Presenting Author

Abstract Title

Talk/Poster

Abraham, Brian J

Three-dimensional super-enhancers

poster

Adelman, Karen L

Enhancer landscapes are established through coordination activities of transcription factors and RNA polymerase II

talk

Akdemir, Kadir C

Pan-cancer analysis of structural alterations in TADs reveals novel insights into genome architecture, gene expression, and mutation rates in human cancers

talk

Amit, Ido

The power of ONE—Immunology in the age of single cell genomics

talk

Andrilenas, Kellen

Characterizing the DNA­binding differences between IRF transcription factors

poster

Ansari, Aseem

Combinatorial bZIP heterodimers display binding to unanticipated "emergent" DNA sites

talk

Ballouz, Sara

Going rogue—Outlier gene expression drives rare disease in the TAF1 syndrome cohort

talk

Beer, Michael

Assessing the impact of feature importance on regulatory mutation predictions

poster

Bekiranov, Stefan

Methods for estimating transcription factor-chromatin dynamics across the yeast genome

talk

Bernardi, Giorgio

The genomic code—Isochores encode and mold chromatin domains

poster

Bhattacharya, Surajit

Dissecting the Knot transcriptional regulatory network in dendritic development via integrative bioinformatics

poster

Booth, Gregory T

Transcriptional control imparted by conserved kinases in fission yeast

poster

Brent, Michael

What do TF binding locations tell us about functional regulation?

poster

Chakraborty, Abhijit

Characterization of genomic rearrangements in cancer cell lines from Hi-C data

poster

Chandrasekharan, Mahesh B

Dynamic modulation of histone H3 lysine-4 post-translational modifications in regulating gene transcription and chromatin structure

talk

Choate, Lauren A

Human-specific changes in transcription of the anthrax toxin receptor

poster

Chou, Shao-Pei

Global identification of transcription factors regulating promoter and enhancer directionality

poster

Combs, Peter A

Spatially varying allele specific expression in Drosophila hybrids

talk

Cramer, Patrick

Investigating gene regulation with functional genomics and structural biology

talk

Cuperus, Josh T

Predicting the translational efficiency of 5' untranslated regions

talk

Danko, Charles G

Chromatin run-on reveals nascent RNAs that differentiate normal and malignant brain tissue

poster

de Boer, Carl G

Deciphering cis-regulatory logic with millions of synthetic promoters

talk

D'Ippolito, Anthony M

Glucocorticoid-mediated gene activation and repression are associated with distinct topological dynamics

talk

Drier, Yotam N

Epigenetic silencing of CTCF binding sites in cancer perturbs DNA folding and rewires gene regulatory networks to drive tumorigenesis

talk

Dueck, Hannah

Using single-cell RNA sequencing measurements to estimate population mean and variability

poster

Eaton, Matthew L

Super-enhancer landscapes reveal novel epigenomic patient subtypes and druggable dependencies in human AML

poster

Engreitz, Jesse

Quantitative control of enhancer function by 3D chromosome conformation

talk

Ercan, Sevinc

Long-distance cooperation and hierarchy between recruitment sites specify the X chromosome for dosage compensation

talk

Eser, Umut

The ground state and evolution of promoter region directionality

talk

Fairchild, Lauren

Discrete chromatin states define tumor-specific T cell dysfunction and therapeutic reprogrammability

talk

Flam, Emily L

Discovery of differentially methylated super-enhancer elements in HPV-related head and neck squamous cell carcinoma

poster

Friedrich, Dhana

Bridging the gap—From p53 dynamics to stochastic gene expression.

poster

Fulco, Charles P

Functional maps of enhancer-promoter connectivity across genes and cell types

poster

Gagneur, Julien

Sequence features explain most of the mRNA stability variation across genes in yeast

talk

Garber, Manuel

Not all regulatory elements are conserved equally—Revisiting enhancer conservation using an innate immune model

poster

Goff, Loyal A

Cell-type specific responses to loss of Ret signaling in the developing enteric nervous system—Implications for Hirschsprung disease

poster

Gray, Jesse M

Transient elevations in neuronal activity induce a subset of the activity-regulated gene program defined by MAPK/ERK-dependent enhancers

talk

Greenside, Peyton

Interpretable deep learning approaches to decipher context-specific encoding of regulatory DNA sequence in hematopoiesis

