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Reading Papers List, 2017-2018

 



As selected at RECOMB/ISCB Regulatory systems Genomics 2019
(Papers are listed alphabetically by title)

  • A web server for comparative analysis of single-cell RNA-seq data (Nat Commun. 2018) Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z
  • Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data (Cell Systems 2018) Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. O'Neill, David M. Gilbert, Jian Ma
  • Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding (Cell Systems 2018) Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R
  • DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. (PLoS Comput Biol. 2018) Mitra S, Biswas A, Narlikar L
  • Enhancer RNA profiling predicts transcription factor activity (Genome Res. 2018) Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD
  • GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs (Bioinformatics 2018) Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A
  • Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data (Nat Biotechnol. 2018) Zhu Q, Shah S, Dries R, Cai L, Yuan GC
  • Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. (Epigenetics Chromatin 2018) Behjati Ardakani F, Kattler K, Nordström K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH
  • Quantifying the similarity of topological domains across normal and cancer human cell types (Bioinformatics 2018) Sauerwald N, Kingsford C
  • Reconstructing differentiation networks and their regulation from time series single-cell expression data (Genome Res. 2018) Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z
  • SCENIC: single-cell regulatory network inference and clustering. (Nat Methods 2017) Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S
  • SigMat: a classification scheme for gene signature matching (Bioinformatics 2018) Xiao J, Blatti C, Sinha S
  • The impact of rare variation on gene expression across tissues (Nature 2017) Xin Li, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna, Michael C. Bassik, Jason D. Merker, GTEx Consortium, Ira M. Hall, Alexis Battle, Stephen B. Montgomery
  • Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. (Nat Commun. 2017) Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B


CONGRATULATIONS TO ALL AUTHORS!


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CALL FOR SUBMISSIONS FOR TOP 10 READING PAPERS, 2017-2018



As in previous years, we are again planning to assemble a "top 10 papers reading list" in Regulatory and Systems Genomics. Our goal is to identify seminal papers that introduced not only new biological insights, but also key computational methodologies for interpreting biological datasets that we except to have a lasting impact in the field of Computational Regulatory and Systems Genomics. Relevant areas include Motifs, Grammars, Networks, Systems, Variation, Disease, Personal Genomics, GWAS interpretation, Regulatory Evolution, Comparative Genomics, Epigenomics, Physical Modeling, Dataset Integration, Splicing Regulation, Transcriptional Regulation, and all areas of gene and genome regulation at the systems level.

Based on feedback from the community, we modified the format and the timeline of the competition in order to encourage more participation, focus on the papers that are most relevant to our community, and remove any perceived biases during the nomination and voting processing.

The new nomination process is as follows:

  • Authors are asked to nominate their own papers using the nomination form available Here . An author can nominate at most 1 paper. (Please note that during the voting process the nominators will be asked to vote for 5 papers on which they are not authors, in order for their nominated paper to continue to be eligible for this competition. Please use the same email address for nomination and voting.)
  • The deadline for nominations is August 1, 2019.
  • Papers published between Sep 1, 2017 to Dec 31, 2018 are eligible for this year’s competition, as long as the work described in the paper has been presented orally (i.e. selected for platform presentation from the submitted abstracts) at either RegSys at ISMB or RECOMB/ISCB RegSys in 2016, 2017, or 2018. Abstracts selected for short 1-min poster talks are not eligible.


Voting will start on August 2, 2019 and will be open until November 4, 2019 (the first day of the 2019 RECOMB/ISCB RegSys meeting).  Winners will be announced on the last day of the 2019 RECOMB/ISCB RegSys meeting.

We note that if less 25 nominations are received, then we will not move on to the voting phase. So please also encourage your colleagues and collaborators to nominate their papers for the competition.

For additional information and to submit: Click Here


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DREAM Submissions



Call for Papers for DREAM Conference Session and Poster

The DREAM Challenges are crowdsourcing challenges examining questions in biology and medicine.

The DREAM Challenges are an open science effort of crowdsourcing challenges to examine questions in biology and medicine. We are a non-profit, collaborative community effort with contributors from across the research spectrum including universities; technology companies like IBM Research; not for profits, like Sage Bionetworks; and biotechnology and pharmaceutical companies. Since the beginning of the DREAM Challenges in 2006, we have been an innovator and leader in open science and crowdsourcing. The DREAM Challenge participants and organizers have numerous publications in top journals such as Science and Nature. Since the dawn of the DREAM Challenges, commercial crowdsourcing efforts have sprung up which utilize techniques that we pioneered.

