Presenting Author

Abstract Title

Talk/Poster

Adelman, Karen L

Controlling the transition into productive elongation

talk

Alfonso Gonzalez, Carlos

ELAV regulates the neuronal circRNA landscape

poster

Allen, Mary A

A transcription factor inference method that broadly measures TF activity and identifies mechanistically distinct TF networks

poster

Arda, Efsun

Predictive prioritization of enhancer function in human pancreas cells

poster

Azukas, Joshua

Unveiling heterogeneity in synthetic gene circuit dynamics through single-cell time-lapse imaging

poster

Badal, Dushyant Y

Investigating dependence of transcriptional onset time on transcription factor-driven accessibility of enhancers

poster

Baderna, Valentina

Investigating the assembly rules used by transcription factors to open chromatin using a chromatin-integrated reporter assay

poster

Bai, Gali

Chromatin accessibility profiling with small molecule intercalation and long-read sequencing

poster

Barbadilla Martinez, Lucia

Uncovering the principles of human promoter regulation using lightweight MPRA-trained deep learning models

poster

Bartley-Dier, Emma L

Integration of cis regulatory grammar and biomolecular condensates in transcription

poster

Battistoni, Giorgia

Light-driven combinatorial barcoding for tuneable spatial profiling

poster

Bayanjargal, Ariunaa

The DBD-α4 helix of EWS::FLI is required for GGAA microsatellite binding that underlies genome regulation in Ewing sarcoma

poster

Beavers, Deidre A

ReactomeIDG—A web-based platform to predict dark proteins’ functions in the context of reactome pathways

poster

Beyer, Daniel

Transcription factors with similar DNA-binding domains avoid redundancy through alternative effector domain activity

poster

Bintu, Lacramioara

Dynamics and mechanisms of bifunctional transcriptional effectors in human cells

talk

Boeren, Jeffrey

Large scale X-linked deletions identify HCFC1 as activator of Xist

poster

Boettiger, Alistair N

Super-enhancer interactomes from single-cells link clustering and transcription

poster

Brewster, Robert C

Characterizing individual TF function in E. coli to predict their regulation of diverse promoters

talk

Bulyk , Martha

DNA binding analysis of rare variants in homeodomains reveals novel homeodomain specificity-determining residues

poster

Bulyk , Martha

Genomic sequence context and histone marks regulate pioneer binding to nucleosomes

talk

Bulyk , Martha

Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity

poster

Burge , Christopher

Interpretable models of RNA splicing

talk

Chang, Ting-Ya

Single nucleus multiOmics identifies mouse liver open chromatin regions showing sex-biased, growth hormone-responsive enhancer activity using in vivo STARR-seq

poster

Chen, Dawn

Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes

poster

Chen, Ziheng

High-throughput reporter assays reveal the impacts of Alzheimer's disease-associated genetic variants on cis-regulatory activities

poster

Chu, Jiangbangrui

Understanding roles of fucoxanthin in treating Alzheimer‘s disease by both traditional 2D cell culture and 3D organoid culture using 3D bioprinting

poster

Chung, Wen-Yu

Using differential co-expression networks to identify disease-related genes

poster

Cohen, Lianne B

Identifying enhancers and dissecting the regulatory logic of the Drosophila innate immune system

poster

Contreras, J. Sebastian

Integrative genomics and machine learning approach to identify master transcription factors of drought adaptation in Arabidopsis thaliana

poster

Dai, Min

Development of PIASO, an efficient framework for single cell multiomics analysis, and establishment of an enhancer-based toolkit to target and manipulate distinct interneuron populations

poster

Dalakishvili, Lasha

Decoding gene regulation at the single molecule level—Insights from biophysical modeling of DNA footprinting data

poster

de Almeida, Bernardo P

The Nucleotide Transformer—building and evaluating robust foundation models for genomics

talk

Dhar, Riddhiman

Translational regulation of cell-to-cell variation in gene expression

poster

Do, Catherine

Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizer

poster

Dolsten, Gabriel

3D genome architecture precedes zygotic genome activation in Drosophila melanogaster

poster

Dooley, Peyton

Thymic epithelial cellular plasticity depends on dosage of the transcriptional coactivator AIRE