talk

Grossman, Shari

Systematic dissection of genomic features determining transcription factor binding and enhancer function

poster

Guo, Yuchun

K-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants

poster

Guvenek, Aysegul

Differential gene and mRNA isoform expression in Down syndrome neurons

poster

Han, Xinwei

Epigenomic patterns predict haploinsufficiency and enable discovery of novel risk genes of developmental disorders

poster

Hansen, Anders S

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

talk

Hawkins, David

Genome-wide identification of silencer elements and their functional validation

talk

Huang, Di

Epigenetic and genetic alterations and their influence on gene regulation in CLL

poster

Huang, Jialiang

Dissection of super-enhancer hierarchy based on chromatin interactions

poster

Hughes, Tim R

Sequence specificity of unconventional RNA binding proteins

talk

Ietswaart, Robert

Cell size scaling of RNA dynamics at FLC are altered by antisense transcription

talk

Jacobs, Jelle

Decoding epithelial enhancer logic using natural variation and single-cell ATAC-seq

talk

Jordan III, William T

Clustering of cis-elements open chromatin to promote X-specificity of Drosophila dosage compensation

poster

Kakumanu, Akshay

Characterizing regulatory sequence features that discriminate between overlapping annotation labels

poster

Kalita, Cynthia A

Accurate allele-specific analysis for high-throughput reporter assays

poster

Kang, Jee youn

STAT1/2-mediated high order chromatin structure enhances therapeutic efficacy through viral mimicry

poster

Kaplow, Irene M

An integrative analysis of C2H2 zinc finger ChIP-seq datasets reveals novel roles and motifs of C2H2 zinc finger transcription factors

poster

Keenan, Jessica L

A high-throughput approach for designing novel cell-based signal integrators

poster

Kim, Daniel S

Learning dynamic regulatory networks in skin differentiation

poster

King, Dana M

Understanding the grammar of regulatory sequences in mouse embryonic stem cells

poster

Kreimer, Anat

Leveraging massive parallel reporter assays for functional regulatory elements prediction

poster

Kumar, Vivek

Transcriptomic analysis in the open-science community platform, KBase

poster

Kundaje, Anshul B

The ENCODE-DREAM in vivo transcription factor binding site prediction challenge

talk

Lareau, Liana F

A neural network to model translation and design sequences optimized for expression

talk

Larson, Daniel

Intrinsic dynamics of a single human gene reveal the limits of information transfer

talk

Larsson, Ola

Estrogen receptor alpha coordinates homeostatic gene expression programs via translational buffering

poster

Lee, Young Koung

Regulation of HB34 involved in plant architecture via miR157 in Arabidopsis thaliana

poster

Li, Shan

Quantifying deleterious effects of regulatory variants

poster

Lihm, Jayon

Meta-analysis of chromatin accessibility to determine variable features

poster

Litterman, Adam J

Functional activity of RNA-binding protein binding sites drives 3’ UTR evolution

talk

Liu, Guojing

5’captured transcriptome sequencing profiling across neuronal differentiation

poster

Liu, Nian

N⁶-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

poster

Maicas, Mirren

Transcriptional regulatory logic of C.elegans ADF serotonergic neuron

poster

Mariani, Luca

Transcription factor-8mer glossary with GENRE genomic background enables precise identification of lineage-specific co-regulators

talk

Marquez, Eladio J

Efficient identification of regulatory interactions via dynamic network discovery from TF footprinting data

poster

Martins, Andrew J

Environment tunes propagation of cell-to-cell variation in the human macrophage gene network

talk

Matharu, Navneet

Enhancer/promoter activation by CRISPRa as a novel therapeutic strategy for haploinsufficiency disease model

talk

McDowell, Ian

Glucocorticoid receptor binds to nearly all enhancers and dramatically alters activation

poster

McKay, Daniel

The hormone-dependent transcription factor E93 controls temporal specific gene expression by regulating the accessibility of temporal specific enhancers

talk

Mele Messeguer, Marta

Transcriptional regulation distinguishes lincRNAs and mRNAs

poster

Mellis, Ian

Visualizing adenosine to inosine RNA editing with single-molecule resolution in mammalian cells

poster

Mirny, Leonid

Genome in 3D—Models of chromosome folding

talk

Mishmar, Dan

Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

poster

Moily, Nagaraj

Transcriptional signatures of huntingtin exon 1 aggregation states yield a neuroprotective therapeutic target

poster

Moon, Kevin R

PHATE—Potential heat-diffusion affinity-based trajectory embedding for visualizing and annotating branching trajectory structure in biological data

poster

Morris, Samantha A

Dissecting direct reprogramming from fibroblasts to induced endoderm progenitors using single-cell RNA-seq

talk

Morse, Randall H.

