial Rule-based Modeling of Cellular Biochemistry with MCell/BioNetGen/CellBlender
James Faeder, University of Pittsburgh School of Medicine
Markus Dittrich, Pittsburgh Supercomputing Center
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
TUTORIAL 2
12:00 pm - 2:00 pm
Exploring and Enabling Biomedical Data Analysis with Galaxy
Chair: Anton Nekrutenko, Penn State University
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
TUTORIAL 3
2:30 pm - 4:30 pm
Machine Learning in High Dimension for Genomic Data Analysis
Chairs: Seyoung Kim, Machine Learning in Biology

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Great Lakes Bioinformatics Conference 2013

Key Dates

FOR QUESTIONS, PLEASE CONTACT

Meeting Coordinator:
Joyce Perhac
Ph: (412) 372-1899
Email:  This email address is being protected from spambots. You need JavaScript enabled to view it.

Great Lakes Bioinformatics Conference 2013

Registration

• ONSITE REGISTRATION
  Registration will be in the Wean Commons (1st Floor) of University Center on Monday, May 13 from 4pm to 6pm and again Tuesday, May 14 at 8:00am.  The registration desk will be open throughout the conference hours. 
  

• Registration form (.pdf) >> Click Here <<

Updated May 09, 2013

Links within this page:  Regular Registration Rates  |  Other Items  |  Cancellation Policy

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Great Lakes Bioinformatics Conference 2013

Accommodations

Updated April 10, 2013

Discounted rates have been secured for the GLBIO2013 conference.

Wyndham Pittsburgh University Center
(Previously the Holiday Inn University Center. All current reservations will be valid.)

100 Lytton Avenue
Pittsburgh, PA 15213
Phone: (412) 682-6200
Fax: (412) 681-4749

GLBIO rooms: Single or Double $141.00 plus tax until April 23, 2013. After this date, rooms are on availability basis only. Current room tax is 14%.

Reservations:

Reservations can be made by using this link to the Wyndham Pittsburgh University Center hotel (formerly Holiday Inn University Center). www.wyndham.com/hotels/47154 

Enter your arrival and departure dates and the Group Code:  05136841GLB to receive the discount rate of $141/night.

By Phone: Call the Hotel reservation directly at (412) 682-6259 during regular business hours and mention GLBIO Conference for discounted rates.

A credit card is required to reserve a room.

Hotel Reservation Information: For general registration questions or any difficulties, call during regular business hours and ask for Reservation Manager, Lauren Cahill (412) 682-6259.

Checkin Time: 4:00pm
Checkout Time: 11:00am

Cancellation Policy: Individual reservations may be cancelled up to 4:00pm 24 hours prior to arrival without penalty. Cancellations received within 24 hours or less prior to arrival will be subject to a penalty of one night’s room and tax.

Parking Charges: Parking is available for hotel guests at $10.00 per day

Driving Directions
Follow signs for I-376 East, take Exit 3A (Forbes Avenue/Oakland). This will put you right onto Forbes Avenue. Follow until you get to South Bellefield Avenue and make a Left. Follow South Bellefield to Fifth Avenue and make a Left. Follow Fifth Avenue to Lytton Avenue and make a Right. Hotel will be on Right.

Airport or train to hotel: See website information  www.wyndham.com/hotels/pennsylvania/pittsburgh/wyndham-pittsburgh-university-center/hotel-overview

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Great Lakes Bioinformatics Conference 2013

Conference Location

The GLBIO 2013 conference is being held at Carnegie Mellon University Campus at the University Center in Pittsburgh, Pennsylvania, southwestern Pennsylvania approximately 22 miles from the Pittsburgh International Airport.

UNIVERSITY CENTER

5032 Forbes Ave.           
Pittsburgh, PA 15213       
(412) 268-2107   

CAMPUS MAP

Campus Map - www.cmu.edu/about/visit/campus-map.shtml (University Center #30 on map)

Directions/Parking:  www.cmu.edu/about/visit/directions-parking.shtml 

TRANSPORTATION

By Air
The Pittsburgh International Airport is 22 miles (approximately 45 minutes driving time) from the Carnegie Mellon campus. For more information, please visit FlyPittsburgh (www.flypittsburgh.com/) or call 412-472-3525.

Ground Transportation
Once you arrive at the Pittsburgh International Airport there are several transportation options to bring you to campus or to your hotel:

• Taxi service.The average taxi fare from the airport to campus is about $40-$45, plus gratuity. There are typically taxi cabs outside of the airport, but if you need to call a service, call Yellow Cab (412-321-8100) or Classy Cab (412-322-5080).
  
  
• Rental Car. You can rent a car on-site at the Pittsburgh International Airport. For more information, including a list of car rental agencies and phone numbers, please refer to the transportation services (www.flypittsburgh.com/car_rental) section of the Pittsburgh International Airport website.
  
  
• Public Bus Transportation with Port Authority Transit. The 28X Airport Flyer (www.portauthority.org/paac/) bus stops in the heart of the Carnegie Mellon campus and typically takes 45 minutes en route to the airport. The trip is free for Carnegie Mellon students and costs $2.75 for other passengers. For more information about schedules and rates, please visit the official PAT website (www.portauthority.org/paac/)  or call 412-442-2000.
  
