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DREAM POSTERS


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D# = Cytoscape related work

Poster
Number
Authors Title
D1 Istvan Ladunga, Avi Knecht, Adam Caprez, Timothy Bailey, Tao Liu, Pedro Madrigal and David Swanson ChIPathlon: community-wide performance assessment of tools for mapping transcription factor binding sites and histone modifications
D2 Ana Stanescu and Gaurav Pandey Learning parsimonious ensembles for biomedical prediction problems and DREAM challenges
D3 Robert Vogel, Mehmet Eren Ahsen and Gustavo Stolovitzky Unsupervised aggregation of rank predictions for binary classification in translational systems biology tasks
D4 David Tanenbaum Phd, Eldred Ribeiro Phd, Wenling Chang Phd, Peter Gutgarts, Ari Abrams-Kudan, William Kim, Lisa Tutterow, Lauren Quattrochi Phd and Erin Williams Jd Catalyzing Biomedical Research through the NIH Commons Credit Cloud Computing Paradigm
D5 Dennis Wang, Michael P. Menden, Michael Mason, Thomas Yu, Krishna C. Bulusu, Elias Chaibub Neto, In Sock Jang, Zara Ghazoui, John Vincent, Eric Tang, Giovanni Di Veroli, Gustavo Stolovitzky, Jonathan R. Dry, Justin Guinney, Julio Saez-Rodriguez Community analysis to predict therapeutic synergy within the AstraZeneca-Sanger Drug Combination Challenge
D6 Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Hyeokyoon Chang, Minhwan Yu, Kwanghun Choi, and Jaewoo Kang Drug Synergy Prediction using High Performance Computing and Support Vector Regression
D7 Tin Nguyen, Bence Szalai, Gábort Turu, Miklós Cserző, László Hunyady, Sorin Draghici, Russ Wolfinger Boosted Tree Based Prediction of Drug Synergisms in the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge
D8 Weijia Zhang, Thuc Le, Taosheng Xu, Junpeng Zhang, Lin Liu, Jiuyong Li Disease module identification with balanced multi-layer regularized Markov cluster algorithm
D9 Chi W Pak Bootstrap feature selection of early differentially expressed genes in human respiratory viral challenge studies: viral shedding and patient symptoms
D10 Maria Suprun, Joel Correa-da-Rossa, Mayte Suarez-Farinas and Lewis E Tomalin Estimating a generalizable ‘final model’, suitable for clinical classification applications, using Monte Carlo resamples of patient data
 D11  Artem Lysenko, Piotr J. Kamola, Keith A. Boroevich and Tatsuhiko Tsunoda  Strategies for discovering disease-associated modules in integrated biological networks
 D12  Emilie Ramsahai and Melford John  M-Reach pathways from networks combined on V-Structures
 D13  Jake Crawford, Junyuan Lin, Xiaozhe Hu, Benjamin Hescott, Donna Slonim and Lenore J. Cowen  A double spectral approach to the DREAM module identification challenge
 D14  Sergio Gómez, Manlio De Domenico and Alex Arenas  Module Identification by Adjusting Resolution in Community Detection Algorithms
 D15 Shana White, Lixia Zhang and Mario Medvedovic  Application of diffusion kernels of network graphs and subsequent clustering approaches for identification of disease modules
D16 Hongjiu Zhang and Yuanfang Guan An ultra-fast tumour heterogeneity inference method using density-based infinite mixture model
D17 Liye He, Eemeli Leppäaho, Motoki Shiga, Bhagwan Yadav, Jussi Gillberg, Suleiman Khan, Zia ur Rehman, David Tamborero, Pekka Marttinen, Mehmet Gönen, Hiroshi Mamitsuka, Krister Wennerberg, Samuel Kaski, Tero Aittokallio, and Jing Tang Target-based ensemble drug combination predictions for the DREAM10 challenge
D18 Eduardo G. Gusmao, Zhijian Li, Ivan G. Costa Prediction of Active Transcription Factor Binding Sites Using Computational Footprinting Data
D19 Andrey S. Lando, Ilya E. Vorontsov, Valentina Boeva, Grigory V. Sapunov, Irina A. Eliseeva, Vsevolod J. Makeev, and Ivan V. Kulakovskiy Preselection of training cell types improves prediction of transcription factor binding sites
D20 Zafer Aydın Discovering Biomarkers for Early Prognosis of Respiratory Virus Infection
D21 Sandeep Kumar Dhanda, Kumardeep Chaudhary, Ritesh ‬Kumar‬, Deepak Singla  ViResPred: A Solution for Respiratory Viral Dream Challenge
D22 Michał Łopuszyński and Miron Bartosz Kursa The application of the feature hashing and the mutual information based feature filter in predicting susceptibility to respiratory viruses

