List of works - Saurabh Sinha

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

scientific article

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

scientific article (publication date: December 2009)

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

scientific article published on 26 April 2018

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

scientific article published in March 2011

A probabilistic method to detect regulatory modules

scientific article published in January 2003

A statistical method for alignment-free comparison of regulatory sequences

scientific article published in July 2007

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

scientific article

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

scientific article

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

scientific article published on 22 February 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

scientific article

Assessing computational tools for the discovery of transcription factor binding sites

scientific article

Automated prostate tissue referencing for cancer detection and diagnosis

scientific article

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

scientific article published on 13 July 2020

Big Data: Astronomical or Genomical?

scientific article published on 7 July 2015

ChIPs and regulatory bits.

scientific article published in February 2010

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

scientific article published on 28 January 2008

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy

scientific article (publication date: 2013)

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

scientific article published in October 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

scientific article

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

scientific article published on 16 July 2018

Discovery of novel transcription factor binding sites by statistical overrepresentation

scientific article

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

scientific article

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

scientific article

Evolution of cis-Regulatory Sequences in Drosophila ⬇️

scientific article published on January 1, 2010

Evolution of regulatory sequences in 12 Drosophila species

scientific article

Evolutionary origins of transcription factor binding site clusters

scientific article published on 10 November 2011

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

scientific article

Genome Surveyor 2.0: cis-regulatory analysis in Drosophila

scientific article

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

scholarly article

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

scientific article

Global parameter estimation for thermodynamic models of transcriptional regulation.

scientific article published on 30 May 2013

Global shape of Toll activation is determined by wntD enhancer properties

scientific article published on 03 January 2020

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

scientific article published on 21 August 2009

Identification of pathways associated with chemosensitivity through network embedding

scientific article published on 20 March 2019

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

scientific article published on 5 August 2011

Improving prediction of prostate cancer recurrence using chemical imaging

scientific article

Incorporating chromatin accessibility data into sequence-to-expression modeling

scientific article

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

scientific article published on 15 November 2006

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

scientific article published on 22 December 2020

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

scientific article

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.

scientific article published on 11 August 2017

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

scientific article published on January 2007

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

scientific article published on 24 September 2007

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

scientific article

Motif enrichment tool

scientific article

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

scientific article published on October 2009

Multimodal microscopy for automated histologic analysis of prostate cancer

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in October 2017

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

scientific article

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

scientific article

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

scientific article published on June 2016

Redeployment of a conserved gene regulatory network during Aedes aegypti development

scientific article published on 21 June 2016

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

scientific article

SigMat: a classification scheme for gene signature matching.

scientific article published in July 2018

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

scientific article published on 04 October 2013

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

scientific article

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

scientific article published on 08 July 2020

The Role of Chromatin Accessibility in cis-Regulatory Evolution

scientific article published on 01 July 2019

The role of chromatin accessibility in cis-regulatory evolution

The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression

scientific article (publication date: 2012)

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

scientific article published on September 16, 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

scientific article

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

scientific article

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

scientific article published on 29 March 2017

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

scientific article

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

scientific article

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

scientific article

List of works by Saurabh Sinha

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 role of chromatin accessibility in cis-regulatory evolution

The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression

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