Call for late-breaking posters for DREAM Challenge Session
(we are currently accepting abstracts for posters for past DREAM Challenges)

View Open DREAM Challenges

We are excited to have 3 challenges underway and will be part of this year’s conference so look forward to presentations and posters from these challenge’s participants.

Follow the links for each for the challenges to go that challenge’s pages to register and participate in the challenge to present at the conference.  Presenters for papers and posters will submit abstract information for the conference through the Synapse system used for their specific DREAM challenge. 

 

 

Malaria DREAM Challenge: An open innovation framework for discovery of anti-malarial drug combinations

The malaria parasite can quickly adapt to anti-malarial drugs resulting in drug resistance. Understanding the changing biology of malaria parasites as they acquire resistance may be key to preventing the spread of resistance. The goal of the Malaria DREAM challenge is to develop computational models that predict Artemisinin (Art) drug resistance level of a test set of malaria parasites using their in vitro transcription data and a training set consisting of published in vivo and unpublished in vitro transcriptomes.

 

DREAM Preterm Birth Prediction Challenge: Transcriptomic

This DREAM challenge is about developing a molecular clock of pregnancy and assess the risk of preterm birth using maternal whole blood transcriptomics data

 

Illuminating the Druggable Genome (IDG) Drug-Kinase Binding Prediction DREAM Challenge: Catalyzing compound-target interaction mapping

Round 1b of the IDG-DREAM Drug-Kinase Binding Prediction Challenge just ended and Round 2 will be opening to submissions on March 28th, 2019. In the upcoming round, participants are being asked to predict the binding affinity of a brand new set of drug-like molecules and kinases.


DREAM Talk/Poster Track - The DREAM Challenges welcome poster submissions on past DREAM Challenges from groups who have done further retrospective data analysis on the Challenge data. The list of previous DREAM Challenges and links to their data is available here. We also welcome other challenge initiatives to present posters/talks at the DREAM session to share what they are doing and their experiences. We believe this conference is an opportunity to learn from one another on all aspects of the challenges of Challenges.


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RSG Oral and Poster Presentation Submissions



Links within this page:
Late-Breaking Posters | Submit an Oral Presentation | How to Submit your Abstract | Topics | Special Session on Cancer Systems Biology


Late-Breaking Posters

Abstracts are now being accepted for poster presentations in the late-breaking poster track.  Abstracts may be either original unpublished work or original work that was published or accepted for publication at a high-impact journal between January 1, 2019 and November 1, 2019.

Click Here to Submit!

Poster Display Size: - When preparing accepted posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board.

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Submit a Short Talk

The RECOMB/ISCB Conference on Regulatory and Systems Genomics invites abstracts for consideration for oral presentations or participation in a poster session. Abstracts may be either original unpublished work or original work that was published or accepted for publication at a high-impact journal between January 1, 2019 and November 1, 2019. Unpublished work will be considered for either an oral or a poster presentation. Work already accepted for publication will be considered for an oral presentation only.

Key Dates:
Abstract Submission for Oral Presentation deadline: Monday, September 9, 2019
- Author notifications will occur on or around Monday, September 30, 2019
Abstract Submission for Poster deadline: Monday, September 9, 2019
- Author notifications will occur on or around Monday, September 30, 2019

Abstracts received before the due date will be considered for oral and poster presentations.

Any abstracts submitted after the deadline will be included only at the discretion of the conference chairs, and will be eligible for poster presentations only.  Please also note that we can only allow one abstract per presenting author.

Authors reserve the right to publish their work elsewhere.

Poster Display Size: - When preparing accepted posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board.

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How to Submit your Abstract


Please use this link to EasyChair to submit your abstract (400 words or less). You will be asked to provide information about yourself and your coauthors, including name, e-mail address, and affiliation. Please check one box for corresponding author to indicate who would be speaking or would be primarily responsible for your poster. You will also be asked to provide an abstract title, the text of your abstract, and keywords.