 


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RSG POSTERS


Link within this page:  Download Mobile App
P# = Cytoscape related work

Poster
Number
Authors Title
P1 Anastasia Baryshnikova Functional Annotation of Large-Scale Biological Networks
P2 Christopher Maher, Nicole White, Shuang Zhao, Jin Zhang, Emily Rozycki, Ha Dang, Sandra McFadden, Abdallah Eteleeb, Mohammed Alshalalfa, Ismael Vergara, Nicholas Erho, Jeffrey Arbeit, Jeffrey Karnes, Robert Den and Elai Davicioni Integrative transcriptome analyses reveals PCAT14 promotes lethal prostate cancer
P3 Yaron Orenstein, Lin Yang, Arttu Jolma, Yimeng Yin, Jussi Taipale, Ron Shamir and Remo Rohs DNA Shape Readout Specificities of Different TF Families
P4 Yaron Orenstein, Ryan Kim, Polly Fordyce and Bonnie Berger Sequence libraries to cover all k-mers using degenerate characters
P5 Mark Grimes, Nicolas Fernandez, Neil Clark, Avi Ma’ayan, Klarisa Rikova and Peter Hornbeck Tandem Mass Tag Data Analysis Reveals Post-translational Modification Signaling Pathways in Lung Cancer Cell Lines
P6 Daniela Börnigen, Francisco Ojeda, Stefan Blankenberg and Tanja Zeller A genetic evaluation of multiple cardiovascular risk factors in the European population
P7 Daniela Börnigen, Francisco Ojeda, Stefan Blankenberg and Tanja Zeller Metabolomics analyses in cardiovascular diseases for biomarker discovery
P8 Simon J. van Heeringen Motif activity by ensemble learning for multi-experimental transcription factor motif analysis
P9 Simarjeet Negi and Chittibabu Guda Functional characterization of the healthy adult human brain and its application to study neurological disorders
P10 Tamir Tuller COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana
P11 Alon Diament and Tamir Tuller Inter-organismal analysis of Hi-C data demonstrates a relation between phenotypic divergence and gene re-organization
P12 Florian Schmidt, Tzung-Chien Hsieh, Nina Gasparoni, Gilles Gasparoni, Wei Chen, Karl Nordström, Oliver Gorka, Jürgen Roland, Anupam Sinha, Philip Rosenstiel, Julia K. Polansky, Alf Hamann, Joern Walter and Marcel Schulz A discriminatory method for the identification of transcriptional key regulators using epigenetic data
P13 Krystelle Nganou Makamdop, Slim Fourati, Jianfei Hu, Amy Ransier, Farida Laboune, Rafick-Pierre Sekaly and Daniel Douek Activation of IFNγ-signaling in myeloid dendritic cells is a new marker of risk of HIV-1 acquisition in the HVTN505 cohort
P14 Kimberly Kanigel Winner and James Costello A Spatiotemporal Model To Simulate Chemotherapy Regimens For Heterogeneous Bladder Cancer Metastases To The Lung
P15 Heeju Noh, Ziyi Hua and Rudiyanto Gunawan Inferring molecular targets and mechanism of action from time course expression data
P16 Rahul Mohan, Michael Wainberg, Nasa Sinnott-Armstrong and Anshul Kundaje kmer2vec: Unsupervised embedding of regulatory DNA sequences
P17 Pascal Fieth, Gilles Monneret, Andrea Rau, Florence Jaffrezic, Alexander Hartmann and Gregory Nuel Improving Causal Gaussian Bayesian Network Inference using Parallel Tempering
P18 Morteza Chalabi Hajkarim Computational Approaches to Decipher Composition and Regulation of Complexes by Large-scale Analysis of Mass Spectrometry (MS) Data
P19 Zohar Zafrir and Tamir Tuller Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression prediction
P20 Hatice Osmanbeyoglu, Eneda Toska, Carmen Chan, Jose Baselga and Christina Leslie Modeling the impact of somatic alterations on signaling pathways and transcriptional programs in human cancers
P21 Brian Ross and James Costello Modeling heterogeneous cell populations using Boolean networks
P22 Xiangjia Min Comprehensive cataloging and analysis of alternative splicing events in maize
P23 Oana Ursu, Nathan Boley, Maryna Taranova, Rachel Wang and Anshul Kundaje A graph diffusion framework for multi-scale reproducibility and differential analysis of 3D chromatin contact maps
P24 Jayoung Kim Interstitial Cystitis-Associated Urinary Metabolites
P25 Michaela Willi and Lothar Hennighausen Super-enhancers and CTCF in the regulation of mammary-specific genes
P26 Avanti Shrikumar, Peyton Greenside, Anna Shcherbina, Johnny Israeli, Nasa Sinnott-Armstrong and Anshul Kundaje Not Just a Black Box: Interpretable Deep Learning for Genomics
P27 Mijin Kwon, Jinmyung Jung, Hasun Yu and Doheon Lee Network-based inference of the effects of hormones on drug efficacy
P28 Daniela Börnigen, Francisco Ojeda, Stefan Blankenberg and Tanja Zeller Computational ten-steps workflow for large-scale metabolomics analysis in cardiovascular diseases
P29 Alexendar Perez, Yuri Pritykin, Joana Vidigal, Sagar Chhangawala, Lee Zamparo, Christina Leslie and Andrea Ventura GuideScan: a comprehensive and customizable guide RNA design tool