poster

Doughty, Benjamin

Quantitative models of transcription factor occupancy and gene expression from millions of single-molecule measurements

talk

Dowell, Robin D

Atlas of nascent RNA transcripts reveals enhancer to gene linkages

poster

Edginton-White, Benjamin

The role of epigenetic regulation of haemato-endothelial cell differentiation by class IIa histone deacetylases

poster

Elkon, Ran

Distinct roles of spatial genome organization in cell identity and transient stress response induced by p53

poster

El-Sherif, Ezzat

How enhancers modulate developmental timing and mediate dynamic gene expression patterns

poster

Engreitz, Jesse

An encyclopedia of enhancer-gene regulatory interactions in the human genome

talk

Enriquez, Sandy

Identifying the role of SoxC factors in retinal ganglion cell (RGC) development

poster

Erceg, Jelena

Novel gene evolution and 3D chromatin organization

talk

Fan, Jingyu

Expanding the transcription factor motif lexicon of the genome regulatory code

poster

Feldmann, Angelika

Time-resolved promoter interaction analysis identifies transient enhancer activity

talk

Fiszbein, Ana

U1snRNP regulates alternative promoters by inhibiting premature polyadenylation

talk

Fleck, Katherine

Intron classes within 3D genome landscape in development and disease

poster

Flores, Mario A

Oncogenic KSHV induces cellular transformation by hijacking FAM50A to alter RNA splicing

poster

Francois, Mat

Direct observation of SOX2 clustering dynamics at the Nanog locus during transcription burst in live stem cells

talk

Furlong, Eileen

How do enhancers function to regulate embryonic development?

talk

Fursova, Nadezda A

Live-cell imaging uncovers dynamic coupling between enhancer transcription and gene activation.

talk

Fuxman Bass, Juan I

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

talk

Gambetta, Maria Cristina C

Megabase-range control of neuronal gene transcription in Drosophila

talk

Gerard , Matthieu

The cBAF complex generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers

talk

Girardini, Kaitlin N

Reclassification of introns, a tale of more than two

poster

Guertin, Michael

Mechanisms of direct cis repression by a transcriptional activator

poster

Guharajan, Sunil

Probing the regulatory landscape of E. coli transcription factors by assessing the interplay of TF binding sequence, location, and promoter strength on gene expression

poster

Gunsalus, Laura

Model-driven strategies for regulatory element miniaturization

poster

Ha, Taekjip

Electrostatic encoding of genome organization principles within single native nucleosomes

talk

Hafner, Antonina

Super-enhancer interactomes from single-cells link clustering and transcription

talk

Hahne, Salome

Phenotypic consequences of alternative RNA isoform regulation in the mammalian brain

poster

Hall, Matt R

Controlling the transcriptional regulatory network of Streptococcus pneumoniae to combat antibiotic resistance

poster

Hastings, Renee

Conformational ensembles determine selectivity in orthologous transcription factors

poster

Hepkema, Jacob

Can AI predict how human cells interpret dinosaur DNA?

poster

Higgs, Douglas

Interactions between the enhancers and promoters of the alpha globin gene complex during differentiation

talk

Hilgers, Valerie

Cross-talk between transcription initiation and co-transcriptional RNA processing

talk

Hu, Peinan

Mapping heritable chromatin loop variants in genome imprinting with allele-specific Hi-C analysis

poster

Hughes , Tim

Codebook—Sequence specificity of uncharacterized human transcription factors

talk

Ioannidou, Zoi

Characterising stress response variability in oligodendrocyte precursor cells and immature oligodendrocytes in the context of inflammation at single-cell resolution

poster

Jensen, Christina

Long range regulation of transcription scales with genomic distance in a gene specific manner

talk

Jiang, Haining

Deep learning models reveal separable sequence rules for chromatin accessibility and enhancer activation

poster

Jolma Sidhu, Arttu K

Unexpectedly high intrinsic sequence specificity of human transcription factors

poster

Kaiser, Caroline

Promiscuous enhancer activity enables transcriptional plasticity in thymic epithelial cells for immune tolerance

poster

Kaplan, Noam

MChIP-C—Sensitive nucleosome-resolution mapping of promoter-centered interactions corroborates the enhancer-promoter looping model

poster

Kaplow, Irene M

Computational and experimental evaluations of machine learning models’ abilities to quantify enhancer activity differences between species

poster

Karollus, Alexander

Species-aware DNA language models capture regulatory elements and their evolution

poster

Karshenas, Arman

Uncovering enhancer regulatory mechanisms in D. melanogaster using high throughput deep learning and CRISPR methods

poster

Kentro, James A

Chromatin regulatory networks underlying coordinated synaptic gene expression.