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Topics

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Some possible topics include:

  • Network visualization and analysis
  • Regulatory motifs and modules
  • Epigenomics and chromatin state
  • Non-coding RNAs
  • Regulatory networks
  • Co-transcriptional, post-transcriptional, and translational regulation
  • Signal transduction networks
  • Genetic, molecular, and phenotypic variation and human disease
  • Cellular signatures of biological responses and disease states
  • Mathematical modeling and simulation of biological systems
  • Methods for systematic validation of high-throughput biological predictions
  • Single-cell transcriptomics
  • Single-cell proteomics
  • Metabolomics
  • Microbiome
  • Machine learning methods for systems biology
  • Translational systems biology

 
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Special Session on Cancer Systems Biology

Regulatory and Systems Genomics 2019 will include an abstract submissions track for a Special Session of Cancer Systems  We welcome submissions on computational and experimental advances in the systems-level modeling of cancer.  Topics include but are not limited to: regulatory programs and signaling pathways in cancer cells, tumor-immune interactions and the tumor microenvironment, developmental plasticity in tumors and epigenetic analyses, tumor metabolism, genetic and non-genetic sources of heterogeneity, drug response and precision oncology.  The session will include presentations from keynote speakers as well as talks from selected abstracts. This special session is sponsored by the Research Center for Cancer  Systems Immunology at Memorial Sloan Kettering Cancer Center, an NCI-funded Cancer Systems Biology Consortium (CSBC) Center.

Click Here to Submit!


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Getting Here and Around



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

Getting Around
Subway
| Buses | Taxi | Car | Roosevelt Island Tram | Bike | Ferry | Helicopter | NYC Cruise | Traveling with Pets


NYC Marathon 11.3.19

Attendees, travel to RSGDREAM may be disrupted or take longer due to the NYC Marathon.

Please visit the NYC Marathon website for route closures on November 3. 

Travel on November 2 if possible, earlier in the day will be easier than afternoon or evening travel.
Additionally, please view the course map for an idea of where the runners and spectators will be throughout the day on November 3.


Getting Here

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


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:


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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Getting Around

If you can't walk to your destination, mass transit is the next-best way to get around. The City's rail and bus system is run by the Metropolitan Transportation Authority (MTA) and known as MTA New York City Transit. It's inexpensive, environmentally friendly and a great way to see sights throughout the five boroughs—and it operates 24 hours a day, seven days a week.

The system is accessible to passengers with visual, hearing and mobility disabilities. For more information, consult the MTA's accessibility guide and its list of accessible subway stations.

Purchasing a MetroCard is your first step to getting around on subways and buses; you must put a minimum value of $5.50 on the card when initially buying it. You can do so at subway stations, from either automated machines (which accept cash, ATM bank cards and regular credit cards) or booth attendants (cash only). When you use a pay-per-ride MetroCard, a single subway or bus ride costs $2.75. An Express Bus ride costs $6.50. Riders can buy a pay-per-ride card, an unlimited MetroCard or a SingleRide card—the last of these costs $3, is sold at vending machines only, doesn't allow transfers and must be used within two hours of purchase. An unlimited MetroCard allows users to ride as often as they like within a fixed time period: options include unlimited cards that last for seven days ($31) or 30 days ($116.50). There's also a $1 surcharge on the purchase of a new MetroCard. To avoid the charge, customers can refill an existing card. The MTA offers discounts for seniors (over age 65) and disabled riders, as well as a "bonus" credit of 11% for purchases of $5.50 or more on pay-per-ride cards. Also, up to three children with a maximum height of 44 inches each can get on subways and buses for free when they are traveling with a fare-paying adult. For the most up-to-date information on MetroCard prices, visit mta.info.

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Subway

The easiest and quickest way to travel around NYC is by public subway train. Riding the subway is also a fantastic way to feel like a local during your stay in New York.

Fast facts:

  • Subway trains operate 24 hours a day, seven days a week.
  • For $2.75 (the cost of a single ride when using a pay-per-ride MetroCard), you can use the system citywide and transfer to other subway lines as many times as you need, as long as you don't exit the system through a turnstile.
  • You can transfer from bus to subway or vice versa within two hours of using your MetroCard. (The free transfer does not apply if you leave a subway station through a turnstile and want to get on another subway line.)
  • Subway stations on the same line are generally about 8 to 10 blocks apart.
  • The subway does not travel to Staten Island. To get there, board the free Staten Island Ferry or take a bus.
    You can get a free subway map from booth attendants or at any Official NYC Information Center, or download one from our Maps & Guides section. You can also visit the MTA's Trip Planner for a customized route (but it's still a good idea to carry a subway map when you're out and about). The Trip Planner offers routes for MTA bus lines as well. Subway lines sometimes change routes or temporarily stop running—especially on weekends and late nights during weekdays—so be sure to check for up-to-date MTA service information at mta.info or by calling 718-330-1234.


