Quick links
- Conference DREAM Content Table Information
- Conference DREAM Video and Presentation links
- Conference RICCI Content Table Information
- Conference RICCI Video and Presentation links
- Conference RECOMB SYSTEMS BIOLOGY (1st day) Content Table Information
- Conference RECOMB SYSTEMS BIOLOGY (1st day) Video and Presentation links
- Conference RECOMB REGULATORY GENOMICS (1st day) Content Table Information
- Conference RECOMB REGULATORY GENOMICS (2nd day) Content Table Information
- Conference RECOMB REGULATORY GENOMICS Video and Presentation links
- All Conference Photos
Conference: DREAM
Date: October 2011, Friday 14th
| Hour | Speaker | Title | Presentation | Video |
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| 08:45 | Emilià Pola Gustavo Stolovitzky Andrea Califano Miquel Ángel Pujana |
Introduction to DREAM6 |  |
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| 09:00 | Edda Klipp | Cellular stress response on different levels: zooming in and out in networks | |
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| 09:40 | Don Sharon | Long-Read RNA-Seq as a Novel Tool for Identifying Splice Variants | |
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| 10:00 | Nikolay Ivanov | DREAM6 Challenge 1: Alternative Splicing challenge | |
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| 10:20 | Ramya Rangan | De Novo Splice Form Discovery from RNA-Seq data | |
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| 10:40 | Massimiliano Orsini | AuARS: A Pipeline for Transcript Discovery from RNAseq Data | |
N/A |
| 11:30 | Deepak Chandran | Design and Implementation of the Estimation of Model Parameters Challenge | |
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| 11:50 | Pablo Meyer | DREAM6 Challenge 2: Estimation of Model Parameters | |
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| 12:10 | Po-Ru Loh | Targeted Stepwise Maximum-Likelihood Estimation of Gene Regulatory Network Parameters | |
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| 12:30 | Clements Kreutz | Experimental design and parameter estimation applied to the DREAM6 challenge | |
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| 14:00 | Ewan Birney | ENCODE | N/A | |
| 14:40 | Danny Zeevi | The Promoter Activity (Gene Expression) Predicition Challenge - Motivation and Data | |
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| 15:00 | Pablo Meyer | DREAM6 Challenge 3: Gene Expression Prediction | |
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| 15:20 | Geoffrey H. Siwo | A FIrST DREAM Best Performer Algorithm for Promoter Activity Prediction | |
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| 15:40 | Chien-Yu Chen | Predicting promoter activities by non-linear combination of sequence motifs | |
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| 16:30 | Wade Rogers | Description of the Acute Myeloid Leukemia (AML) Data Set | |
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| 16:50 | Rachel Norel | DREAM6 Challenge 4: Molecular Classification of Acute Myeloid Leukaemia Challenge | |
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| 17:10 | José Vilar | Multidimensional entropies for diagnosing Acute Myeloid Leukemia from patient samples using flow cytometry data | N/A | |
| 17:30 | Michael Biehl | Molecular Classification of Acute Myeloid Leukaemia Challenge | |
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Conference: RICCI
Date: October 2011, Saturday 15th
| Hour | Speaker | Title | Presentation | Video |
|---|---|---|---|---|
| 08:45 | Miguel Àngel Pujana | Introduction | |
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| 09:00 | Manel Esteller | Human Cancer Epigenomes | N/A | N/A |
| 09:40 | Heidi Dvinge | The transcriptional landscape of miRNAs in breast cancer | |
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| 10:00 | Raymond Cho | Temporal Dissection of Tumorigenesis in Primary Cancers | |
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| 10:40 | Gabriel Capellá | Activating KRAS, BRAF and PIK3CA mutations converge at a transcriptional level and predict treatment response to cetuximab in colorectal cancer | |
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| 11:30 | Franziska Michor | Evolution of the cancer genome | N/A | |
| 12:10 | Bernat Gel | Characterirzation and interpretation of MPNST-associated transcriptional imbalances | |
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| 13:30 | Núria López-Bigas | Integration and data-mining of multidimensional oncogenomic data | N/A | |
| 14:30 | Alfonso Valencia | Computational Challenges in Personalize Medicine | |
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| 15:10 | Eva Szczurek | Epistasis and more: Modeling genetic interactions in cancer | |
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| 15:30 | Dana Peer | On the road to personalized therapy, a systems approach | |
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| 16:10 | Álvaro Aytes | FoxO3a drives a regultatory network associated with therapeutic response in metastatic prostate cancer | |
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| 17:00 | Gustavo Stolovitzky | Quantitative modeling in Cancer Research: Two Dynamic Stories | |
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| 17:40 | Gwenael Leday | A flexible framework for modeling the association between DNA copy number and gene expression | |
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| 18:00 | Julio Sáez-Rodríguez | Comparative logical models of signaling networks in normal and transformed hepatocytes | N/A | N/A |