P30 Istvan Ladunga, Avi Knecht, Adam Caprez, Timothy Bailey, Tao Liu, Pedro Madrigal and David Swanson ChIPathlon: community-wide performance assessment of tools for mapping transcription factor binding sites and histone modifications
P31 Hyunghoon Cho, Bonnie Berger and Jian Peng Mashup: Compact Integration of Multi-Network Topology for Functional Analysis of Genes
P32 Yongxiao Yang and Xinqi Gong Protein-protein interface prediction: from several accurately predicted interface residue to the whole interface
P33 Alberto Giaretta, Barbara Di Camillo, Luisa Barzon, Gianna Maria Toffolo and Timothy Charles Elston Stochastic modeling of HPV early promoter gene regulation
P34 Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev and Sushmita Roy A phylogenetic framework to study the evolution of transcriptional regulatory networks
P35 Alireza Fotuhi Siahpirani and Sushmita Roy A prior-based integrative framework for functional transcriptional regulatory network inference
P36 H. Tomas Rube, Chaitanya Rastogi and Harmen J. Bussemaker Revisiting the relationship between DNA shape, base sequence, and transcription factor binding
P37 Qi Song and Song Li CoReg: Identification of co-regulators in genome scale transcription regulatory networks
P38 Xuewei Wang, Zhifu Sun, Jean-Pierre Kocher and Burgrim Andrej Pathway-based approach to predict drug response of cancer cells
P39 Khader Ghneim, Dan Barouch, Jeffrey Lifson and Rafick-Pierre Sekaly Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys
P40 Cynthia Kalita, Gregory Moyerbrailean, Christopher Brown, Francesca Luca and Roger Pique-Regi A novel allele-specific data analysis method for high-throughput reporter assays
P41 Huy Pham and Alioune Ngom A new effective feature selection method and its application for classification on biological data
P42 Lingfei Wang and Tom Michoel Scalable causal gene network inference from genetics of gene expression data
P43 Gil Speyer, Jeff Kiefer, Hai J. Tran, Harshil Dhruv, Michael Berens and Seungchan Kim Identification of personalized therapeutic targets via single-cell transcriptomic analysis
P44 Anasuya Pal, Jia Zeng, Laura Gonzalez-Malerva, Seron Eaton, Jin Park and Joshua Labaer Integrated pathway analysis on phenotypic and molecular alterations induced by different missense mutant p53 proteins in mammary epithelial cells
P45 Yungil Kim, Xin Li, Emily Tsang, Joe Davis, Farhan Damani and Colby Chiang The impact of rare variation on gene expression across tissues
P46 Casey Hanson, Junmei Cairns, Liewei Wang and Saurabh Sinha A Probabilistic Graphical Model integrates genotype, gene expression and ChIP-seq data to identify transcription factors associated with drug response variation
P47 Robert Vogel, Mehmet Eren Ahsen and Gustavo Stolovitzky Unsupervised aggregation of rank predictions for binary classification in translational systems biology tasks
P48 Ning Shen, Jingkang Zhao and Raluca Gordan Comparing the specificity of siblings in transcription factor families
P49 Andrea Repele, Shawn Krueger and Manu Manu Experimental test of a novel de novo regulatory decoding methodology in the context of the Cebpa locus
P50 Michael Saul, Wei Yang, Laura Sloofman, Abbas Burkhari, Charles Blatti, Chris Seward, Joe Troy, Hagai Shpigler, Sriram Chandrasekaran, Alison Bell, Gene Robinson, Lisa Stubbs, Dave Zhao and Saurabh Sinha Cross-species network analyses reveal conserved genomic toolkits involved in response to social challenge
P51 Emily Miraldi, Maria Pokrovskii, Jason A. Hall, Dayanne Martins de Castro, Nicholas Carriero, Aaron Watters, Ren Yi, Dan R. Littman and Richard Bonneau Learning how diverse gut immune cell types contribute to autoimmune disease through reverse-engineered transcriptional regulatory networks
P52 Mehmet Eren Ahsen, Amanda Craig, Carlos Villacorta-Martin, Xintong Chen, Ismail Labgaa, Ashley Stueck, Delia D’avola, Stephen Ward, Maria Isabel Fiel, Ganesh Gunasekaran, Josep Llovet, Swan Thung, Myron Schwartz, Bojan Losic, Augusto Villanueva and Gustavo Stolovitzky Multi-regional integrative genomic analysis reveals intra-tumor heterogeneity in a subset of early-stage hepatocellular carcinoma
P53 Ana Stanescu and Gaurav Pandey Learning parsimonious ensembles for biomedical prediction problems and DREAM challenges
P54 Chen Chen, Min Zhang and Dabao Zhang A Parallel Algorithm to Construct the Entire Gene Regulatory Network of an Organism
P55 Johnny Israeli, Nathan Boley and Anshul Kundaje Integrative deep regulatory genomic neural networks for predicting in-vivo transcription factor binding sites