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Busses

Public buses are a scenic way to see the City and reach destinations not convenient to a subway stop. It's also worth noting that mass transit is central to New York City's efforts to become more environmentally friendly, and a growing number of NYC's buses are hybrid-electric models.

Fast facts:

  • All City buses accept the MetroCard and exact coin change (no pennies or paper money).
  • Check the route sign on the front of the bus before boarding to ensure it's the bus you want, and make sure you know if it's making all stops or only "limited" stops (the limited buses don't make all stops along the route).
  • Enter and pay at the front of the bus. The exception to this is on SBS (Select Bus Service) routes, where payment kiosks are on the sidewalk next to the bus stop.
  • A single fare will take you any distance until the end of the route.
  • Many buses are available 24 hours a day, seven days a week, but be sure to check whether your route offers overnight service. A schedule and route map posted at the bus stop indicate when the bus should arrive and where it will go.
  • Buses run about every 5 to 15 minutes, or at longer intervals, depending on the time of day.
  • If you have a smartphone, you can scan the QR code at the bus stop to receive information about when the next bus is expected to arrive.
  • Buses generally stop every other block on avenue routes and every block on cross-street routes. Late at night, from 11pm to 5am, bus drivers will stop wherever you ask them to—as long as they feel it's safe.
  • MTA service information is available at mta.info or by calling 718-330-1234.


The MTA website tripplanner.mta.info is the most reliable source for up-to-date information about routes and fares.

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The Roosevelt Island Tram

With the swipe of a MetroCard, the Roosevelt Island Tram gives you an aerial view of Midtown East along its path from 59th Street and Second Avenue in Manhattan to Roosevelt Island, located in the East River between Manhattan and Queens. The tram got its start in the early 1900s, taking passengers halfway across the Queensboro Bridge, where an elevator would then transport them down to the island. Today, it provides direct service for more than 2 million riders seven days a week (Sunday–Thursday, 6am–2am; Friday–Saturday, 6am–3:30am), with transfers available to MTA subways and buses. For more information, visit rioc.ny.gov.

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Taxi

The City's fleet of yellow taxicabs and green Boro Taxis is regulated by the Taxi and Limousine Commission. Grabbing a cab can be ideal when tired feet, heavy luggage or shopping bags weigh you down.

Fast facts:

  • Taxis are available 24 hours a day.
  • Hail taxis whose numbers are illuminated on top—they're on duty.
  • Board and exit the cab curbside.
  • Hotel doormen can hail a cab for you; a $1 tip is customary for this service.
  • Minimum metered fare is $2.50, which increases 50 cents every fifth of a mile or every minute, depending on how fast you're traveling; there is also a New York State tax surcharge of 50 cents per ride.
  • An additional $1 surcharge is added to the meter Monday–Friday, 4–8pm, and a 50-cent surcharge is added at night, 8pm–6am.
  • All taxis accept cash and most accept credit cards.
  • Tip 15–20% at the end of a trip; tolls are extra and added to the metered fare.
  • Dial 311 in NYC to inquire about lost items or other concerns; visit the Taxi and Limousine Commission website for more info and the organization's fare information page for additional fare details as well as specifics regarding different destinations.


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Car

If you're planning to drive around the City, use Google Maps to help you navigate New York City roads. Also, make sure you know where to park. You may want to use a site like bestparking.com to compare parking rates and locations from a number of companies or an app like SpotHero where you can book a parking spot in advance. Be aware, though, that the site's listings are not complete. If you need to rent a car, it may be worth considering Zipcar and Enterprise which offer car-share programs that allow members to book vehicles for as little as an hour and as long as a week, 24 hours a day.

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NYC by Bike

Biking the City is good for the environment and your body, and can often be faster and cheaper than fuel-powered transportation. Cycling hotspots like Central, Riverside and Prospect Parks are great options for hitting the City on two wheels, as are bike paths along the Hudson and East Rivers and on many bridges—but all of NYC is bikeable. Check out Ride the City to find the safest route from point A to point B and Transportation Alternatives for NYC biking resources. In addition, the NYC Department of Transportation publishes a downloadable bike map and a guide to biking in the City.

