Lista de obras -

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

artículo científico publicado en 2015

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data

artículo científico publicado en 2009

A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models.

artículo científico publicado en 2018

A new segmentation framework for infrared spectroscopic imaging using frequent pattern mining

artículo científico publicado en 2011

A probabilistic method to detect regulatory modules

artículo científico publicado en 2003

A statistical method for alignment-free comparison of regulatory sequences

artículo científico publicado en 2007

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

artículo científico publicado en 2008

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution

artículo científico publicado en 2009

An epigenomic shift in amygdala marks the transition to maternal behaviors in alloparenting virgin female mice

artículo científico publicado en 2022

An information theoretic treatment of sequence-to-expression modeling

scientific article published on 26 September 2018

An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes

scientific article published on 07 January 2021

Analysis of variance in spectroscopic imaging data from human tissues

artículo científico publicado en 2011

Assessing computational tools for the discovery of transcription factor binding sites

artículo científico publicado en 2005

Automated prostate tissue referencing for cancer detection and diagnosis

artículo científico publicado en 2016

Behavior-related gene regulatory networks: A new level of organization in the brain

artículo científico publicado en 2020

Big Data: Astronomical or Genomical?

artículo científico publicado en 2015

ChIPs and regulatory bits

artículo científico publicado en 2010

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

artículo científico publicado en 2008

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy

artículo científico publicado en 2013

Correction to 'Transcriptional regulation of brain gene expression in response to a territorial intrusion in sticklebacks'.

artículo científico publicado en 2016

Correction: Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

article by Majid Kazemian et al published 24 October 2013 in PLOS Biology

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

artículo científico publicado en 2004

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

artículo científico publicado en 2018

Discovery of novel transcription factor binding sites by statistical overrepresentation

artículo científico publicado en 2002

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data.

artículo científico publicado en 2013

Evidence for deep regulatory similarities in early developmental programs across highly diverged insects

artículo científico publicado en 2014

Evolution of cis-Regulatory Sequences in Drosophila ⬇️

artículo científico publicado el 1 de enero de 2010

Evolution of regulatory sequences in 12 Drosophila species

artículo científico publicado en 2009

Evolutionary Origins of Transcription Factor Binding Site Clusters ⬇️

artículo científico publicado el 10 de noviembre de 2011

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

artículo científico publicado en 2011

Genome Surveyor 2.0: cis-regulatory analysis in Drosophila

artículo científico publicado en 2011

Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees

artículo científico publicado en 2006

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

artículo científico publicado en 2013

Global parameter estimation for thermodynamic models of transcriptional regulation.

artículo científico publicado en 2013

Global shape of Toll activation is determined by wntD enhancer properties

artículo científico publicado en 2020

Honey bee aggression supports a link between gene regulation and behavioral evolution.

artículo científico publicado en 2009

Identification of pathways associated with chemosensitivity through network embedding

artículo científico publicado en 2019

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

artículo científico publicado en 2011

Improving prediction of prostate cancer recurrence using chemical imaging

artículo científico publicado en 2015

Incorporating chromatin accessibility data into sequence-to-expression modeling

artículo científico publicado en 2015

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment

artículo científico publicado en 2006

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks

artículo científico publicado en 2020

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

artículo científico publicado en 2015

Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

scientific article published on 23 January 2020

Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.

artículo científico

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

artículo científico publicado en 2007

MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules

artículo científico publicado en 2007

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

artículo científico publicado en 2007

Motif enrichment tool

artículo científico publicado en 2014

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse

artículo científico publicado en 2009

Multimodal microscopy for automated histologic analysis of prostate cancer

artículo científico publicado en 2011

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

artículo científico publicado en 2014

New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior

artículo científico publicado en 2012

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

artículo científico publicado en 2004

Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.

artículo científico publicado en 2017

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials

artículo científico publicado en 2010

Quantitative modeling of a gene's expression from its intergenic sequence.