P56 Chenyue Hu, Alex Bisberg and Amina Qutub Visually Guided Clustering: an integration of semi-supervised clustering with interactive visualization
P57 Chenyue Hu, Steven Kornblau and Amina Qutub Meta-Proteomic Analysis for the Clinic: A Guide Towards Personalized Therapy in Leukemia
P58 Allison Richards, Athma Pai, Daniel Kurtz, Gregory Moyerbrailean, Omar Davis, Chris Harvey, Adnan Alazizi, Yoram Sorokin, Nancy Hauff, Xiaoquan Wen, Roger Pique-Regi and Francesca Luca Gene expression and splicing responses to environmental perturbations across 250 cellular conditions
P59 Yan Kai, Alexandros Tzatsos and Weiqun Peng Predicting CTCF-mediated chromosomal long-range interactions using genomic and epigenomic features
P60 Victor Solovyev and Ramzan Umarov Prediction of Prokaryotic and Eukaryotic Promoters Using Convolutional Deep Learning Neural Networks
P61 Madhavi Ganapathiraju, Srilakshmi Chaparala and Sandeep Subramanian DNA Palindrome variants and their association with diseases
P62 Xi Gu and Chung-Jui Tsai Gene co-expression analyses of parasitic plants reveal non-photosynthetic functions of phylloquinone in transmembrane parasitic signaling
P63 Artur Jaroszewicz and Jason Ernst Modeling of spatial organization of chromatin states facilitates discovery of various types of exon splicing patterns
P64 Sebastian Winkler and Oliver Kohlbacher Identifying deregulated subnetworks bridging different omics-layers via fractional and bi-level integer programming
P65 Shun-Yuen Kwan, Jia-Hsin Huang, Zing Tsung-Yeh Tsai and Huai-Kuang Tsai Expansion of transcription binding specificities in the promoters of humans
P66 Ying Liu Discovering Structures in Biological networks using pattern-based network decomposition
P67 Tsu-Pei Chiu and Remo Rohs Genome-wide prediction of minor groove electrostatics enables biophysical modeling of protein-DNA binding
P68 Tunca Dogan, Ece Akhan, Marcus Baumann, Ahmet Süreyya Rifaioğlu, Diego Poggioli, Andrew Nightingale, Ian R. Baxendale, Maria Martin and Rengul Cetin-Atalay Automated compound-protein interaction estimation and validation on PI3K/AKT/mTOR pathway
P69 Anthony Findley, Gregory Moyerbrailean, Francesca Luca and Roger Pique-Regi Transcription factor footprints predict the gene expression response to environmental stimuli
P70 Jianwen Fang Tight Integration of Multi-Omics Data Using Tensor Decomposition
P71 Abiel Roche-Lima, Kelvin Carrasquillo-Carrion, Pablo Vivas and Dayanara Velazquez-Morales Associating miRNA and Cancer in Hispanics Populations using Bioinformatics Analysis
P72 Andrew Rouillard, Mark Hurle and Pankaj Agarwal Selection of Features from Omic Datasets for Prioritizing Drug Targets
P73 Tristan Bepler, Ryan Chung and Bonnie Berger Protein secondary structure annotation using long-short term memory recurrent neural networks
P74 George Steinhardt and David Waxman PREDICTION OF TRANSCRIPTIONF FACTOR BINDING SITES USING ATAC-SEQ AND DNASE-SEQ.
P75 Luis Santos, Robert Vogel, Marc Birtwistle, Jerry Chipuk, Pablo Meyer and Gustavo Stolovitzky Mitochondria variability confers resilience to pro‐apoptotic stimulation and is associated with drug resistance
P76 Gracia Bonilla and David Waxman Chromatin state preferences of transcription factors in male and female mouse liver
P77 Rosario Corona, Emily Adler, Janet Lee, Kate Lawrenson, Simon Gayther and Dennis Hazelett Characterization of the Pax8 regulatory network in epithelial ovarian cancer
P78 Padmapriya Swaminathan, Anne Fennell, Kalley Besler, Yuxin Yao, Somchai Rice, Jacek Koziel, Murli Dharmadhikari, Devin Maurer, Emily Del Bel, Zata Vickers, Katie Cook, Adrian Hegeman and Jim Luby Characterization of Grape berry ripening - Genomics to Sensory
P79 Simon Coetzee, Zack Ramjan, Huy Dinh, Benjamin Berman and Dennis Hazelett StateHub-StatePaintR: a tool for creating and documenting reproducible chromatin state annotations.
P80 Prathik Naidu and Caleb Lareau A Machine Learning Approach to Identify Genome-Wide 3D DNA Interactions
P81 Satyanarayan Rao, Harmen Bussemaker and Remo Rohs High-throughput predictions of DNA shape features for methylated DNA reveal mechanisms of TF binding
P82 David Tanenbaum Phd, Eldred Ribeiro Phd, Wenling Chang Phd, Peter Gutgarts, Ari Abrams-Kudan, William Kim, Lisa Tutterow, Lauren Quattrochi Phd and Erin Williams Jd Catalyzing Biomedical Research through the NIH Commons Credit Cloud Computing Paradigm
P83 Jared Sagendorf, Helen Berman and Remo Rohs DNAproDB: A Web-Based Database and Visualization Tool for the Analysis of DNA-Protein Complexes
P84 Murat Cokol and Bree B. Aldridge Efficient and robust measurement of high order drug interactions
P85 Christopher Michael Pietras, Diana W. Bianchi, and Donna K. Slonim TEMPO: Temporal Modeling of Pathway Outliers