poster

Khetan, Shubham

Synthetic genetic circuit reveals overlapping binding sites underlie TF genomic occupancy

poster

Khullar, Saniya

NetREm—Network regression embeddings reveal cell-type transcription factor coordination for gene regulation

poster

Kim, Jongmin

Polycomb paralog switching and somatic gene silencing in spermatogenesis

poster

Kim, Yeojin

Predicting spatial location from gene expression—A new analytical approach to spatial transcriptomics

poster

Kinney, Justin B

Specificity, synergy, and mechanisms of splice-modifying drugs

poster

Klaassen, Noud

Scalable promoter-focused MPRAs to study promoter activity across many cell types

poster

Klose, Rob J

Understanding polycomb-mediated gene repression

talk

Knoetze, Nicole

Elucidating the regulatory logic of T-cell gene expression

poster

Kosfeld, Tim D

Transcription factor motif-based supervised regression of single-cell chromatin accessibility

poster

Koulle, Andria

Unveiling the context-dependent roles of ChAHP in chromatin and transcriptional regulation

poster

Krebs, Arnaud R

Combinatorial transcription factor binding increases the frequency of enhancer usage in cell populations

talk

Krup, Alexis L

The transcription regulatory network of the integrated stress response

poster

Kukreja, Kalki

Cell division dictates proportions but not identities of cell types in vertebrate development

poster

Kundaje, Anshul B

Deep learning sequence models of diverse regulatory profiling experiments reveal a polysyntactic, context-specific window into the cis-regulatory sequence code

talk

Kvon, Evgeny

Conserved Cis-acting range extender element mediates extreme long-range enhancer activity in mammals

talk

Lal, Avantika

regLM—Designing realistic regulatory DNA with autoregressive language models

poster

Lalanne, Jean-Benoit

Exploring cis-regulatory grammar plasticity with sequence-transformed and phylogenetically diverse regulatory elements

talk

Larschan , Erica

Competition versus synergy between similar pioneer transcription factors regulates global versus local gene expression

poster

Lehman, Jesse W

Temporal regulation of mRNA biogenesis in the innate immune response

poster

Levo, Michal

A transcriptional metronome—Coupled ON-OFF durations govern gene activity

talk

Lin, Xueqiu

Decoding synergistic networks of multiple non-coding variants linked to cancer risk

poster

Liu, Annie

FACS-based CRISPR screening reveals a novel transcriptional regulator of the tumor suppressor gene PTEN

poster

Liu, Shaoxun

Predicting the DNA binding specificity of mutated transcription factors using family-level biophysically interpretable machine learning

poster

Lloyd, Catrin T

The ground-truth developmental function of H3K27me3

poster

Loell, Kaiser

Learning genotype-phenotype maps from genome-wide datasets

poster

Lorbeer, Franziska K

A genome-wide silencer screen identifies a new class of silencer elements with distinct sequence- and chromatin properties and a novel mechanism of repression

poster

Loubiere, Vincent

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

poster

Luchsinger Morcelle, Samuel Jesus

An expanded interactome of the silencing factor SPEN identifies novel proteins that act in X chromosome inactivation

poster

Ma, Zhaoxia

Dory—A computational method for differential chromatin tracing analysis

poster

Maher, Kelsey A

Topology-informed regulatory element collections coordinate cell identity gene expression programs

poster

Maurano, Matthew

Synthetic genomic dissection of enhancer context sensitivity and synergy

poster

Mayr, Juliane

Revealing the nature of transcriptional bursting variation across mouse tissues and cell types

poster

Melo, Lucas

Benchmarking DNA binding affinity models using allele-specific transcription factor binding data

poster

Menet, Jerome S

Circadian regulation of stereotypic chromatin conformations at enhancers

poster

Messina, Olivier M

Multiplexed imaging approach reveals that single-cell 3D structures is organized in discrete chromatin folding motifs

