Shandar Ahmad

Dean School of Computational and Integrative Sciences (SCIS)
Jawaharlal Nehru University (JNU), New Delhi

Shandar Ahmad is interested in developing data-driven algorithms and applications for biological data with an integrative perspective. His core research in basic science relates to investigating biomolecular interactions using machine learning approaches and developing novel algorithms for it. He has developed methods to predict DNA-binding proteins and their binding sites from sequence and has pioneered in integrating sequence information with gene expression for such predictions.
His current interests are in using DNA-shape for investigating genome-wide interaction patterns of transcription factors in local and higher dimensional chromatin structures.
In addition Shandar’s lab is developing methods for single cell transcriptome analysis, dimension reduction of Biological data and genotype-phenotype associations from genomic sequence contents.
Shandar also enjoys reading and writing poetry. His works on English Ghazals have recently been published by Studera Press. He blogs about science and society and posts his poetry on

Principal Investigator | Supervisor | Administrator

Further information

RTG Projects
Research interest
Field of Expertise
Selected publications
Complete list of publications
Contact details
Network within Big Data

RTG Projects

PhD supervisor for: Arfa Jabin (start of PhD 2018)

Research interest

  • Transcription factor dynamics and Genome-wide DNA local and higher structures using Biological big data sets.
  • Meta-analysis of Gene expression and other heterogenous Biological data.
  • Genotype-Phenotype association predictions from integratives data analytics.
  • Dimensionality reduction of Biological data and single cell transcriptomics
  • Computational diagnostics and prenatal disease prediction.

Field of Expertise

Biological big data analytics; machine learning

Selected publications

  • Hutchins, Andrew Paul; Diez, Diego; Takahashi, Yoshiko; Ahmad, Shandar; Jauch, Ralf; Tremblay, Michel Lucien; Miranda-Saavedra, Diego; (2013) Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions, Nucleic acids research, 41,4, 2155-2170
  • Andrabi, Munazah; Hutchins, Andrew Paul; Miranda-Saavedra, Diego; Kono, Hidetoshi; Nussinov, Ruth; Mizuguchi, Kenji; Ahmad, Shandar; (2017) Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences, Scientific Reports, 7,1, 4071
  • Ahmad, Shandar; Keskin, Ozlem; Mizuguchi, Kenji; Sarai, Akinori; Nussinov, Ruth; (2010) CCRXP: exploring clusters of conserved residues in protein structures, Nucleic acids research, 38, suppl_2, W398-W401
  • Ahmad, Shandar; Keskin, Ozlem; Sarai, Akinori; Nussinov, Ruth; (2008)
    Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins, Nucleic acids research, 36,18,5922-5932
  • Andrabi, Munazah; Mizuguchi, Kenji; Sarai, Akinori; Ahmad, Shandar; (2009) Prediction of mono-and di-nucleotide-specific DNA-binding sites in proteins using neural networks, BMC structural biology, 9,1,30
  • Ahmad, Shandar; Kono, Hidetoshi; Arauzo-Bravo, Marcos J; Sarai, Akinori; (2006) ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition,Nucleic acids research, 34, suppl_2, W124-W127
  • Ahmad, Shandar; Prathipati, Philip; Tripathi, Lokesh P; Chen, Yi-An; Arya, Ajay; Murakami, Yoichi; Mizuguchi, Kenji; (2017)Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism,Nucleic acids research, 46,1,54-70

Contact details


Room #9  
School of Computational and Integrative Sciences,  
Jawaharlal Nehru University,  
New Delhi-110067  

Phone: +91-11-2670-4171;  +91-11-2674-8788 

Network within Big Data

Heidelberg Principal Investigator: Matthias Schlesner

PhD candidate: Arfa Jabin Phase 2

Carl Herrmann