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TOP 10 PAPERS READING LIST, 2015-2016


 As selected at RECOMB/ISCB Regulatory and Systems Genomics 2016

(Papers are listed alphabetically by title)

A widespread role of the motif environment in transcription factor binding across diverse protein families, Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. Genome Research 2015 Sep;25(9):1268-80

Affinity regression predicts the recognition code of nucleic acid-binding proteins, Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Nature Biotechnology 2015 Dec;33(12):1242-1249

Analysis of computational footprinting methods for DNase sequencing experiments, Gusmao E, Allhoff M, Zenke M, Costa I. Nature Methods 2016 Apr;13(4):303-9

Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks, Kelley DR, Snoek J, Rinn J. Genome Research 2016 Jul;26(7):990-9

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes, Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Proc Natl Acad Sci U S A 2015 Nov 24;112(47):E6456-65

Evaluating the impact of single nucleotide variants on transcription factor binding, Shi W, Fornes O, Mathelier A, Wasserman WW. Nucleic Acids Research 2016 Aug 4. pii: gkw691

Inferring causal molecular networks: empirical assessment through a community-based effort, Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Nature Methods 2016 Apr;13(4):310-8

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens, Chasman D, Walters KB, Lopes TJ, Eisfeld AJ, Kawaoka Y, Roy S. PLoS Computational Biology 2016 Jul 12;12(7):e1005013

Models of human core transcriptional regulatory circuitries, Saint-Andre V, Federation AJ, Lin CY, Abraham BJ, Reddy J, Lee TI, Bradner JE, Young RA. Genome Research 2016 Mar;26(3):385-96

Pathways on demand: automated reconstruction of human signaling networks, Ritz A, Poirel CL, Tegge AN, Sharp N, Simmons K, Powell A, Kale SD, Murali TM. Npj Systems Biology And Applications, vol. 2 p. 16002.

CONGRATULATIONS TO ALL AUTHORS!


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AGENDAS - CONFERENCE & DREAM


Links within this page*: Conference Agenda | DREAM Agenda | Download Mobile App

Link to maps and floor plans: Click here

*Proposed Programs. Agendas subject to change.