talk

Mitra, Sneha

Role of regulatory T cells in colorectal cancer

poster

Moffitt, Jeffrey

Imaging the transcriptome—Lessons for microbe-host interactions from MERFISH

talk

Molina, Nacho

Unraveling the cell-cycle dynamics of mRNA metabolism and chromatin accessibility through integration of single-cell multiome data

poster

Montgomery, Michael

Rewriting regulatory DNA to dissect and reprogram gene expression

poster

Moore, Jill E

An expanded registry of candidate cis-regulatory elements for studying transcriptional regulation

poster

Moyano, Tomas C

Gene regulatory network analysis to uncover conserved plant drought stress responses

poster

Nandu, Tulip S

Characterizing the genomic effects of low-dose estrogen in breast cancer cells

poster

Naqvi, Sahin

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

poster

Nawar, Noshin

Developing a quantitative understanding of heterogeneity in D. melanogaster’s innate immune responses

poster

Nemcko, Filip

Proteome-scale tagging and functional screening in mammalian cells by ORFtag

poster

Ness, Jillian

Exploring the functional significance of shadow enhancer architecture in development

poster

Oksanen, Marika

The mechanisms of HNRNPU-mediated RNA regulation in neuronal development and HNRNPU-related neurodevelopmental syndrome

poster

Oliva, Baldo

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements

poster

Osato , Naoki

Discovery of regulatory motifs associated with human insulator sites reveals the role of directional bias in insulator function

poster

Otto, Dominik J

Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon

poster

Ozbulut, Hasan-Can

ELAV regulates neuronal isoform choice at transcription initiation

poster

Pai, Athma A

mRNA initiation and termination are spatially coordinated

talk

Pampari, Anusri

ChromBPNet—Bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

poster

Pe'er, Dana

The role of inhibitory TFs during regeneration and tumor tumor progression

talk

Pena-Martinez, Edwin G

High-throughput validation of machine learning prediction of CHD-associated SNPs on cardiac TF-DNA binding

poster

Perkins, Mindy L

Chromatin enables precise and scalable gene regulation with factors of limited specificity

poster

Petreczky, Julia

Engineering a chromosomally integrated mammalian genetic toggleswitch with enhanced inducibility

poster

Pinheiro, Kyle

Towards predictive models of transcription factor-mismatch repair competition.

poster

Pritykin, Yuri

Ultra-long-range and interchromosomal looping and compartmentalization in regulatory T cell genome

poster

Rothkegel, Karin

Unraveling the role of cell ploidy in gene regulation of nitrate-induced leaf growth in Arabidopsis thaliana

poster

Rottenberg, Jaice T

Uncovering the functions of human viral transcriptional regulators

poster

Roy, Roshni

Epigenetic and transcriptomic landscape of IgM, IgG, and IgA influenza-specific plasma cells

poster

Rudrapatna, Akshata N

Application of maxATAC transcription factor binding predictions for gene regulatory network inference from scRNA-seq and scATAC-seq data

poster

Sahay, Harshit

A pan-cancer catalog of mutation enrichment at transcription factor binding sites

poster

Sahni, Nidhi

Systems biology coupled with transfer learning enables scalable precision medicine discovery

poster

Sakellaropoulos, Theodoros

MethNet—A robust approach to identify regulatory hubs and their distal targets from cancer data

poster

Sakharova, Helen

Combining large language models and genome-wide screens to identify codon constraints in yeast

poster

Saraswat, Manu

Regulatory network inference using single-cell multi-omics decodes determinants of Glioblastoma subtype plasticity

poster

Schroeder, Jeremy

Feedback regulation of cyclic di-GMP levels promotes an efficient transition between biofilm and dispersion in Vibrio cholerae

poster

Shah, Devina

The NuRD complex drives sequence-level and spatial changes in chromatin accessibility to regulate transcription

poster

Shepherdson, James L

Mutational scanning of CRX reveals biochemical properties of the transcriptional effector domain and classifies human variants

poster

Shi, Meihong

Transcriptomic difference of in vitro produced male and female early embryos in bovine

poster

Siggers , Trevor

Profiling transcription factor-cofactor complexes to understand gene regulatory logic and the function of non-coding single-nucleotide variants (ncSNPs)