  
• Super Shuttle. Super Shuttle (www.supershuttle.com/Locations/PITAirportShuttlePittsburgh.aspx) provides shuttle service between the airport and downtown hotels. For reservations, contact Super Shuttle at 1-800-258-3826.
  
  
• Hotel Shuttle Service. Because many hotels offer a complimentary shuttle from the airport to the hotel and then on to Carnegie Mellon, please inquire about this option when making your lodging reservations. Please refer to the transportation services  (www.flypittsburgh.com/limousines_taxis_buses) section of the Pittsburgh International Airport website for further contact information.
  

By Bus 
The Greyhound Lines (www.greyhound.com/en/locations/terminal.aspx?city=171150) bus terminal is located less than eight miles from campus in downtown Pittsburgh. For a detailed transportation schedule, call Greyhound at 1-800-231-2222. The Pittsburgh station is located at 55 11th Street and can be reached at 412-392-6513.

By Train
The Amtrak Train Station-Pittsburgh (www.amtrak.com/servlet/ContentServer?pagename=am/am2Station/Station_Page&code=PGH) is located at 1100 Liberty Avenue, less than five miles from campus. For information on rates and schedules, call Amtrak at 1-800-872-7245.

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Great Lakes Bioinformatics Conference 2013

Travel Fellowships

Travel Awards are available through FASEB MARC Travel Award opportunities (www.faseb.org/MARC-and-Professional-Development/Travel-Awards.aspx). The deadline for submitting a request is April 2, 2013.

Great Lakes Bioinformatics Conference 2013

Full Agenda

Connect with us!

Great Lakes Bioinformatics Conference 2013

Agenda at a Glance

Please check back for updates to this page. 