Citi Bike is New York City's bike-sharing system, and it has gained a quick adoption since its inception in May 2013. There are thousands of bikes at hundreds of stations, available 24/7 every day of the year. Unlock a bike at any station, ride wherever you want and check in the bike at any other station. Daily, weekly and annual passes are available.

Plenty of operations rent bikes by the half day and full day, with many such places located near the major biking destinations mentioned above. Some, like Bike and Roll New York and Blazing Saddles, also offer guided tours or suggested itineraries for independent exploration.

If you want someone else to do the pedaling for you, hop in a pedicab (sometimes called a "bike taxi" or "bicycle rickshaw"). You won't have to look too hard in the busier parts of Manhattan—the drivers aren't shy about offering their services.

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NYC by Ferry

As a waterfront city, New York is home to an extensive ferry system that can get you uptown, downtown and across the rivers to Staten Island, Brooklyn, Queens, the Bronx and New Jersey.

  • The Staten Island Ferry is a staple of many morning commutes—and taking a ride on it is a must-do on any sightseeing itinerary. In use since 1905, the route between Staten Island and Manhattan's Whitehall Ferry Terminal is a glorious 5-mile, 25-minute mini-cruise with great views of the Statue of Liberty, New York Harbor and Lower Manhattan—and it's free.
  • New York Water Taxi is another popular aquatic shuttle. Hop-on and hop-off stops include Pier 84 (at West 44th Street), Christopher Street, the World Financial Center and Pier 1 in DUMBO. Check nywatertaxi.com for information on schedules and package deals.
  • NY Waterway operates commuter ferries between points in Manhattan and New Jersey, and harbor and sightseeing cruises. The East River Ferry also provides a refreshing alternative to more traditional public transportation in the City (and breathtaking skyline views), with regular service to seven locations across three boroughs. A 74-foot ferry departs every 20 to 30 minutes from approximately 7am to 8:30pm on weekdays and every 45 minutes from approximately 9:30am to 9pm on weekends. Check the official schedule to confirm, as departure times vary in different seasons.


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NYC by Helicopter

Seeing New York by air is an unforgettable experience, and the City offers helicopter tours for the adventurous and just plain curious. Here are some choices:

Liberty Helicopters (800-542-9933) runs several tours of the City; Helicopter Flight Services, Inc. (212-355-0801), will personalize sightseeing tours and charters; and New York Helicopter Charter, Inc. (212-361-6060), allows you to choose from three options: the Liberty Tour, the Central Park Tour and the Grand Tour, which combines the first two tours and also flies over many other essential NYC attractions.

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NYC Cruise Information

New York City is one of America's top cruise ports. Passengers from New York City can cruise to the Caribbean year-round and may also cruise to the Northeast, Canada, Bermuda, England and many other destinations around the world.

Recent infrastructure improvements ensure smooth sailing for the cruise passengers who pass through New York City. In Manhattan, the renovated Manhattan Cruise Terminal welcomes some of the world's most prestigious ships, while the state-of-the-art Brooklyn Cruise Terminal in Red Hook is the port for Cunard and Princess Cruise ships, including the luxurious Queen Mary 2 and the Royal Princess. Below is a listing of information for each terminal.

  • New York Cruise Terminal
    Piers 88, 90 and 92
    711 Twelfth Ave. (at W. 55th St.)
    212-246-5450
  • Brooklyn Cruise Terminal
    Pier 12 at Clinton Wharf
    72 Bowne St. (bet. Van Brunt and Imlay Sts.)


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Travelling with Pets

If you're bringing a dog or cat along on your NYC adventure, you'll have no trouble getting around—but it's important to know the rules.

Only small-size pets in carriers are allowed on MTA buses, subways and trains, as well as in taxis. Properly harnessed service animals are also permitted on mass transit. Taxi drivers may, at their discretion, pick up dogs without carry cases. The City is also home to several pet-taxi companies that can help transport pets that are not allowed on ordinary public transit.

  • Pet Chauffeur: 212-696-9744
  • K9 Cars: 718-683-2152

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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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Accommodations



The Bentley Hotel

The headquarters hotel for RSG 2019, The Bentley Hotel provides an unmatched New York City hotel experience. Settled just outside of the epicenter of the buzzing Midtown activity, you can enjoy a quieter stay while only being a short walk from the conference, Central Park and the historic 5th Avenue shopping district.

