Julia Zeitlinger
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View article: GAME: Genomic API for Model Evaluation
GAME: Genomic API for Model Evaluation Open
The rapid expansion of genomics datasets and the application of machine learning has produced sequence-to-activity genomics models with ever-expanding capabilities. However, benchmarking these models on practical applications has been chal…
View article: PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data
PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data Open
Sequence-to-function neural networks learn cis-regulatory rules of many types of genomic data from DNA sequence. However, a key challenge is to interpret these models to relate the sequence rules to underlying biological processes. This ta…
View article: Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model
Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model Open
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of si…
View article: Perspective on recent developments and challenges in regulatory and systems genomics
Perspective on recent developments and challenges in regulatory and systems genomics Open
Summary: Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this pe…
View article: Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis
Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis Open
View article: Gene regulatory network co-option is sufficient to induce a morphological novelty in<i>Drosophila</i>
Gene regulatory network co-option is sufficient to induce a morphological novelty in<i>Drosophila</i> Open
Identifying the molecular origins by which new morphological structures evolve is one of the long standing problems in evolutionary biology. To date, vanishingly few examples provide a compelling account of how new morphologies were initia…
View article: Interpretable deep learning reveals the sequence rules of Hippo signaling
Interpretable deep learning reveals the sequence rules of Hippo signaling Open
Summary The response to signaling pathways is highly context-specific, and identifying the transcription factors and mechanisms that are responsible is very challenging. Using the Hippo pathway in mouse trophoblast stem cells as a model, w…
View article: Gene Regulatory Network Co-Option is Sufficient to Induce a Morphological Novelty in Drosophila
Gene Regulatory Network Co-Option is Sufficient to Induce a Morphological Novelty in Drosophila Open
View article: The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5
The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5 Open
View article: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development Open
While the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor,…
View article: Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation Open
View article: Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression"
Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression" Open
Here you can find the data supporting the conclusions in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression." The accompanying code repository can be found at https://doi.org/10.5281/zenodo.8161422.
View article: Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression"
Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression" Open
Here you can find the data supporting the conclusions in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression." The accompanying code repository can be found at https://doi.org/10.5281/zenodo.8161422.
View article: <i>De novo</i>distillation of thermodynamic affinity from deep learning regulatory sequence models of<i>in vivo</i>protein-DNA binding
<i>De novo</i>distillation of thermodynamic affinity from deep learning regulatory sequence models of<i>in vivo</i>protein-DNA binding Open
Transcription factors (TF) are proteins that bind DNA in a sequence-specific manner to regulate gene transcription. Despite their unique intrinsic sequence preferences, in vivo genomic occupancy profiles of TFs differ across cellular conte…
View article: Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation
Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation Open
Summary Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep le…
View article: Off the deep end: What can deep learning do for the gene expression field?
Off the deep end: What can deep learning do for the gene expression field? Open
View article: De novo inference of thermodynamic binding energies using deep learning models of in vivo transcription factor binding
De novo inference of thermodynamic binding energies using deep learning models of in vivo transcription factor binding Open
We introduce Affinity Distillation (AD), a method for extracting thermodynamic affinities de-novo from in-vivo immunoprecipitation experiments using deep learning. We show that neural networks modeling base-resolution in-vivo binding profi…
View article: Short tandem repeats bind transcription factors to tune eukaryotic gene expression
Short tandem repeats bind transcription factors to tune eukaryotic gene expression Open
Short tandem repeats (STRs) are enriched in eukaryotic cis -regulatory elements and their polymorphisms alter gene expression, yet how they regulate transcription remains unknown. We find that STRs can modulate transcription factor (TF)-DN…
View article: Stochastic mRNA production by a three-state gene
Stochastic mRNA production by a three-state gene Open
We consider a model of mRNA production governed by the dynamics of a gene that exists in three possible states -- inactive, poised and active. The transitions between the adjacent states are controlled by stochastic processes characterized…
View article: Lola-I is a developmentally regulated promoter pioneer factor
Lola-I is a developmentally regulated promoter pioneer factor Open
While enhancers are often regulated at the level of accessibility by pioneer factors, promoters tend to be constitutively accessible and poised for activation by paused Pol II — thus are often not considered as sites of developmental regul…
View article: The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters
The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters Open
The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene expression is not well understood. During Drosophila oogenesis, th…
View article: The SAGA core module is critical during<i>Drosophila</i>oogenesis and is broadly recruited to promoters
The SAGA core module is critical during<i>Drosophila</i>oogenesis and is broadly recruited to promoters Open
The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene activation in specific biological contexts is not well understood.…
View article: Base-resolution models of transcription-factor binding reveal soft motif syntax
Base-resolution models of transcription-factor binding reveal soft motif syntax Open
View article: TATA and paused promoters active in differentiated tissues have distinct expression characteristics
TATA and paused promoters active in differentiated tissues have distinct expression characteristics Open
Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this affects their tissue-specific gene expression characteristics is not well understood. While promoters with Pol II pausing el…
View article: Seven myths of how transcription factors read the cis-regulatory code
Seven myths of how transcription factors read the cis-regulatory code Open
Genomics data are now being generated at large quantities, of exquisite high resolution and from single cells. They offer a unique opportunity to develop powerful machine learning algorithms, including neural networks, to uncover the rules…
View article: β-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells
β-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells Open
Mouse embryonic stem cells (ESCs) cultured in defined medium resemble the pre-implantation epiblast in the ground state, with full developmental capacity including the germline. β-Catenin is required to maintain ground state pluripotency i…
View article: TATA and paused promoters active in differentiated tissues have distinct expression characteristics
TATA and paused promoters active in differentiated tissues have distinct expression characteristics Open
Core promoter types differ in the extent to which RNA polymerase II (Pol II) pauses after initiation, but how this difference affects their tissue-specific gene expression characteristics is not well understood. While promoters with Pol II…
View article: An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of<i>Drosophila melanogaster</i>
An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of<i>Drosophila melanogaster</i> Open
During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mappi…
View article: Base-resolution models of transcription factor binding reveal soft motif syntax
Base-resolution models of transcription factor binding reveal soft motif syntax Open
Summary The arrangement of transcription factor (TF) binding motifs (syntax) is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution…
View article: An atlas of transcription factors expressed in the<i>Drosophila melanogaster</i>pupal terminalia
An atlas of transcription factors expressed in the<i>Drosophila melanogaster</i>pupal terminalia Open
During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mappi…