PROGRAM SCHEDULE

*Children under 18 MUST be accompanied by their parent (parents also need to register individually for a ticket).

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KEYNOTE SPEAKER

Dr. David Fenstermacher is currently the Vice President R&D-Bioinformatics at Medimmune, LLC. With more than 30 years of research experience as a molecular biologist and bioinformaticist, he has held several academic appointments at multiple universities and participated in several national and international informatics projects.

During his eighteen years in biomedical informatics, David has designed and directed the implementation of numerous bioinformatics and biomedical informatics distributed computing systems to support basic, translational and clinical research, including multiple institution research projects. He has also designed data warehouses that integrate patient-level clinical data, genomics (genome-wide association studies, massively parallel sequencing, array-based technologies) and other ‘omics data to support studies focused on cancer and other human diseases. Data management systems designed by David have included: collection and integration of subject clinical data; data quality methodologies, development of web-based forms for input, storage and retrieval of clinical and research data, customized data representations using data governance principles and data sharing technologies. Most recent academic research focused on developing informatics resources that span the informatics continuum of Bioinformatics, Biomedical Informatics and Clinical/Medical Informatics specifically for precision medicine including clinical decision support, and health outcomes research.

Before joining MedImmune, David served as the Chief Research Information Officer for Virginia Commonwealth University (VCU) and was Founding Chair of the Department of Biomedical Informatics at the H. Lee Moffitt Cancer Center.

David received his B.S. in Biology from Bloomsburg University of Pennsylvania and his PhD in Molecular Biology and Genetics from the University of North Carolina at Chapel Hill.

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LOCATION & PARKING

Click here to download PDF of the George Mason University map.

Parking: There is about a 5-10 minute walk from Mason Pond Parking Deck to Innovation Hall. Please plan accordingly.

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THE STORY BEHIND THE SYMPOSIUM

Please check back soon for updates.

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ISCB Hosts the Second Youth Bioinformatics Symposium

The International Society for Computational Biology (ISCB) in partnership with George Mason University, will host the Youth Bioinformatics Symposium (YBS), Exploring Computational Biology at George Mason University in winter 2019.

At our first YBS, in 2016, nearly 100 students from the greater Washington DC area gathered for this event. This engaging one-day event introduces students to the amazing world of computational biology, allowing them to engage with and learn about three popular tools used in research in our hands-on workshop, inform them of the many career areas that bioinformatics is now appearing in, and spark the spirit of competition in our team-based mini science challenges.

We hope you join us to make YBS 2019 just as successful!

REGISTRATION IS NOW CLOSED

Click here to see the 2016 symposium photos.

What IS computational Biology?! Watch this video to find out and click here for additional resources.

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TECHNOLOGY TALKS

Bioinformatics as the main protagonist of the microbiome field

Speaker: Dr. Daniel Almonacid

The human microbiome, the microorganisms that live in and on the human body, is one of the most diverse ecosystems on Earth. Our mission at uBiome is to advance the science of the microbiome and make useful products that improve human life. The company’s technological platform is based on the largest microbial dataset in the world (over 300,000 samples), allowing us unprecedented coverage of the microbial diversity across multiple sites of the human body. Using nucleotide sequencing, including our own approach called Precision Sequencing TM, bioinformatics, and machine learning methods, we are developing precision medicine solutions based on microbiome information, empowering doctors, patients, and citizen scientists to improve their quality of life.

Our current portfolio goes from tools for citizens scientists to study their own microbial communities (Explorer TM), to screening tests that can inform doctors of conditions associated with intestinal health (SmartGut TM) and vaginal health (SmartJane TM). The information generated with these analyses allow us continuous improvement of these products.  Additionally, we continually monitor the scientific literature to add new targets as well as novel correlations in our tests. Moreover, the sequencing information combined with the metadata collected from patients has allowed us to discover novel correlations between the microbiome and host conditions, some of which we have been able to understand mechanistically. This knowledge has presented uBiome with the opportunity to in silico design and test drugs that target the microbiome (drugs for bugs), drugs that are naturally produced by the microbiota to modulate the host (drugs from bugs), in addition to identifying and testing potential live biotherapeutics for different health conditions (bugs as drugs).