CONFERENCE AGENDA
Go directly to: [Monday - Nov 7] [Tuesday - Nov 8]
SUNDAY – DAY 1 – Cytoscape Workshop - November 6, 2016
START TIME END TIME SESSION TYPE
Registration
12:00pm - 5:00pm
Location: Anasazi Lobby
1:00 pm 3:00 pm Cytoscape Workshop
Location: Kachina Room
3:00 pm 3:30 pm Break
3:30 pm 5:00 pm Cytoscape Workshop (continued) - Location: Kachina Room
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RSG AGENDA
MONDAY – DAY 2 – November 7, 2016
START TIME END TIME SESSION TYPE
Registration
8:00am - 6:00pm
Location: Anasazi Lobby
8:00 am 8:45 am Coffee Break with Pastries and Fruit
Location: Kiva Room
Keynote 1
Location: Kachina Room
9:00 am 9:45 am Keynote - Gordon B. Mills
Systems approach to rational drug combinations
9:45 am 10:00 am Coffee Break
Location: Kiva Room
Regulatory Genomics: Session 1
Location: Kachina Room
10:00 am 10:15 am Alexendar Perez, Yuri Pritykin, Joana Vidigal, Sagar Chhangawala, Lee Zamparo, Christina Leslie and Andrea Ventura
GuideScan: a comprehensive and customizable guide RNA design tool
10:15 am 10:30 am Istvan Ladunga, Avi Knecht, Adam Caprez, Timothy Bailey, Tao Liu, Pedro Madrigal and David Swanson
ChIPathlon: community-wide performance assessment of tools for mapping transcription factor binding sites and histone modifications
10:30 am 10:45 am Alberto Giaretta, Barbara Di Camillo, Luisa Barzon, Gianna Maria Toffolo and Timothy Charles Elston
Stochastic modeling of HPV early promoter gene regulation
10:45 am 11:00 am Alireza Fotuhi Siahpirani and Sushmita Roy
A prior-based integrative framework for functional transcriptional regulatory network inference
11:00 am 11:15 am Buffer for Q&A
11:15 am 11:30 am Coffee Break
Location: Kiva Room
Regulatory Genomics: Session 2
Location: Kachina Room
11:30 am 11:45 am Lingfei Wang and Tom Michoel
Scalable causal gene network inference from genetics of gene expression data
11:45 am 12:00 pm Allison Richards, Athma Pai, Daniel Kurtz, Gregory Moyerbrailean, Omar Davis, Chris Harvey, Adnan Alazizi, Yoram Sorokin, Nancy Hauff, Xiaoquan Wen, Roger Pique-Regi and Francesca Luca
Gene expression and splicing responses to environmental perturbations across 250 cellular conditions
12:00 pm 12:15 pm H. Tomas Rube, Chaitanya Rastogi and Harmen J. Bussemaker
Revisiting the relationship between DNA shape, base sequence, and transcription factor binding
12:15 pm 12:30 pm Cynthia Kalita, Gregory Moyerbrailean, Christopher Brown, Francesca Luca and Roger Pique-Regi
A novel allele-specific data analysis method for high-throughput reporter assays
12:30 pm 1:45 pm Lunch On Own
Poster Viewing in the Kiva Room
Keynote 2
Location: Kachina Room
1:45 pm 2:30 pm Keynote - Christopher Burge
Protein-RNA interactions and function of alternative 3’ UTRs
Systems Biology: Session 1
Location: Kachina Room
2:30 pm 2:45 pm Yuval Itan, Laurent Abel and Jean-Laurent Casanova
Finding a needle in a haystack: new approaches to select disease-causing mutations in patients’ genomes
2:45 pm 3:00 pm Janhavi Moharil, Daniel Gaile, Paul May and Rachael Hageman Blair
Probabilistic reasoning in genotype-phenotype networks
3:00 pm 3:15 pm Heeju Noh, Ziyi Hua and Rudiyanto Gunawan
Inferring molecular targets and mechanism of action from time course expression data
3:15 pm 3:30 pm Hatice Osmanbeyoglu, Eneda Toska, Carmen Chan, Jose Baselga and Christina Leslie
Modeling the impact of somatic alterations on signaling pathways and transcriptional programs in human cancers
3:30 pm 3:45 pm Joseph J. Muldoon, Yishan Chuang, Neda Bagheri and Joshua N. Leonard
A dynamical model for the regulation of heterogeneous macrophage activation by apparent quorum sensing
3:45 pm 4:00 pm Brian Ross and James Costello
Modeling heterogeneous cell populations using Boolean networks
4:00 pm 4:10 pm Buffer for Q&A
4:10 pm 4:30 pm Tech Talk
Presenter:  Blake Borgeson