artículo científico publicado en 2014

Quantitative modeling of gene expression using DNA shape features of binding sites.

artículo científico publicado en 2016

Redeployment of a conserved gene regulatory network during Aedes aegypti development

artículo científico publicado en 2016

Sequence turnover and tandem repeats in cis-regulatory modules in drosophila

artículo científico publicado en 2005

SigMat: a classification scheme for gene signature matching.

artículo científico publicado en 2018

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

artículo científico publicado en 2013

Stubb: a program for discovery and analysis of cis-regulatory modules

artículo científico publicado en 2006

Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature

artículo científico publicado en 2020

The Role of Chromatin Accessibility in cis-Regulatory Evolution

scientific article published on 01 July 2019

The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression ⬇️

artículo científico publicado el 29 de marzo de 2012

The role of chromatin accessibility in cis-regulatory evolution

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression ⬇️

artículo científico publicado el 16 de septiembre de 2010

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

scientific article published on 22 January 2020

Towards realistic benchmarks for multiple alignments of non-coding sequences

artículo científico publicado en 2010

Transcriptional regulation of brain gene expression in response to a territorial intrusion ⬇️

artículo científico publicado el 24 de octubre de 2012

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

artículo científico publicado en 2017

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

artículo científico publicado en 2017

What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation

artículo científico publicado en 2015

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

scientific article published on 11 July 2013

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

artículo científico publicado en 2003

Lista de obras de

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data

A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models.

A new segmentation framework for infrared spectroscopic imaging using frequent pattern mining

A probabilistic method to detect regulatory modules

A statistical method for alignment-free comparison of regulatory sequences

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution

An epigenomic shift in amygdala marks the transition to maternal behaviors in alloparenting virgin female mice

An information theoretic treatment of sequence-to-expression modeling

An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes

Analysis of variance in spectroscopic imaging data from human tissues

Assessing computational tools for the discovery of transcription factor binding sites

Automated prostate tissue referencing for cancer detection and diagnosis

Behavior-related gene regulatory networks: A new level of organization in the brain

Big Data: Astronomical or Genomical?

ChIPs and regulatory bits

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy

Correction to 'Transcriptional regulation of brain gene expression in response to a territorial intrusion in sticklebacks'.

Correction: Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Discovery of novel transcription factor binding sites by statistical overrepresentation

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data.

Evidence for deep regulatory similarities in early developmental programs across highly diverged insects

Evolution of cis-Regulatory Sequences in Drosophila ⬇️

Evolution of regulatory sequences in 12 Drosophila species

Evolutionary Origins of Transcription Factor Binding Site Clusters ⬇️

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

Genome Surveyor 2.0: cis-regulatory analysis in Drosophila

Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Global parameter estimation for thermodynamic models of transcriptional regulation.

Global shape of Toll activation is determined by wntD enhancer properties

Honey bee aggression supports a link between gene regulation and behavioral evolution.

Identification of pathways associated with chemosensitivity through network embedding

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

Improving prediction of prostate cancer recurrence using chemical imaging

Incorporating chromatin accessibility data into sequence-to-expression modeling

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

Motif enrichment tool

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse

Multimodal microscopy for automated histologic analysis of prostate cancer

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials

Quantitative modeling of a gene's expression from its intergenic sequence.

Quantitative modeling of gene expression using DNA shape features of binding sites.

Redeployment of a conserved gene regulatory network during Aedes aegypti development

Sequence turnover and tandem repeats in cis-regulatory modules in drosophila

SigMat: a classification scheme for gene signature matching.

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

Stubb: a program for discovery and analysis of cis-regulatory modules

Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature

The Role of Chromatin Accessibility in cis-Regulatory Evolution

The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression ⬇️

The role of chromatin accessibility in cis-regulatory evolution

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression ⬇️

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

Towards realistic benchmarks for multiple alignments of non-coding sequences

Transcriptional regulation of brain gene expression in response to a territorial intrusion ⬇️

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation