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!
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 themicrobiome 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 thehuman body. Using nucleotide sequencing, including our own approach called PrecisionSequencing TM, bioinformatics, and machine learning methods, we are developing precisionmedicine solutions based on microbiome information, empowering doctors, patients, and citizenscientists 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 informationgenerated with these analyses allow us continuous improvement of these products.Additionally, we continually monitor the scientific literature to add new targets as well as novelcorrelations in our tests. Moreover, the sequencing information combined with the metadatacollected 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 thattarget 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 livebiotherapeutics 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 andimplementation of clinical tests, toward the development of therapeutics products, having bioinformatics as the main protagonist.
Many of the sessions listed below will consider submissions for contributed talks, including full papers in addition to our regular track. All such papers should be submitted through EasyChair, by the relevant GLBIO 2019 submission deadline. Please contact the organizer of the individual sessions for more information.
Accepting abstracts only for oral presentations through EasyChair. The GLBIO 2019 Special Session on Bioinformatics Education seeks to create a platform for presentation and discussion on the topic of bioinformatics education broadly defined. The session will mix invited talks from leaders in bioinformatics education with contributed talks and posters from the community. The intention is to provide a broad representation of perspectives, goals, and topics engaging the bioinformatics education community. The session is soliciting short abstracts for proposed talks or posters. Topics of interest include but are not limited to
bioinformatics curriculum development for bioinformatics professionals, life scientists, healthcare professionals, K-12 students, or other communities
education policy and practices
pedagogical strategies or experiences
community education resources
outreach and diversity efforts
case studies in bioinformatics education
The session will conclude with a Panel Discussion and Community Forum organized around the theme of identifying the aims for Bioinformatics Education community over the next five years.
Accepting abstracts only for oral presentations through EasyChair. Microbiome research is a rapidly growing area of science. Over the last decade, the number of microbiome sequencing studies has expanded enormously, exploring the intricate communities of microbes within soil, water, the built environment, and the human body, amongst others. There is a need to ensure that adequate expertise and infrastructure is in place to meet the challenge of analyzing the data generated as well as a robust and reliable framework for interpreting the data. This session will cover (1) different computational and statistical methods for analyzing microbiome data sets, and (2) investigations of microbiomes uncovering new insight into functions and dynamics.
Accepting full papers and abstracts for oral presentations through EasyChair. Post-transcriptional processes play a key role in eukaryotic gene regulation, yet it is not well understood how such processes contribute to the level of functional RNAs within the cell. Such regulation is orchestrated through a variety of mechanisms acting on all aspects of RNA metabolism, including pre-mRNA splicing, stability, polyadenylation, localization, editing, modification, and translation. The diversity of these mechanisms as well as the the increase in RNA-related high-throughput sequencing approaches highlight the need for research into new computational tools addressing post-transcriptional gene regulation.
This session focuses on research findings and methods related to the sequence and structure of RNA as well as its post-transcriptional gene regulation. These include but are not limited to the analysis of transcriptomics and protein-RNA interaction datasets, novel methods for interpretation of single-cell transcriptomes and approaches for RNA structure prediction. The session comprises of invited and selected talks, as well as a workshop on analyses of RNA splicing from high-throughput transcriptome-wide sequencing, and identification of protein/RNA binding sites from CLIP-seq data. The audience is expected to have a basic understanding and experience with computational biology, but not to be experts on RNA biology or the current computational and experimental approaches used in RNA research.
Accepting abstracts only for oral presentations through EasyChair. Advances in computing have led to a data-driven revolution in biology and promise to guide progress in precision medicine. This session will explore the spectrum of challenges and opportunities in precision medicine, including genomics, electronic health record analytics, and drug discovery. Confirmed speakers apply systems approaches to disease, biomarker, and other complex trait prediction by building computational models that leverage and integrate similarity in genetic, transcriptomic and other omics-level data. The intended audience for this session includes those interested in integrative genomics, statistical modeling, machine learning, and human population genetics applications in medicine.
Half-day Tutorial. Will not accept submissions. This workshop aims to be the next step in reproducibility for computational biologists and will focus on using and developing software containers. We will review best practices for practicing reproducible research and teach participants how to use Docker, a popular software for containerization (which can also be used by Singularity, another commonly used containerization platform). Using containers can help overcome the many interoperability and dependency issues often encountered when distributing or installing software. Docker images used conjunction with continuous integration is considered to be a possible solution for the reproducibility crisis plaguing research at large. Similar to a Carpentries workshop, a majority of the proposed workshop will be hands-on live-coding. Workshop attendees are expected to have familiarity with the Unix shell and git/github, bring their own laptops, and follow along with the training.
Half-day Tutorial. Will not accept submissions. As the flood of data from high-throughput sequencing threatens to overwhelm scientists with data generated within individual labs and distributed on the web, visualization becomes even more important. The UCSC Genome Browser has developed tools that assist in understanding the import of data and provides a platform to view data from multiple sources together. The endpoint of a data pipeline need not be statistical or tabular. A potent visualization tool such as the Browser can add an important dimension to data analysis.
This UCSC Genome Browser workshop will offer a tour through recent data releases and new features. New data include a pre-computed CRISPR guides track on human, mouse and other genome assemblies, a mapping of transcript-specific GTEx expression data, a Gene Interactions track which collects data from multiple curated databases and from data-mining of the literature, and gnomAD. Recently added features include multi-region mode, which allows for display of exons only or of any regions specified by the user, whether contiguous in the genome or not and Track Collections, which allows co-configuration of multiple tracks and new data formats for loading your data (interation and barChart).
Evening Tutorial. Will not accept submissions. Many real-world datasets are high-dimensional in their raw form but have low-dimensional structure, groupings, or representations. Dimensionality reduction methods have been applied to various biomedical datasets with the aim of cancer subtype extraction from mutational signatures, genotype-to-phenotype mapping, gene regulatory program identification, unsupervised multi-omics data integration, and cell differentiation trajectory visualization. This workshop will provide an opportunity to explore a handful of powerful dimensionality reduction methods: matrix factorization, PCA/LDA/GDA, t-SNE and UMAP, diffusion map, and autoencoders. All demos and exercises will use real biomedical datasets from single cell RNA-seq, Hi-C, and de-identified medical records.
Topic: ISCB Town Hall Date: Sunday, July 8 (12:45 PM - 1:45 PM) Room: Columbus IJ
Description Join us at the ISCB Town Hall meeting on Sunday, July 8, from 12:45 PM - 1:45 PM to learn more about the latest programs, initiatives, and conferences. This is also your chance to help shape the future of ISCB by providing feedback and suggestions. The Town Hall will close with a celebration of achievement with the announcement of the Student Council Symposium award winners.
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
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.
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).
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.
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).
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.
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.
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.
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.