TALKS SCHEDULE



Links within this page*: DREAM Schedule | RSG Schedule
*Proposed Programs. Agendas subject to change.

DREAM Schedule

Saturday - Day 1 – December 8, 2018
Go directly to: Sunday, Dec 9 - Monday, Dec 10
START
TIME
END
TIME
SESSION
TYPE
8:00 am 5:00 pm REGISTRATION
8:40 am 9:00 am Welcome and Introductory Remarks. Pablo Meyer and Gustavo Stolovitzky
Challenges Papers
9:00 am 9:15 am Mi Yang
Target functional similarity based workflows for drug synergy prediction and stratification
9:15 am 9:30 am Lenore Cowen
The Disease Module Identification DREAM Challenge: An Update
9:30 am 9:45 am Michael Banf
Enhancing gene regulatory network inference through data integration with markov random fields
9:45 am 10:25 am Keynote - Daphne Koller
A fireside chat
10:25 am 10:55 am Coffee Break with Posters
Challenge Updates
10:55 am 11:10 am Andrew Gentles
Tumor Deconvolution DREAM Challenge
11:10 am 11:25 am Pei Wang
A precision FDA NCI-CPTAC Multiomics Mislabeling Challenge
11:25 am 11:40 am Geoffrey Siwo
Malaria Challenge
11:40 am 11:55 am Anna Cichonska
IDG-DREAM Drug-Kinase Binding Prediction Challenge
11:55 am 12:40 pm The Challenge of Imaging Challenges: A Panel Discussion
12:40 pm 2:25 pm Lunch on Own
Multi-Targeting Drug DREAM Challenge
2:25 pm 3:05 pm Keynote - Ross Cagan
A Fly DREAM
3:05 pm 3:25 pm Challenge Overview Talk
3:25 pm 3:45 pm Best Performance Talk
3:45 pm 4:05 pm Best Performance Talk
4:05 pm 4:35 pm Coffee Break with Posters
Single-Cell Transcriptomics Challenge
4:35 pm 4:55 pm Shibiao Wan
Hyper-fast and accurate processing of large-scale single-cell transcriptomics data via ensemble random projection
4:55 pm 5:15 pm Single-Cell Transcriptomics Overview: Nikolaus Rajewsly
5:15 pm 5:20 pm Best Performer Announcements
5:20 pm 5:40 pm Best Performer Talk 1
5:40 pm 6:00 pm Best Performer Talk 2
6:00 pm 7:00 pm Dream Reception and Posters
7:00 pm   Adjourn