In this talk I will provide an overview of the work that we are currently doing at uBiome, emphasizing the use of reproducible approaches (both in the laboratory and bioinformatics).  This talk will also highlight the road that uBiome is taking from the research and implementation of clinical tests, toward the development of therapeutics products, having bioinformatics as the main protagonist.

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TOP 10 PAPERS READING LIST, 2016-2017

As selected at RECOMB/ISCB Regulatory systems Genomics 2017
(Papers are listed alphabetically by title.  Due to a draw, this year's list contains 11 papers.)

A prior-based integrative framework for functional transcriptional regulatory network inference, Siahpirani A, Roy S. Nucleic Acids Res 45(4):e21

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data, Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. Nat Methods 14(10):975-978

Denoising genome-wide histone ChIP-seq with convolutional neural networks, Koh PW, Pierson E, Kundaje A. Bioinformatics 33(14):i225-i233

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions, Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M. Nat Biotechnol 34(11):1180-1190

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility, Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. PLoS Comput Biol 13(1):e1005311

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network, Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Genome Biol 18:141

Is a super-enhancer greater than the sum of its parts?, Dukler N, Gulko B, Huang YF, Siepel A. Nat Genet 49:2-3

Quantifying the impact of non-coding variants on transcription factor-DNA binding, Zhao J, Li D, Seo J, Allen AS, Gordan R. Res Comput Mol Biol 10229:336-352

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet 49(10):1428-1436

SMiLE-seq identifies binding motifs of single and dimeric transcription factors, Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. Nat Methods 14(3):316-322

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models, Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Mol Syst Biol 13(2):910

CONGRATULATIONS TO ALL AUTHORS!

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PROMOTION

Click here to download flyer (pdf)

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GETTING TO NYC

Links within this page:
Plane | Train | Bus | Car

Whether you live across the Hudson or across the Atlantic, getting to NYC is easy. If you’re coming from outside the United States, check this page for visa information.

See below for the best ways to reach the five boroughs from anywhere in the world.

By plane If you’re coming from far away, you’ll probably want to fly into one of the New York City area’s major airports. There are a number of hotels conveniently located near the City’s airports.

• By Plane
• By Train
• By Bus
• By Car

By Plane

Below, you'll find a list of NYC-area airports, along with the best ways to get from those airports to Manhattan. There are more than a hundred air carriers traveling to NYC from all over the country and the world, including American Airlines, Delta, JetBlue and United.

Air travelers to New York City may arrive at John F. Kennedy International Airport (JFK) or LaGuardia Airport (LGA), both in Queens, or Newark Liberty International Airport (EWR) in neighboring New Jersey. LaGuardia primarily serves domestic destinations, and also offers flights to select Canadian and Caribbean destinations. Kennedy and Newark both serve domestic and international destinations. Visitors can reach Manhattan from all three airports by using taxis, buses, subways and/or commuter trains. Other metropolitan-area airports include Stewart International Airport (SWF), Westchester County Airport (HPN) and MacArthur Airport (ISP). For those interested, there are a number of hotels conveniently located near the City's airports.

John F. Kennedy International Airport (JFK)
Jamaica, Queens, NY 11430
718-244-4444

New York's largest airport serves more than 80 airlines, most of which are international. It is approximately 15 miles from Midtown Manhattan. Here's how to get to Midtown Manhattan from JFK:

• Taxi: $52.50 flat fare (non-metered), plus bridge and tunnel tolls and gratuity; 30 to 60 minutes to Midtown Manhattan, depending on traffic and road conditions. For more information, call 212-NYC-TAXI or visit the Taxi and Limousine Commission website.
• AirTrain JFK: $5 (children under 5 are free); AirTrain links the airport to the subway and Long Island Rail Road. AirTrain also offers free service between points in the airport.
• Subway: one ride (in addition to AirTrain fare) from the A subway stop at the Howard Beach/JFK Airport station or the E, J or Z subway stop at the Sutphin Blvd./Archer Ave./JFK Airport station; 60 to 75 minutes to Midtown Manhattan.
• Long Island Rail Road (LIRR): $7.25–$10 (children under 5 are free), depending on time of day (in addition to AirTrain fare) for the trip between LIRR's Jamaica Station and Penn Station; on Saturday and Sunday, the fare is $4.25. The trip is 20 minutes to Midtown Manhattan (not including AirTrain ride).
• City bus: For details, visit tripplanner.mta.info.
• Shuttle bus: NYC Airporter, Go Airlink NYC and SuperShuttle.
• Private car service: See this list of providers.
• Car rental: Companies at JFK include Avis, Budget, Dollar, Enterprise, Hertz and National.

LaGuardia Airport (LGA)
Jackson Heights, Queens, NY 11371
718-533-3400

This is New York's second-largest airport, with nearly 20 airlines serving mostly domestic destinations, as well as Canada and the Caribbean, from four passenger terminals. LaGuardia is on the northern shore of Queens, directly across the East River (about 8 miles from Midtown Manhattan). Here's how to get to Midtown Manhattan from LaGuardia:

• Taxi: Approximately $29–$37 metered fare, plus bridge and tunnel tolls and gratuity; 20 to 25 minutes to Midtown Manhattan. For more information, call 212-NYC-TAXI or visit the Taxi and Limousine Commission website.
• City bus: Two express buses serve LaGuardia; the M60 and Q70. The Q70 goes nonstop to Jackson Heights/Roosevelt Avenue, a major subway hub in Queens with five lines. The M60 runs to Harlem and connects to all the major subway lines in Manhattan. For details, visit tripplanner.mta.info.
• Shuttle bus: NYC Airporter, Go Airlink NYC and SuperShuttle.
• Private car service: Dial 7, Carmel and Uber.
• Car rental: Companies at LGA include Avis, Budget, Dollar, Enterprise, Hertz and National.

Newark Liberty International Airport (EWR)
Newark, NJ 07114
973-961-6000

Newark Airport, with more than 30 airlines (many of which are international), is across the Hudson River from New York City—16 miles from Midtown Manhattan. Here's how to get to Midtown Manhattan from Newark Liberty:

• Taxi: Traveling to Manhattan, metered fare; approximately $50 to $75, plus bridge and tunnel tolls and gratuity; 45 to 60 minutes to Midtown Manhattan. During weekday rush hours (6–9am and 4–7pm) and on weekends (Saturday–Sunday, noon–8pm), there is a $5 surcharge for travel to anywhere in New York State except Staten Island. When traveling to the airport from Midtown Manhattan, service is via New York City’s regulated yellow taxis. Metered fares range $69–$75, plus a $17.50 surcharge in addition to tolls and gratuity.
• AirTrain Newark: Costs vary by destination. AirTrain links to the airport via NJ Transit and Amtrak's Newark (or EWR) train station; 45 to 90 minutes to Midtown Manhattan, requiring a transfer from the AirTrain line to the NJ Transit line (be sure to keep your ticket after using it to exit the AirTrain station, as it is also used for the NJ Transit fare) or Amtrak. AirTrain also offers free service between points in within the airport complex, including hotels and parking. Look for signs marked “Monorail/AirTrain Link” (do not follow signs for Ground Transportation).
• Shuttle bus: NYC Airporter, Go Airlink NYC, Olympia Airport Express and SuperShuttle.
• Private car and limousine service: Dial 7, Carmel and Uber.
• Car rental: Companies at Newark include Avis, Budget, Dollar, Enterprise, Hertz and National.

Stewart International Airport (SWF)
New Windsor, NY 12553
845-838-8200

Stewart International Airport is 60 miles north of New York City. Here's how to get to Midtown Manhattan from Stewart:

• Bus/train: Leprechaun Lines runs a $1 shuttle bus on their Newburgh-Beacon-Stewart commuter line, which connects to the Beacon train station. There, use Metro-North Railroad for direct service to Grand Central Terminal ($16 off-peak, $21.25 peak); 70 to 90 minutes to Midtown Manhattan.
  

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By Train

New York City has two main rail stations in Midtown: Grand Central Terminal (on the east side) and Penn Station (on the west side). Each is also served by numerous bus and subway lines. Grand Central is served by Metro-North Railroad, which goes to NYC suburbs in New York and Connecticut. Penn Station is served by the following: Long Island Rail Road, a commuter railroad serving Long Island; Amtrak, the US national passenger railroad, serving many points throughout the country; and NJ Transit, a commuter line serving points in New Jersey.

• Rail Terminals
  • Grand Central Terminal
    Park Avenue and East 42nd Street (between Lexington and Vanderbilt Avenues)
    212-532-4900
    Grand Central is the main terminal for Metro-North Railroad services. Subway lines here include the 4, 5, 6, 7 and S (shuttle between Grand Central and Times Square). For MTA bus details, visit tripplanner.mta.info.
    
    Aside from being a transit hub, Grand Central is also a landmark and an attraction unto itself. The Main Concourse boasts an immense 88,000 square feet of space, and on sunny days is bathed in light from its giant arching windows. Grand Central's 12-story ceiling is painted with stars and gilded zodiac constellations. Not only might Grand Central be the globe's most beautiful train station, the 49-acre terminal is also one of the world's largest. There are numerous shops of all varieties here, including an Apple Store, MAC Cosmetics and Tumi. The dining concourse on the lower level features a wide selection of eateries, and in Grand Central Market, fresh and prepared foods—ranging from baked goods to gourmet teas—are available.
    
  • Penn Station
    Seventh to Eighth Avenues, between West 31st and West 33rd Streets
    Penn Station is the main terminal for Long Island Rail Road, and a terminal for Amtrak and NJ Transit. Subway lines here include the 1, 2, 3, A, C and E. For MTA bus details, visit tripplanner.mta.info.
    
    Penn Station's main concourse features information booths, restaurants, waiting rooms and public restrooms to accommodate the thousands of passengers who pass through the terminal each day. In 2016, the new West End Concourse will open providing additional access to the station from 8th avenue. Car rental offices are nearby.
    
• Rail Services
  • Amtrak
    800-872-7245, 212-630-6400
    Amtrak is the national passenger railroad of the United States. New York City's Penn Station is their busiest station in the nation, serving hundreds of thousands of passengers each year. The company offers numerous packages and deals, including special passes allowing international visitors to make multiple stops throughout the country.
  • Long Island Rail Road (LIRR)
    718-217-5477
    This commuter railroad operates out of Penn Station and serves 124 stations in Nassau County, Suffolk County, Queens, Brooklyn and Manhattan, transporting some 81 million customers each year. Destinations include the Belmont Park racetrack, Citi Field, Jones Beach, the Hamptons and Montauk.
  • Metro-North Railroad
    212-532-4900, 877-690-5114
    The second-largest commuter train line in the United States, Metro-North operates out of Grand Central Terminal. The historic roots of the operation go back to 1832, when the enterprise was known as the New York & Harlem Railroad, a horsecar line in Lower Manhattan. Today, with 775 miles of track, Metro-North goes to 121 stations (in seven New York State counties—Dutchess, Putnam, Westchester, Rockland, Orange, Bronx and New York (Manhattan)—and Connecticut's New Haven and Fairfield counties).
  • NJ Transit
    973-275-5555, TTY 800-772-2287
    This rail system features 12 lines in three divisions (Hoboken, Newark and the Atlantic City Rail Line) with frequent service throughout New Jersey (Atlantic City and the Jersey Shore are popular stops) and New York (Rockland and Orange counties)—and, of course, into and out of New York City via Penn Station. For schedules and fares, visit the NJ Transit website.
  • PATH (Port Authority Trans Hudson)
    800-234-PATH
    The PATH provides rapid transit between several stops in New York City, along with locations in Newark, Harrison, Jersey City and Hoboken in New Jersey. Air travelers can connect to the PATH from Newark Liberty International Airport. The service operates from the Penn Station in Newark (not the same as Manhattan's Penn Station) to Lower and Midtown Manhattan. The PATH's 33rd Street station (on Sixth Avenue, in Herald Square) in Manhattan is one avenue from Amtrak, Long Island Rail Road and NJ Transit trains at Penn Station.

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By Bus

There are a number of affordable, convenient bus lines that travel to New York City from around the United States and parts of Canada. These include BoltBus, Megabus and Greyhound.

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By Car

Use Google Maps for driving directions to New York City. Also, make sure you know where to park: you may want to use an app like SpotHero to find and compare parking spots and locations.

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RSG and DREAM General Questions

Bel Hanson, Conference Manager
Tel: 1-571-293-0286

Source: NYC The Official Guide

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