| 18:40 | Christopher Maxwell | BRCA1: From network analysis to carcinogenesis | |
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Conference: RECOMB SYSTEMS BIOLOGY PROGRAM (1st day)
Date: October 2011, Sunday 16th
| Hour | Speaker | Title | Presentation | Video |
|---|---|---|---|---|
| 08:45 am | Andrea Califano | Introduction | N/A | |
| 09:00 am | Barry Honig | Structure-based prediction of protein-protein interactions on a genome-wide scale | |
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| 09:40 am | Federica Eduati | Dynamic modeling of miRNA-mediated Feed-Forward Loops | |
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| 10:00 am | Carlo Consentino | Structural Bistability of the GAL Regulatory Network and Characterization of its Domains of Attraction | |
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| 10:20 am | Anthony Wright | Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions (IDRs) in proteins | |
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| 11:10 am | Sylvia Plevritis | Inferring Biological Progression from High Dimensional Data | |
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| 11:50 pm | Jaanika Kronberg | High level dynamical models in non-model species | |
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| 12:10 pm | Francesco Vallania | Modeling the relationship between Mean and Variance in Gene Expression | |
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| 12:30 pm | Xiling Shen | A microRNA Mediated Switch Regulates Asymmetric Division of Colon Cancer Stem Cells | |
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| 02:10 pm | Manolis Kellis | Epigenomic views of complex disease reveal 1000s of causal variants | |
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| 02:50 pm | Liram Vardi | A Linearized constraint based approach for modeling signaling networks | |
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| 03:10 pm | Yang Yinyi | An S-System Parameter Estimation Method for Biological Networks | |
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| 03:30 pm | Tanja Vavouri | Does the promoter type affect the chromatin organization within the gene? | N/A | |
| 03:50 pm | Michele Caselle | The role of miRNA-mediated Feed Forward Loops in the Human Regulatory Network | |
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| 04:40 pm | Rune Linding | Modeling of cancer kinome networks | N/A | |
| 05:20 pm | Giusseppe Jurman | Biological network comparison via Ipsen-Mikhailov distance | |
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| 05:40 pm | Federico Morán | Multi-criteria Optimization Of Regulation in Metabolic Networks |
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| 06:00 pm | Janusz Dutkowski | Protein networks as logic functions in development and cancer | |
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| 06:20 pm | Merja Heinaniemi | Gene circuit signatures in cell type transcriptomes reveal lineage control | N/A | N/A |
| 06:40 pm | Daniel Marbach | NetworkInference.org - A community platform for gene network inference | |
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Conference: RECOMB SYSTEMS BIOLOGY PROGRAM (2nd day)
Date: October 2011, Monday 17th
| Hour | Speaker | Title | Presentation | Video |
|---|---|---|---|---|
| 08:45 am | Andrea Califano | Introducción | N/A | |
| 09:00 am | Scott Armstrong | Gene Expression and Epigenetic Control Of Leukemia Stem Cell Development | |
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| 09:40 am | Yael Silberberg | Large Scale Elucidation of Drug Response Pathways in Humans | |
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| 10:00 am | Francesco Falciani | A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease | |
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| 10:20 am | Miguel Rocha | Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression | |
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| 11:10 am | Luis Serrano | M pneumoniae: Towards a full quantitative understanding of a free-living system | |
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| 11:50 pm | Mukesh Bansal | Dissecting signaling transduction network in non small cells lung cancer | |
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| 12:10 pm | David Amar | Using differentially correlated gene pairs for classification and regulatory analysis of expression profiles from multiple diseases | |
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| 12:30 pm | Antonina Mitrofanova | Interrogating therapeutic response in a mouse model of aggressive prostate cancer | |
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| 02:20 pm | Xavier Solé | Master Regulators of metastasis in early-stage colon cancer | |
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| 02:40 pm | Alexandra Dana | Efficient manipulations of synonymous mutations for controllingtranslation rate |
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| 03:00 pm | Roee Amit | Anti-cooperative and cooperative protein-protein interactions between TetR isoforms on synthetic enhancers | N/A | |
| 03:20 pm | Joan Planas-Iglesias | To Bind or not To Bind: Predicting protein-protein interactions from favouring and disfavouring local structural features | N/A | |
| 04:10 pm | Dennis Vitkup | Complex Genetics and Systems Biology of Autism | |
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| 04:50 pm | Milana Morgenstern | Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts | |
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| 05:10 pm | Tamir Tuller | Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions | |
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| 05:30 pm | Edwing Wang | The human phosphotyrosine signaling network- evolution and hotspots of hijacking in cancer | |
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[still not available] Download Available Recomb SB 2011 Presentations
Conference: RECOMB REGULATORY GENOMICS PROGRAM
Date: October 2011, Tuesday 18th
| Hour | Speaker | Title | Presentation | Video |
|---|---|---|---|---|
| 08:45 am | Manolis Kellis | Introduction | |
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| 09:00 am | Gary D Stormo | Predicting DNA-binding specificity from protein sequence | N/A | |
| 09:40 am | Emi Tanaka | Improved similarity scores for comparing motifs | |
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| 10:00 am | Roee Amit | Building enhancers from the ground up: a synthetic biology approach | N/A | |
| 10:20 am | Gary D Stormo | Fast, sensitive discovery of conserved genome-wide motifs | N/A | |
| 11:10 am | Alexander Stark | Regulatory genomics in Drosophila | N/A | |
| 11:50 pm | Armita Nourmohammad | Formation and Conservation of Regulatory Binding Site Complexes |
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| 12:10 pm | Marina Naval | Cross-‐species Tag-‐Seq reveals a conserved Glass targetome underlying photoreceptor cell specification in Drosophila | |
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| 12:30 pm | Rahul Siddharthan | Evolution of binding sites in yeast | |
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| 12:50 pm | Quaid Morris | Profiling and initial analysis of 56 Drophosila RNA-binding protein binding preferences using RNAcompete | N/A | |
| 02:30 pm | Jonathan K Pritchard | Variation in chromatin accessibility is a key determinant of heritable variation in gene expression | N/A | |
| 03:10 pm | Mathieu Clément-Ziza | Determining the genetic contribution to transcript variation through RNA deep sequencing |
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| 03:30 pm | Marit Ackermann | The impact of genetic variation on gene expression dynamics |
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| 03:50 pm | Roger Pique-Regi | Variation in transcription factor binding inferred by DNase-seq assays provides molecular mechanisms for gene expression variation |
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| 04:10 pm | Daphne Ezer | Mechanistic model of how AT repeats influence gene expression | |
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| 05:00 pm | Mitchell Guttman | Functional integration of lincRNAs in the molecular circuitry of the cell | |
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| 05:20 pm | Andrea Tanzer | Regulation of Regulators: Small ncRNA - Host Gene Relationships | |
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| 06:00 pm | Hadas Zur | Determinants of Translation Initiation in Eukaryotes | |
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| 06:20 pm | Aly Azeem Khan | Identifying non-canonical microRNA targeting with differential CLIP-seq | |
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Conference: RECOMB REGULATORY GENOMICS PROGRAM
Date: October 2011, Wednesday 19th
| Hour | Speaker | Title | Presentation | Video |
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| 08:45 am | Manolis Kellis | Introduction | N/A | N/A |
| 09:00 am | Martha L Bulyk | Transcription Factors and DNA Regulatory Elements | |
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| 09:40 am | Carine Gubelmann | DNA-centered identification and mapping of metazoan transcription factor-DNA interactions within regulatory elements | |
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| 10:00 am | Aleksander Jankowski | Predicting cell type-specific transcription factor cooperative binding | |
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| 10:20 am | Stein Aerts | CisTargetX 2.0 Genome-wide integration of regulatory features for the discovery of CRMs in Drosophila | |
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| 11:10 am | Eileen E Furlong | Making global predictions of cis-regulatory activity | N/A | |
| 11:50 pm | Thu Hang Pham | Dynamic epigenetic enhancer signatures are predictive for key transcriptional regulators associated with cellular di!erentiation states | |
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| 12:10 pm | Thomas Sakoparnig | Binding pro les of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing | |
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| 12:30 pm | Ivan Costa | Inferring gene expression from histone modifications and transcription factor affinity on lymphoid cell development | |
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| 12:50 pm | Christel Goudot | The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins | N/A | |
| 02:30 pm | Andrea Califano | MicroRNA-mediated regulation accounts for missing genetic variability in Glioblastoma | |
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| 03:10 pm | Thierry Forné | Modulated contact frequencies at gene-rich loci support a statistical helix model for mmalian chromatin organization | |
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| 03:30 pm | Sagi Shapira | N/A | N/A | |
| 03:50 pm | Francis Chin | MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species | |
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| 04:10 pm | Alex Greenfield | Incorporating Prior Knowledge Into Network Inference |
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[still not available] Download Available Recomb RG 2011 Presentations
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