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Conference Schedule

Sunday – Day 2 – December 9, 2018
Go directly to: Saturday, Dec 8 (DREAM)Monday, Dec 10
START
TIME
END
TIME
SESSION
TYPE
8:00 am 5:00 pm REGISTRATION
9:00 am 9:15 am Welcome
9:15 am 10:00 am Keynote - Aravinda Chakravarti
10:00 am 10:15 am Anat Kreimer, Fumitaka Inoue, Tal Ashuah, Nadav Ahituv and Nir Yosef
Massively parallel characterization of regulatory dynamics during neural induction
10:15 am 10:30 am Tobias Zehnder, Philipp Benner and Martin Vingron
Predicting enhancers in mammalian genomes using supervised hidden Markov models
10:30 am 10:45 am William Lai, Kylie Bocklund, Kate Mistretta and B Franklin Pugh
Methods of defining “success” in ChIP-seq/exo experiments
10:45 am 11:15 am Coffee Break with Posters
11:15 am 11:30 am Alireza Fotuhi Siahpirani, Rupa Sridharan and Sushmita Roy
Incorporating noisy prior networks for estimating latent transcription factor activities and inferring genome-scale regulatory network in yeast and mammalian systems
11:30 am 11:45 am Amir Alavi, Matthew Ruffalo, Aiyappa Parvangada, Zhilin Huang and Ziv Bar-Joseph
scQuery: a web server for comparative analysis of single-cell RNA-seq data
11:45 am 12:30 pm Keynote - Shirley Liu
12:30 pm 2:00 pm Lunch on Own
2:00 pm 2:15 pm Special Session Welcome
2:15 pm 3:00 pm Keynote - Peter Kharchenko
Analysis of transcriptional dynamics with single-cell transcriptomics
3:00 pm 3:15 pm Florian Wagner and Itai Yanai
Moana: A Robust and Scalable Cell Type Classification Framework for Single-cell RNA-Seq Data
3:15 pm 3:30 pm Joseph A. Wayman, Diep Nguyen, Peter DeWeirdt, Bryan D. Bryson and Emily R. Miraldi
Benchmarked methods for transcriptional regulatory network inference from single-cell RNA-seq data
3:30 pm 3:45 pm Gunsagar Gulati, Shaheen Sikandar, Daniel Wesche, Anjan Bharadwaj, Anoop Manjunath, Francisco Ilagan, Mark Berger, Michael Clarke and Aaron Newman
Robust Reconstruction of Single Cell Differentiation Trajectories using CytoTRACE
3:45 pm 4:15 pm Coffee Break with Posters
4:15 pm 4:30 pm Qian Zhu, Sheel Shah, Ruben Dries, Long Cai and Guo-Cheng Yuan
Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity
4:30 pm 4:45 pm Nelson Johansen and Gerald Quon
Characterizing cell type-specific responses to stimuli using single cell RNA sequencing
4:45 pm 5:30 pm Keynote - Miriam Merad
5:30 pm 7:00 pm Reception with poster viewing
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Monday – Day 3 – December 10, 2018
Go directly to: Saturday, Dec 8 (DREAM)Sunday, Dec 9
START
TIME
END
TIME
SESSION
TYPE
8:00 am 5:00 pm REGISTRATION
9:00 am 9:15 am Special Session Welcome
9:15 am 10:00 am Keynote - Adam Siepel
An evolutionary framework for measuring epigenomic information and estimating cell-type specific fitness consequences
10:00 am 10:15 am Akpeli Nordor, Martin Aryee and Geoffrey Siwo
Predicting interactions between small molecules and genome editing technologies
10:15 am 10:30 am Gregory Nuel, Flaminia Zane, Andrea Rau and Florence Jaffrezic
Clustering of Directed Acyclic Graphs in Systems Biology
10:30 am 10:45 am Peter Koo, Praveen Anand, Steffan Paul and Sean Eddy
Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks
10:45 am 11:15 am Coffee Break with Posters
11:15 am 11:30 am Jingyi Jessica Li, Guo-Liang Chew and Mark Biggin
Principles of cis-translational control by general mRNA features in a yeast, a plant and a mammal
11:30 am 11:45 am Svetlana Shabalina
Complexity and evolution of the mammalian transcriptome: the architecture of alternative transcription and splicing
11:45 am 12:30 pm Keynote - Barbara Engelhardt
12:30 pm 2:00 pm Lunch on Own
2:00 pm 2:45 pm Keynote - Bing Ren
Functional Organization of the Human Genome
2:45 pm 3:00 pm Shahin Mohammadi, Jose Davila-Velderrain and Manolis Kellis
Systems biology of schizophrenia at single-cell resolution
3:00 pm 3:15 pm Federica Eduati, Ramesh Utharala, Patricia Jaaks, Mathew Garnett, Thorsten Cramer, Christoph Merten and Julio Saez-Rodriguez
Combining microfluidics and mathematical modelling for prioritisation of personalised cancer treatments from patient biopsies
3:15 pm 3:30 pm Lu Cheng, Siddharth Ramchandran, Tommi Vatanen, Juho Timonen, Niina Lietzen, Riitta Lahesmaa, Aki Vehtari and Harri Lähdesmäki
An additive Gaussian process regression model for interpretable probabilistic non-parametric analysis of longitudinal data
3:30 pm 4:00 pm Coffee Break with Posters
4:00 pm 4:15 pm Jonathan Warrell, Daifeng Wang, Shuang Liu, Hyejung Wong, Xu Shi, Fabio Navarro, Declan Clarke, Mengting Gu, Prashant Emani and Mark Gerstein
Interpretable Deep-learning for Multilevel Models of Psychiatric Disorders
4:15 pm 4:30 pm Hatice Osmanbeyoglu, Fumiko Shimizu, Angela Rynne-Vidal, Tsz-Lun Yeung, Petar Jelinic, Samuel Mok, Gabriela Chiosis, Douglas Levine and Christina Leslie
Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers
4:30 pm 5:15 pm Keynote - Ana Pombo
5:30 pm 7:00 pm Reception with poster viewing

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SPONSORS



Platinum Sponsors

NYU Langone Memorial Sloan Kettering Cancer Center

Gold Sponsors

IBM Research


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CALL FOR SUBMISSIONS FOR TOP 10 READING PAPERS, 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 DREAM Challenges

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 Papers for DREAM Conference Session and Poster

This year we are inviting posters and oral presentations about past DREAM Challenges. We encourage participants to submit abstracts about their published or unpublished work on past Challenges, such as the SMC Challenges, ENCODE challenge, the AZ synergy Challenge, etc. Abstracts may be either original unpublished work related to past DREAM challenges or work that was published or accepted for publication in a journal previously.

Key Dates:
Abstract Submission for Oral Presentation & Poster deadline: Monday, September 24, 2018

- Author notifications will occur on or around Monday, October 15, 2018
Late Breaking Poster deadline: Monday, October 15, 2018

- Author notifications will occur on or around Monday October 29, 2018

 CLICK HERE TO SUBMIT

Abstracts received before the due date will be considered for oral presentations and/or 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: 36 inches wide by 48 inches high. There will be 2 posters per side on the each poster board.


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POSTERS



 Please check back for updates.


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