Extracting the biology of a hundred diseases from a million images
Recursion Pharmaceuticals
4:30 pm 5:00 pm Coffee Break with light snacks
Location: Kiva Room
Keynote 3
Location: Kachina Room
5:00 pm 5:45 pm Keynote - Réka Albert
Control and Damage Mitigation in Regulatory Networks
6:00 pm 8:00 pm Wine and Cheese Reception
with Poster Viewing
Location: Kiva Room
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TUESDAY – DAY 3 – November 8, 2016
START TIME END TIME SESSION TYPE
6:45 am 8:00 am Sunrise Networking Hike - Meet-up location is of South Pointe Lobby.
Leaving lobby at 6:45 to begin the hike.

Hiking trail map is available here.
Registration
8:00am - 6:00pm
Location: Anasazi Lobby
8:00 am 8:45 am Coffee Break with Pastries and Fruit
Location: Kiva Room
Keynote 4
Location: Kachina Room
9:00 am 9:45 am Keynote - Jill Mesirov
Signature and Integrative Computational Approaches to Genomic Medicine
9:45 am 10:00 am Coffee Break
Location: Kiva Room
Systems Biology: Session 2
Location: Kachina Room
10:00 am 10:15 am Xuewei Wang, Zhifu Sun, Jean-Pierre Kocher and Burgrim Andrej
Pathway-based approach to predict drug response of cancer cells
10:15 am 10:30 am Pooya Zakeri, Jaak Simm, Adam Arany, Sarah Elshal and Yves Moreau
Towards a Bayesian Data Fusion Model for Hunting Disease Candidate Genes
10:30 am 10:45 am Anasuya Pal, Jia Zeng, Laura Gonzalez-Malerva, Seron Eaton, Jin Park and Joshua Labaer
Integrated pathway analysis on phenotypic and molecular alterations induced by different missense mutant p53 proteins in mammary epithelial cells
10:45 am 11:00 am Yungil Kim, Xin Li, Emily Tsang, Joe Davis, Farhan Damani and Colby Chiang
The impact of rare variation on gene expression across tissues
11:00 am 11:10 am Buffer for Q&A
11:10 am 11:30 am Coffee Break
Location: Kiva Room
11:30 am 11:45 am Robert Vogel, Mehmet Eren Ahsen and Gustavo Stolovitzky
Unsupervised aggregation of rank predictions for binary classification in translational systems biology tasks
11:45 am 12:00 pm Laura Heiser, James Korkola, Mark Dane, Elmar Bucher, David Kilburn, Rebecca Smith, Wallace Thompson, Sean Gross, Damir Sudar, Michel Nederlof and Joe Gray
Elucidating the role of the microenvironment in modulating cellular phenotypes
12:00 pm 12:15 pm Casey Hanson, Junmei Cairns, Liewei Wang and Saurabh Sinha
A Probabilistic Graphical Model integrates genotype, gene expression and ChIP-seq data to identify transcription factors associated with drug response variation
12:15 pm 12:30 pm Aditya Pratapa, Neil Adames, Pavel Kraikivski, John Tyson, Jean Peccoud and T. M. Murali
Systematic Planning of Genetic Crosses to Validate Mathematical Models
12:30 pm 1:45 pm Grab N' Go Lunch
Includes: sandwich or salad, chips, cookie or whole fruit and a drink
Poster Viewing in the Kiva Room
Keynote 5
Location: Kachina Room
1:45 pm 2:30 pm Keynote - Nicholas Schork
Heterogeneity in Large-Scale Biomedical Data Sets
Regulatory Genomics: Session 3
Location: Kachina Room
2:30 pm 2:45 pm Beibei Xin and Remo Rohs
Protein family-specific relationship between histone modifications and transcription factor binding
2:45 pm 3:00 pm Mark Grimes, Nicolas Fernandez, Neil Clark, Avi Ma’ayan, Klarisa Rikova and Peter Hornbeck
Tandem Mass Tag Data Analysis Reveals Post-translational Modification Signaling Pathways in Lung Cancer Cell Lines
3:00 pm 3:15 pm Alon Diament and Tamir Tuller
Inter-organismal analysis of Hi-C data demonstrates a relation between phenotypic divergence and gene re-organization
3:15 pm 3:30 pm Yaron Orenstein and Bonnie Berger
Structural analysis of the compendium of RNA-binding proteins
3:30 pm 3:45 pm Oana Ursu, Nathan Boley, Maryna Taranova, Rachel Wang and Anshul Kundaje
A graph diffusion framework for multi-scale reproducibility and differential analysis of 3D chromatin contact maps
3:45 pm 4:00 pm Jingkang Zhao, Dongshunyi Li, Andrew Allen and Raluca Gordan
Quantifying the impact of non-coding variants on TF-DNA binding
4:00 pm 4:15 pm Michaela Willi and Lothar Hennighausen
Super-enhancers and CTCF in the regulation of mammary-specific genes
4:15 pm 4:30 pm Buffer for Q&A
4:20 pm 5:00 pm Coffee Break with light snacks
Location: Kiva Room
Keynote 6
Location: Kachina Room
5:00 pm 5:45 pm Keynote - Martha Bulyk
Genetic variation in human transcription factors
6:00 pm 7:00 pm Sponsored Talk
Presenter: Chris Cheadle PhD
Sponsor: Elsevier
Hands-on workshop with Pathway Studio, a high content, molecular modeling software tool
Location: Kachina Room
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DREAM AGENDA - WEDNESDAY – November 9, 2016
START TIME TALK LENGTH CATEGORY EVENT
Registration
7:30 am - 6:00pm
Location: Anasazi Lobby
8:30 0:20 DREAM 11: Welcome and Introductory Remarks.
Gustavo Stolovitzky
9:00 0:20 DRUG COMBO
CHALLENGE