talk

Smeal, Steven W

Evidence that dynamic cytokine stimulation facilitates transcriptional reprogramming mediated by the IKK-NF-κB signaling axis

poster

Smet, Dajo

Insights in plant gene regulatory grammar using explainable machine learning and single cell genomics

poster

Stanton , Lawrence W

Deletion in RMST lncRNA impairs hypothalamic neuronal development in a human stem cell-based model of Kallmann syndrome

poster

Stergachis, Andrew

Haplotype-resolved view of normal and pathogenic gene regulation

talk

Sun, Qian-Quan

Transcriptomic and spatial profiling of projection defined, functionally unique glutamatergic neurons in the mPFC

poster

Tam, Cyrus

Protein language models improve the target prediction of nucleic acid-binding proteins

talk

Tan, Jason

Human enhancer and promoter sequence compatibility at a controlled genomic locus

poster

Tang, Ziqi

Genomic language models struggle to learn cell-type-specific cis-regulatory mechanisms in the non-coding genome

talk

Taslim, Tommy H

Identification and functional characterization of viral cis-regulatory elements

poster

Thurm, Abby R

High-throughput discovery of regulatory domains in RNA-binding proteins

talk

Toneyan, Shushan

Interpreting cis-regulatory interactions from large-scale deep neural networks for genomics

poster

Trinh, Bon

Understanding cis-regulatory codes in lineage-gene expression

poster

Tsagkris, Stylianos

Programming the epigenome to dissect chromatin function

poster

Tullius, Thomas

RNA polymerases reshape chromatin architecture and coordinate transcription on individual fibers

poster

van der Wijst, Monique

Single-cell gene regulatory networks for the fine-mapping and interpretation of genetic variation

poster

van Oudenaarden, Alexander

Novel sequencing tools to explore translation in individual cells

talk

Van Steensel , Bas

Scalable relocation of regulatory elements to study positional logic

talk

Vandepoele , Klaas

Decoding plant transcription factor functions using cell-type specific gene regulatory networks

poster

Vasciaveo, Alessandro

Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury

poster

Velten, Lars

Synthetic genomics uncovers the design rules of lineage-specific enhancers in hematopoietic differentiation

talk

Vock, Isaac W

Uncovering transcript isoform regulatory dynamics with metabolic labeling and EZbakR

poster

Walhout, Marian

Inferring metabolism using large-scale gene expression data

talk

Wan, Yiming

Gene expression tuning via synthetic gene circuits reveals a nonmonotone invasion landscape of metastasis activator BACH1

poster

Wang, Bo

Probabilistic sequence motif usage underlying cell type conservation

talk

Wang, Siyuan

Perturb-tracing enables high-content screening of multiscale 3D genome regulators

talk

Weissman, Jonathan S

Epigenome editing as a tool for basic discovery and therapeutic intervention

talk

White, Michael A

Active machine learning of enhancer and silencer cis-regulatory grammar in a developing neural tissue

talk

Wittbschlager, Sandra

Enhancer screening at nucleotide resolution using dense base editing and allele-based readout

poster

Wong, Emily S

A Bag-of-Motif model captures cell states at distal regulatory sequences

poster

Woolley-Allen, Katherine

Multiplicative transposase cutting bias in ATAC-seq data

poster

Wu, Yawei

A genome-integrated reporter assay for systematic probing of long-range enhancer-promoter interactions

poster

Yang, Rui

Enhancing feature attribution in 3D chromatin analysis via contrastive learning

poster

Yang, Zi

Unraveling genetic insights into inflammatory bowel disease mechanisms from multiome-seq

poster

Yi, Soon

Mapping RNA-protein interactions with subcellular resolution using colocalization CLIP

poster

You, Chris (Dong Shin)

Cell size increase leads to transcriptome remodeling and lysosome vulnerability

poster

Yu, Haiyuan

Map regulatory genomic landscapes across >100 diverse human cell and tissue types through nascent transcriptome studies

poster

Zang, Chongzhi

A bias correction method for bulk and single-cell CUT&Tag

poster

Zeitlinger , Julia

Visualization and discovery of cis-regulatory sequence rules learned by neural networks

talk

Zhao, Yixin

Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells

poster