Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

H. Tomas Rube, Chaitanya Rastogi, Siqian Feng, +10

Nature Biotechnology

Accurate and sensitive quantification of protein-DNA binding affinity

Chaitanya Rastogi, H. Tomas Rube, Judith F. Kribelbauer, +9

Proceedings of the National Academy of Sciences

Transcriptional RegulationFunctional GenomicsNatural SciencesGeneticsGene Recognition +11

SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes

Todd Riley, Matthew Slattery, Namiko Abe, +4

Methods in molecular biology

BioinformaticsSequence MotifComplete RepertoireNatural SciencesGenetics +13

A unified approach for quantifying and interpreting <scp>DNA</scp> shape readout by transcription factors

H. Tomas Rube, Chaitanya Rastogi, Judith F. Kribelbauer, +1

Molecular Systems Biology

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

Siqian Feng, Chaitanya Rastogi, Ryan Loker, +4

Nature Communications

In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module

Carlos Sánchez-Higueras, Chaitanya Rastogi, Roumen Voutev, +2

Nature Communications

Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins

Judith F. Kribelbauer, Ryan Loker, Siqian Feng, +5

Molecular Cell

Transcriptional RegulationShape-readout Deficient ProteinsSignal TransductionMolecular RegulationGenetics +8

Dewetting of the Thin Liquid Bilayers on Topographically Patterned Substrates: Formation of Microchannel and Microdot Arrays

Dipankar Bandyopadhyay, Ashutosh Sharma, Chaitanya Rastogi

Langmuir

EngineeringThin Liquid BilayersPattern TransferThin BilayersMicroscale System +14

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

Liyang Zhang, Gabriella Martini, H. Tomas Rube, +6

Genome Research

22 Evolving insights on how cytosine methylation affects protein-DNA binding

Satyanarayan Rao, Ana Carolina Dantas Machado, Tianyin Zhou, +3

Journal of Biomolecular Structure and Dynamics

Histone ModificationsEpigenetic ChangeGeneticsDna MethylationMolecular Biology +14