Mechanisms of Mediator recruitment in yeast

poster

Mortazavi, Ali

Dynamic gene regulatory networks of human myeloid differentiation

poster

Muhire, Brejnev M

Genome-wide detection of regions of differential chromatin accessibility between different lineages of lymphocyte cells

poster

Murray, John I

Quantifying the mechanisms controlling the robust, context-specific activation of Wnt-responsive developmental enhancers at single-cell resolution

talk

Nandakumar, Vivek

Direct visualization and quantitative spatial annotation of regulatory DNA in situ

talk

Noyes, Marcus B

The capture of low affinity interactions improves our ability to predict protein interactions in vivo

poster

Okamura, Katsutomo

Transcriptional and post-transcriptional mechanisms controlling miRNA expression during Drosophila development

poster

Orenstein, Yaron

Sequence libraries to cover all k-mers using degenerate characters

poster

Orenstein, Yaron

Structure-based prediction of RNA-protein interactions on a transcriptome-wide scale

poster

Orenstein, Yaron

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models

poster

Osmanbeyoglu, Hatice U

Modeling the impact of somatic alterations in ubiquitin pathway genes across human cancers

poster

Pearl, Jocelynn R

Reconstruction of a transcriptional regulatory network for the human brain identifies core regulators of psychiatric disorders

poster

Peng, Pei-Chen

Quantifying the relationships among evolutionary changes in sequence, accessibility, TF binding and regulatory activity of enhancers of a well characterized developmental system

talk

Penvose, Ashley

Elucidating genomic regulation by the class II nuclear receptors

poster

Pinello, Luca

Chromatin state variability—A guide to uncover non-coding functional genomic regions and potential regulated genes

poster

Pollard, Katherine S

Massively parallel dissection of human accelerated regions

talk

Price, Amanda J

Dynamic, cell type-specific cis-regulatory element use in the developing human frontal cortex

poster

Pritykin, Yuri

CLIPanalyze—An algorithm to detect and analyze peaks in CLIP-seq data

poster

Pritykin, Yuri

Computational analysis of genome-wide chromatin accessibility and transcriptional expression data to characterize epigenetics of CD8 T cell tolerance

poster

Radovani, Ernest

Gene regulation by the human C2H2 zinc finger proteins

poster

Rahi, Sahand Jamal

Oscillatory stimuli resolve fundamental circuit topologies for adaptation

talk

Raj, Arjun

Single cell analysis of therapy resistance in cancer

talk

Ramani, Vijay

Massively multiplex single-cell Hi-C

talk

Rao, Satyanarayan

Transcription factor family-specific DNA readout by multiscale specificity models

poster

Rastogi, Chaitanya

Accurate and interpretable quantification of protein-DNA recognition

talk

Reddy, Karen L.

Dynamic in situ chromosome conformation

talk

Rich, Charlotte S

Deciphering the assembly of immunity networks in a complex plant organ using high resolution transcriptomics

poster

Richards, Allison L

Characterization of changes in RNA processing across 89 cellular environments

poster

Rieber, Lila

3-D human genome structures at kilobase resolution

poster

Risca, Viviana I

RICC-seq—Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

talk

Roe, Jae Seok

Enhancer reprogramming as a driver of pancreatic cancer metastasis

poster

Roy, Sushmita

Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

talk

Rumley, Jonathan D

Regulation of opposite Wnt target genes in C. elegans embryonic development

poster

SAGENDORF, JARED

DNAproDB—A web-based tool for structural analysis of DNA-protein complexes

poster

Sahu, Biswajyoti

Enhancer activity of transcription factor-binding motifs identified from HT-SELEX

talk

Samee, Md Abul Hassan

Many transcription factors recognize DNA shape independent of sequence

poster

Santos, Sergio

Systematic assessment of alternative transcript usage in human tissues

poster

Sanz, Joaquin

Genetic contribution to population differences in transcriptional response to infection in primary macrophages

poster

Schönherz, Anna A

A classification system that associates normal myeloid progenitor subsets with  Acute Myeloid Leukaemia prognosis

poster

Segal, Eran

Dissecting the effect of gene expression levels on cellular fitness

talk

Sewell, Jared

Delineation of a cytokine trotein-DNA interaction network

poster

Shao, Yingyao

Optimization of antisense oligonucleotide therapy in a mouse model that exclusively express two copies of human MECP2

poster

Siebenthall, Kyle

The regulatory landscape of endocrine disruptor exposure

poster

Singh, Shashank

Predicting enhancer-promoter interaction using genomic sequence features only

poster

Sonawane, Abhijeet R

Understanding tissue-specific gene regulation

poster

Staller, Max V

Deep mutational scanning of a transcription factor activation domain reveals the role of intrinsic disorder

talk

Stein-O'Brien, Genevieve

Genome specific transcriptional signatures predict differentiation biases in human ES/IPS cells

poster

Sun, Mingan

Deciphering the function of different PcG recruiters for Polycomb regulation

poster

Szczesnik, Tomasz

High-throughput elucidation of Wnt-dependent transcription factor binding grammar

talk

Tang, Mei San

Chromatin structure and transcriptional networks of alternatively activated macrophages derived from recruited monocytes or tissue resident lineages

poster

Taylor, James P

Chromosome conformation in context

poster

Tewhey, Ryan

Direct identification of non-coding variants that modulate expression using high-throughput experimental assays

talk

Thibodeau, Asa J

Cell-type-specific promoters and enhancers are connected differentially in the three-dimensional chromatin space

poster

Tippens, Nathaniel D

Functional comparison of enhancers defined by histone modification or nascent transcription profiles

poster

Trono, Didier

Mobile elements, polydactyl proteins and the genesis of human-specific regulatory networks

talk

Ucar, Duygu

The chromatin accessibility signature of human immune system aging mostly stems from changes in memory CD8 T cells

poster

Ursu, Oana

A graph diffusion framework for measuring multi-scale reproducibility of 3D chromatin contact maps

poster

van Schaik, Tom

Unraveling the spatial organization of the genome near nuclear compartments using DamID

poster

Vierstra, Jeff

Comprehensive Identification of cis- and trans- elements driving hematopoeisis

poster

Vinson, Charles

Using protein binding microarrays (PBMs) to examine transcription factors binding to DNA containing 5mC and 5hmC

poster

Wan, Yihan

Capturing transcription and splicing dynamics across the human genome with single-molecule sensitivity in living cells

talk

Wang, Yuchuan

Integrated genomic analysis of nuclear compartmentalization using probabilistic modeling

talk

Wei, Bei

Limited sets of transcription factors are strongly active in specific cell types

poster

Weirauch, Matthew T

Transcription factors operating across disease loci—EBNA2 in autoimmunity

poster

Weng, Zhiping

ENCODE Encyclopedia—Featuring a registry of candidate regulatory elements and the visualization tool SCREEN for searching them

poster

Wojtowicz, Damian

Genome-wide mapping and computational analysis of non-B DNA structures in vivo

poster

Xie, Shiqi

Multiplexed engineering and analysis of combinatorial enhancer activity in single cells

talk

Yan, Koon-Kiu

MrTADFinder—A network-based approach to identify topologically associating domains in multiple resolutions

poster

Yang, Haiwang

Drosophila positive regulators of transcriptional elongation regulate specific metabolic genes and sex-biased expression in adults

poster

Yuan, Xuefei

From mammals to fish and back again—Discovering new regulators of early cardiac development

talk

Zavolan, Mihaela

Pre-mRNA splicing and polyadenylation in cell type specification

talk

Zeitlinger, Julia

Paused RNA polymerase II inhibits new initiation

talk

Zeng, Zhouhao

Study of regulated intron retention and its impact on mRNA degradation

poster

Zhao, Kangmei

Epigenomic signatures of metabolism in Arabidopsis thaliana

poster

Zhu, Fangjie

Binding of transcription factors to nucleosomal DNA

talk