Chair:
Justin Guinney
Invited Talk: Why AstraZeneca decided to DREAM about better cancer drug combinations. Jonathan Dry
9:20 0:20 Challenge Overview Talk: Community analysis to predict therapeutic synergy within the AstraZeneca-Sanger Drug Combination Challenge.
Michael Menden
9:40 0:20 Best Performer Talk: Boosted Tree Based Prediction of Drug Synergisms in the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge. Tin Nguyen and Bence Szalai
10:00 0:20 Best Performer Talk: Drug Synergy Prediction using High Performance Computing and Support Vector Regression. Minji Jeon
10:20 0:30 Coffee Break with Posters
10:50 0:15 CHALLENGES UPDATES


Chair:
Lara Mangravite
Challenge Update. Respiratory Viral DREAM Challenge: Discovering dynamic molecular signatures in response to viral exposure. Solly Sieberts
11:05 0:15 Challenge Update. Update SMC-RNA. Paul Boutros
11:20 0:15 Challenge Update. The Digital Mammography Challenge Update. Justin Guinney
11:35 0:15 Upcoming DREAM Challenges.
Gustavo Stolovitzky
11:50 0:40 Keynote - Isaac Kohane
Fake and True Names of Disease: Phenome and/or Genome?
12:30 1:30 Lunch with Posters
14:00 0:20 DISEASE MODULE


Chair:
Gustavo Stolovitzky
Challenge Overview Talk. The Disease Module Identification DREAM Challenge. D. Marbach and S. Schoobdar
14:20 0:20 Best Performer Talk: A double spectral approach to the DREAM module identification challenge. Jake Crawford and Lenore Cowen
14:40 0:20 Best Performer Talk: Strategies for discovering disease-associated modules in integrated biological networks.
A. Lysenko and P. Kamola
15:00 0:30 Coffee Break with Posters
15:30 0:20 SMC-HET


Chair:
Pablo Meyer
Challenge Overview Talk.
SMC-Het Challenge: Understanding the subclonality of tumours.
Paul Boutros
15:50 0:20 Best Performer Talk: Subclonal reconstruction from tumor genomic variation data using a cascade ensemble model. Kaiyi Zhu
16:10 0:20 Best Performer Talk:  An ultra-fast tumour heterogeneity inference method using density-based infinite mixture model. Hongjiu Zhang
16:30 0:30 Coffee Break with Posters
17:00 0:40 Keynote - Zhiping Weng
Expanding the ENCODE Encyclopedia: Applications for Annotating Non-coding Variants
17:40 0:20 ENCODE CHALLENGE


Chair:
Laura Heiser
Challenge Overview Talk.
The ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge.
Anshul Kundaje
18:00 0:20 Best Performer Talk: Discriminative learning using iterative background data set complementation. Jens Keilwagen
18:20 0:20 Best Performer Talk: Preselection of training cell types improves prediction of transcription factor binding sites.
Andrey S. Lando
18:40 1:50 DREAM Reception and Posters
20:30   Adjourn
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