Great Lakes Bioinformatics Conference 2013

Keynote Speakers

updated April 04, 2013

	Ivet Bahar University of Pittsburgh www.ccbb.pitt.edu/Faculty/bahar/ Title: Protein Dynamics: Relevance to Sequence Evolution and Drug Discovery Abstract: Most proteins are molecular machines. They undergo collective motions under physiological conditions. These motions are uniquely defined by their 3-dimensional structure. Several studies in the last decade further showed that these structure-encoded motions, also called intrinsic dynamics, are relevant to biological function. For example, transporters alternate between outward- and inward-facing conformers to enable uptake and release of substrate from the extracellular and intracellular media, respectively; many allosteric machines undergo cooperative transitions between tense and relaxed conformers during their allosteric cycles; or many enzymes fluctuate between closed and open substates in order to accommodate ligand binding and stabilization. These observations brought up new questions with regard to the significance of intrinsic dynamics in the evolutionary selection of structure. The selected structures are not only those maintaining their stability in response to possible mutations, but also those possessing suitable intrinsic flexibilities to accomplish functional changes in conformation. Notably, these properties have important implications with regard to drug discovery. Recent years have indeed drawn attention to two challenging issues in computer-aided assessment of protein targets: First, proteins are not static entities, and drugs need to be designed to bind these moving targets. Second, not all proteins present druggable sites. Accurate evaluation of target druggability and flexibility is key to discovering potent inhibitors of allosteric interactions, and this goal is within reach with significant progresses made in recent years on modeling protein dynamics and assessing druggability. Biography: Professor Ivet Bahar is the John K. Vries Chair of Computational & Systems Biology at the University of Pittsburgh (Pitt), School of Medicine. She joined the School of Medicine at Pitt in 2001 to start a new Center for Computational Biology and Bioinformatics, as a Professor in the Department of Molecular Genetics and Biochemistry. She founded the Computational Biology Department in 2004, and the Department of Computational & Systems Biology, in 2009. She also founded the Joint PhD Program in Computational Biology between Carnegie Mellon University (CMU) and the University of Pittsburgh (together with Prof RF Murphy, CMU co-director) in 2005. Prior to joining Pitt, Dr. Bahar worked as an Assistant Professor (1986-87), Associate Professor (1987-1993) and Professor (1993-2001) at the Chemical Engineering Department of Bogazici University, Istanbul Turkey. She served as the Director of the Polymer Research Center at the same university (1993-2000). She authored more than 200 scientific papers, which received more than 8,000 citations to date. She is an elected member of the European Molecular Biology Organization (EMBO) and is currently serving on several national and international scientific review and/or advisory committees.
	Ziv Bar-Joseph Carnegie Mellon University www.cs.cmu.edu/~zivbj/ Title: Reconstructing Dynamic Networks in Development and Disease Abstract: Transcriptional gene regulation is a dynamic process and its proper functioning is essential for all living organisms. We have been developing methods to integrate time series data (including gene expression and protein-DNA interaction data) with static data (including sequence and protein interactions) for reconstructing such networks. The models take into account various aspects of post-transcriptional regulation including temporal regulation by microRNAs and provide a link between regulatory and signaling networks that explains the observed activation of genes. I will discuss the application and experimental validation of predictions made by our methods for studying lung development in mice and immune response in humans. Results from this analysis indicate that some disease progression pathways may represent partial reversal developmental processes. Biography: Ziv Bar-Joseph is an Associate Professor in the Lane Center for Computational Biology and the Machine Learning Department at the School of Computer Science at Carnegie Mellon University. His work focuses on the analysis and integration of static and temporal high throughput biological data for systems biology and on improving algorithms for distributed computational networks by relying on our increased understanding of how biological systems operate and what makes them robust and adaptable. Dr. Bar-Joseph has been the co-chair of the RECOMB meeting on Regulatory Networks and Systems Biology and is currently an associate editor of Bioinformatics. He received his Ph.D. from the MIT in 2003. He was the recipient of the DIMACS-Celera Genomics Graduate Student Award in Computational Molecular Biology and the NSF CAREER award. Most recently he was named the 2012 recipient of the Overton prize in computational biology, awarded annually by the International Society for Computational Biology (ISCB).
	Jing Li Case Western Reserve University http://engr.case.edu/li_jing/ Title: Haplotype Reconstruction in Large Pedigrees: Recent Development and Applications Abstract: Haplotypes can provide important information for understanding genetics of human traits. However haplotypes cannot be obtained directly using current genotyping/sequencing platforms, which stimulates extensive investigations of computational methods to recover such information. In this talk, I will mainly discuss some recent developments in addressing computational challenges for haplotype inference from large families with many ungenotyped members. I will also discuss some applications that can take advantage of the inferred haplotypes. Biography: Dr. Jing Li is an Associate Professor in the department of Electrical Engineering and Computer Science at Case Western Reserve University. He received B.S. in Statistics from Peking University in 1995 and Ph.D. in Computer Science from the University of California - Riverside in 2004. Dr. Li's research mainly focuses on the development of efficient computational algorithms in computational molecular biology and bioinformatics. More information about his work can be found at http://engr.case.edu/li_jing
	Isidore Rigoutsos Thomas Jefferson University http://cm.jefferson.edu/people/rigoutsos.html Title:   Unraveling the Rules of MicroRNA Targeting: Towards an "Expanded" Model Abstract:  MicroRNAs (miRNAs) are short non-coding RNAs that regulate their target's expression in a sequence-dependent manner. Ever since the first reported animal heteroduplex in 1993 it has been clear that a portion of the 5´ region of a miRNA plays a central role in the recognition of the miRNA’s target. This portion typically spans positions 2-7 from the miRNA’s 5´ end and is known as the ‘seed.’ For the past decade, miRNA targeting has been studied largely under the paradigm of the standard model that calls for Watson-Crick base-pairing in the seed region with targets that are located primarily in the 3´ untranslated regions of protein-coding genes and are typically conserved across organisms.   In recent years, we and others have been reporting specific examples of miRNA:mRNA heteroduplexes that are functionally important and transcend the standard model. These examples revealed that base-pairing in the seed region is not contingent solely upon Watson-Crick coupling and that partial sequence complementarity, in the form of G:U wobbles and bulges, within the seed region is in fact permissible and leads to functioning heteroduplexes.  Also, using molecular dynamics simulation of the Argonaute silencing complex, we demonstrated that non-standard heteroduplexes whose ‘seed’ region includes several G:U wobbles and/or bulges are admissible and do not affect the stability of the complex.  These findings support what we have been referring to as the "expanded" model of miRNA:target interactions.  In this presentation, I will describe our latest results on miRNA targeting and miRNA promiscuity, and discuss sequence (Watson-Crick vs. wobble) and architecture (bulge vs. no bulge) preferences in the seed region that emerge from our analyses. Biography:  Dr. Rigoutsos is the Director of the Computational Medicine Center at Thomas Jefferson University (TJU). He joined TJU in early 2010 as a Professor in the Department of Pathology, Anatomy & Cell Biology. He also has joint appointments in the Department of Cancer Biology, and the Department of Biochemistry & Molecular Biology, and is a member of the Kimmel Cancer Center at TJU.  For nearly 18 years prior to joining TJU, Dr. Rigoutsos was with IBM's Thomas J. Watson Research Center where he founded and managed the Bioinformatics and Pattern Discovery group. In parallel to his IBM tenure, Dr. Rigoutsos was for a decade a Visiting Lecturer at MIT's Dept. of Chemical Engineering where he taught graduate-level classes and summer professional courses in Bioinformatics. Dr. Rigoutsos’ involvement in the field of Computational Biology spans more than twenty years. During this time, he has been developing computer algorithms for studying genomic architecture and biological sequences and analyzing very large biological datasets. Since 1996, his efforts have revolved around the theoretical and practical aspects of pattern discovery and the design of pattern-based solutions to a variety of problems from genomics, genetics, molecular biology and medicine.  Starting in 2002, Dr. Rigoutsos’ work placed particular emphasis on the study of non-coding RNAs (microRNAs, pyknons, piRNAs, etc.). Of particular interest are the questions surrounding the biogenesis of such non-coding RNAs, the mechanisms of action and the discovery of their targets, the discovery of novel organism-specific regulatory sequences, and the elucidation of the roles of non-coding RNAs in the onset and progression of disease.
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