It has breathtaking views from the guestrooms of the East River and of the 59th Street Bridge as well as a lobby bar and a penthouse restaurant. Among the multitude of hotels in Manhattan, the Bentley has been ranked as one of the top rated hotels in New York. The convenient location and oasis of comfort featured in each guestroom creates a luxury hotel experience that shouldn’t be missed.

  • Room Rate: $249 for a Superior King per night
  • Includes complimentary WiFi and 24 hour fitness center
  • Discounted room rate is available through October 4, 2019


Please use one of the following to book your reservation:

  • Please use this link to book online.  
  • Call for a reservation at tel: 212-644-6000. Please reference MSK/RSG 2019

ONLINE BOOKING IS NO LONGER AVAILABLE
AND OUR DISCOUNT RATE HAS EXPIRED. 
Please feel free to call the hotel directly to inquire about possibly receiving the group rate.  


Gardens Suites Hotel

Discretely located on the Upper East Side on an intimate, tree-lined street, the all-suite Gardens Suites Hotel is the picture of Manhattan gentility. It’s surrounded by world-class NYC shopping and Manhattan’s famed museums along Central Park, adding grace and charm to its locale. But guests find it’s just right for a tranquil retreat. With such great in-room service, you can simply take to your spacious hotel suite and escape for some alone time.  It is only a  10 minute walk to the conference venue and the Junior suite can accommodate up to Quad occupancy.

215 East 64th St. (between 2nd & 3rd Ave)
New York, NY 10065  

  • Room Rate: $329 for a Junior Suite per night
  • Includes complimentary WiFi, waived facility fee and Wine Hour from 5pm-6pm
  • Discounted room rate is available through October 4, 2019


Please use one of the following to book your reservation: 

  • Book online with our private booking link:  RSGDREAM 2019
  • Call 866-233-4642.  Please identify that you are part of the RSG with DREAM Conference at MSK Block to guarantee the special rate.

ONLINE BOOKING IS NO LONGER AVAILABLE 
AND OUR DISCOUNT RATE HAS EXPIRED.  
Please feel free to call the hotel directly to inquire about possibly receiving the group rate.


NYC Marathon 11.3.19

Attendees, travel to RSGDREAM may be disrupted or take longer due to the NYC Marathon.

Please visit the NYC Marathon website for route closures on November 3. 

Travel on November 2 if possible, earlier in the day will be easier than afternoon or evening travel.
Additionally, please view the course map for an idea of where the runners and spectators will be throughout the day on November 3.


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Venue





Conference Venue:
MSKCC - Rockefeller Research Laboratories
430 E 67th St.
New York, New York 10065

 

 



NYC Marathon 11.3.19

Attendees, travel to RSGDREAM may be disrupted or take longer due to the NYC Marathon.

Please visit the NYC Marathon website for route closures on November 3. 

Travel on November 2 if possible, earlier in the day will be easier than afternoon or evening travel.
Additionally, please view the course map for an idea of where the runners and spectators will be throughout the day on November 3.


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Committees



Steering Committee

  • Grégoire Altan-Bonnet, Center for Cancer Research, National Cancer Institute
  • Bonnie Berger, MIT
  • Andrea Califano, Columbia University
  • Manolis Kellis, MIT
  • Saurabh Sinha, University of Illinois at Urbana-Champaign
  • Gustavo Stolovitzky, IBM Research
  • Lonnie Welch, Ohio University


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Organizing Committee

  • Elise Blaise, DREAM Chair
  • Richard Bonneau, RSG Program Chair
  • Christina Leslie, RSG Program Chair
  • Jian Ma, RSG Program Chair
  • Pablo Meyer, DREAM Chair
  • Itai Yanai, RSG Program Chair


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Additional Support

  • Bel Hanson, ISCB Operations and Programs Manager
  • Ben Hegel, MSKCC, Program Coordinator

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Exclusively for members

  • Member Discount

    ISCB Members enjoy discounts on conference registration (up to $150), journal subscriptions, book (25% off), and job center postings (free).

  • Why Belong

    Connecting, Collaborating, Training, the Lifeblood of Science. ISCB, the professional society for computational biology!

     

Supporting ISCB

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