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Employment (2)

Jawaharlal Nehru University: New Delhi, Delhi, IN

2016-03-16 to present | Professor (School of Computational and Integrative Sciences)
Employment
Source: Self-asserted source
Shandar Ahmad

National Institutes of Biomedical Innovation: Ibaraki, Osaka, JP

2007-01-17 to 2016-03-15 | Research Scientist
Employment
Source: Self-asserted source
Shandar Ahmad

Works (50 of 83)

Items per page:
Page 1 of 2

Global and local genomic features together modulate the spontaneous single nucleotide mutation rate

Computational Biology and Chemistry
2024-10 | Journal article
Contributors: Akash Ajay; Tina Begum; Ajay Arya; Krishan Kumar; Shandar Ahmad
Source: check_circle
Crossref

On Performance and Calibration of Natural Gradient Langevin Dynamics

IEEE Access
2023 | Journal article
Contributors: Hanif Amal Robbani; Alhadi Bustamam; Risman Adnan; Shandar Ahmad
Source: check_circle
Crossref

Sample Size Estimation for Effective Modelling of Classification Problems in Machine Learning

2023 | Book chapter
Contributors: Neha Vinayak; Shandar Ahmad
Source: check_circle
Crossref

Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates

Journal of Molecular Biology
2023-09 | Journal article
Contributors: Anuja Jain; Tina Begum; Shandar Ahmad
Source: check_circle
Crossref

Predictive modeling of moonlighting DNA-binding proteins

NAR Genomics and Bioinformatics
2022-10-06 | Journal article
Contributors: Dana Mary Varghese; Ruth Nussinov; Shandar Ahmad
Source: check_circle
Crossref

Molecular Characterization of HOXA2 and HOXA3 Binding Properties

Journal of Developmental Biology
2021-12-03 | Journal article
Contributors: Joshua Mallen; Manisha Kalsan; Peyman Zarrineh; Laure Bridoux; Shandar Ahmad; Nicoletta Bobola
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Crossref
grade
Preferred source (of 2)‎

Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5

Genes
2021-03-11 | Journal article
Contributors: Ambuj Srivastava; Dhanusha Yesudhas; Shandar Ahmad; M. Michael Gromiha
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Crossref
grade
Preferred source (of 2)‎

Potential of age distribution profiles for the prediction of COVID-19 infection origin in a patient group

Informatics in Medicine Unlocked
2020 | Journal article
Part of ISSN: 2352-9148
Source: Self-asserted source
Shandar Ahmad

Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

Scientific Reports
2020-12 | Journal article
Part of ISSN: 2045-2322
Source: Self-asserted source
Shandar Ahmad

Feature Selection for Topological Proximity Prediction of Single-Cell Transcriptomic Profiles in Drosophila Embryo Using Genetic Algorithm

Genes
2020-12-28 | Journal article
Contributors: Shruti Gupta; Ajay Kumar Verma; Shandar Ahmad
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Crossref
grade
Preferred source (of 2)‎

Intestinal Epithelium-Derived Luminally Released Extracellular Vesicles in Sepsis Exhibit the Ability to Suppress TNF-α and IL-17A Expression in Mucosal Inflammation

International Journal of Molecular Sciences
2020-11-10 | Journal article
Part of ISSN: 1422-0067
Source: Self-asserted source
Shandar Ahmad

Enabling full‐length evolutionary profiles based deep convolutional neural network for predicting DNA‐binding proteins from sequence

Proteins: Structure, Function, and Bioinformatics
2020-01 | Journal article
Contributors: Sucheta Chauhan; Shandar Ahmad
Source: check_circle
Crossref

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability

2014 | Journal article
DOI:

10.1002/prot.24462

EID:

2-s2.0-84898052218

Contributors: Mizuguchi, K.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Integrated pathway clusters with coherent biological themes for target prioritisation

2014 | Journal article
DOI:

10.1371/journal.pone.0099030

EID:

2-s2.0-84903397448

Contributors: Chen, Y.-A.; Tripathi, L.P.; Dessailly, B.H.; Nyström-Persson, J.; Ahmad, S.; Mizuguchi, K.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions

2013 | Journal article
DOI:

10.1093/nar/gks1300

EID:

2-s2.0-84876375138

Contributors: Hutchins, A.P.; Diez, D.; Takahashi, Y.; Ahmad, S.; Jauch, R.; Tremblay, M.L.; Miranda-Saavedra, D.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

2013 | Journal article
DOI:

10.1093/nar/gkt544

EID:

2-s2.0-84886863190

Contributors: Nagarajan, R.; Ahmad, S.; Michael Gromiha, M.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter

2013 | Journal article
DOI:

10.1016/j.bbagen.2013.01.024

EID:

2-s2.0-84876005117

Contributors: Tiwari, P.; Tripathi, L.P.; Nishikawa-Matsumura, T.; Ahmad, S.; Song, S.-N.J.; Isobe, T.; Mizuguchi, K.; Yoshizaki, K.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

2012 | Book
EID:

2-s2.0-84868705269

Contributors: Shibuya, T.; Kashima, H.; Sese, J.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Analysis of electric moments of RNA-binding proteins: Implications for mechanism and prediction

2011 | Journal article
DOI:

10.1186/1472-6807-11-8

EID:

2-s2.0-79351468726

Contributors: Ahmad, S.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

2011 | Journal article
DOI:

10.1186/2046-1682-4-21

EID:

2-s2.0-84862193851

Contributors: Morita, M.; Katta, A.V.S.K.M.; Ahmad, S.; Mori, T.; Sugita, Y.; Mizuguchi, K.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Prediction of dinucleotide-specific RNA-binding sites in proteins

2011 | Journal article
DOI:

10.1186/1471-2105-12-S13-S5

EID:

2-s2.0-84864039064

Contributors: Fernandez, M.; Kumagai, Y.; Standley, D.M. .; Sarai, A.; Mizuguchi, K.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Selective constraints in yeast genes with differential expressivity: Codon pair usage and mRNA stability perspectives

2011 | Journal article
DOI:

10.1016/j.gene.2011.04.009

EID:

2-s2.0-79957642995

Contributors: Kahali, B.; Ahmad, S.; Ghosh, T.C.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

CCRXP: Exploring clusters of conserved residues in protein structures

2010 | Journal article
DOI:

10.1093/nar/gkq360

EID:

2-s2.0-77954277173

Contributors: Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Creation of lysine-deficient mutant lymphotoxin-α with receptor selectivity by using a phage display system

2010 | Journal article
DOI:

10.1016/j.biomaterials.2009.10.015

EID:

2-s2.0-73249150267

Contributors: Yoshioka, Y.; Watanabe, H.; Morishige, T.; Yao, X.; Ikemizu, S.; Nagao, C.; Ahmad, S.; Mizuguchi, K.; Tsunoda, S.-i.; Tsutsumi, Y. et al.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins

2010 | Journal article
DOI:

10.1186/1471-2105-11-533

EID:

2-s2.0-77958502965

Contributors: Ahmad, S.; Singh, Y.H.; Paudel, Y.; Mori, T.; Sugita, Y.; Mizuguchi, K.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin

2010 | Journal article
DOI:

10.1007/s00894-010-0680-1

EID:

2-s2.0-79951769180

Contributors: Malik, A.; Firoz, A.; Jha, V.; Sunderasan, E.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

On nucleotide solvent accessibility in RNA structure

2010 | Journal article
DOI:

10.1016/j.gene.2010.05.001

EID:

2-s2.0-77954660742

Contributors: Singh, Y.H.; Andrabi, M.; Kahali, B.; Ghosh, T.C.; Mizuguchi, K.; Kochetov, A.V.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

PROCARB: A database of known and modelled carbohydrate-binding protein structures with sequence-based prediction tools

2010 | Journal article
DOI:

10.1155/2010/436036

EID:

2-s2.0-78349288066

Contributors: Malik, A.; Firoz, A.; Jha, V.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines

2010 | Journal article
DOI:

10.1021/ci1000532

EID:

2-s2.0-77954071785

Contributors: Fernandez, M.; Ahmad, S.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis

2009 | Journal article
DOI:

10.1186/1472-6807-9-25

EID:

2-s2.0-66149176906

Contributors: Singh, H.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network

2009 | Journal article
DOI:

10.1016/j.gene.2008.09.032

EID:

2-s2.0-57049156519

Contributors: Kahali, B.; Ahmad, S.; Ghosh, T.C.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

2009 | Journal article
DOI:

10.1186/1472-6807-9-30

EID:

2-s2.0-67649337519

Contributors: Andrabi, M.; Mizuguchi, K.; Sarai, A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Recognition of drug-target interaction patterns using genetic algorithm-optimized Bayesian-regularized neural networks and support vector machines

2009 | Conference paper
DOI:

10.1109/ICSMC.2009.5346852

EID:

2-s2.0-74849090431

Contributors: Fernandez, M.; Sarai, A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen

2008 | Journal article
DOI:

10.1016/j.ijbiomac.2007.11.004

EID:

2-s2.0-38549174619

Contributors: Malik, A.; Arif, S.A.M.; Ahmad, S.; Sunderasan, E.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea)

2008 | Journal article
DOI:

10.1016/j.bpc.2007.12.006

EID:

2-s2.0-38949138456

Contributors: Singh, R.; Ali Dar, T.; Ahmad, S.; Moosavi-Movahedi, A.A.; Ahmad, F.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

ATP-binding site as a further application of neural networks to residue level prediction

2008 | Conference paper
DOI:

10.1109/IJCNN.2008.4634136

EID:

2-s2.0-56349160697

Contributors: Ahmad, S.; Ahmad, Z.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Benchmarking and analysis of DNA-binding site prediction using machine learning

2008 | Conference paper
DOI:

10.1109/IJCNN.2008.4634034

EID:

2-s2.0-56349144356

Contributors: Andrabi, M.; Ahmad, S.; Mizuguchi, K.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Lecture Notes in Bioinformatics: Preface

2008 | Book
EID:

2-s2.0-57049153992

Contributors: Chetty, M.; Ngom, A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Neural network based prediction of protein structure and function: Comparison with other machine learning methods

2008 | Conference paper
DOI:

10.1109/IJCNN.2008.4634033

EID:

2-s2.0-56349100748

Contributors: Gromiha, M.M.; Ahmad, S.; Suwa, M.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Protein-DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

2008 | Journal article
DOI:

10.1093/nar/gkn573

EID:

2-s2.0-54549096025

Contributors: Ahmad, S.; Keskin, O.; Sarai, A.; Nussinov, R.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Specific 5′CpG island methylation signatures of FHIT and p16 genes and their potential diagnostic relevance in Indian breast cancer patients

2008 | Journal article
DOI:

10.1089/dna.2007.0660

EID:

2-s2.0-50849143775

Contributors: Naqvi, R.A.; Hussain, A.; Raish, M.; Noor, A.; Shahid, M.; Sarin, R.; Kukreti, H.; Khan, N.J.; Ahmad, S.; Deo, S.V.S. et al.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

uORFs, reinitiation and alternative translation start sites in human mRNAs

2008 | Journal article
DOI:

10.1016/j.febslet.2008.03.014

EID:

2-s2.0-41449117605

Contributors: Kochetov, A.V.; Ahmad, S.; Ivanisenko, V.; Volkova, O.A.; Kolchanov, N.A.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Dynamic outlier exclusion training algorithm for sequence based predictions in proteins using neural network

2007 | Book
EID:

2-s2.0-38349039924

Contributors: Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

2007 | Journal article
DOI:

10.1186/1472-6807-7-1

EID:

2-s2.0-33847317012

Contributors: Malik, A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

SVM-cabins: Prediction of solvent accessibility using accumulation cutoff set and support vector machine

2007 | Journal article
DOI:

10.1002/prot.21422

EID:

2-s2.0-34249898391

Contributors: Wang, J.-Y.; Lee, H.-M.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Atom-wise statistics and prediction of solvent accessibility in proteins

2006 | Journal article
DOI:

10.1016/j.bpc.2006.06.013

EID:

2-s2.0-33750165508

Contributors: Singh, Y.H.; Gromiha, M.M.; Sarai, A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Classification of Protein-DNA Complexes Based on Structural Descriptors

2006 | Journal article
DOI:

10.1016/j.str.2006.06.018

EID:

2-s2.0-33748290192

Contributors: Prabakaran, P.; Siebers, J.G.; Ahmad, S.; Gromiha, M.M.; Singarayan, M.G.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Databases and QSAR for cancer research

2006 | Journal article
EID:

2-s2.0-33746668097

Contributors: Malik, A.; Singh, H.; Andrabi, M.; Husain, S.A.; Ahmad, S.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

2006 | Journal article
DOI:

10.1016/j.compbiolchem.2005.12.003

EID:

2-s2.0-33645859913

Contributors: Araúzo-Bravo, M.J.; Ahmad, S.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier

ReadOut: Structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

2006 | Journal article
DOI:

10.1093/nar/gkl104

EID:

2-s2.0-33747827908

Contributors: Ahmad, S.; Kono, H.; Araúzo-Bravo, M.J.; Sarai, A.
Source: Self-asserted source
Shandar Ahmad via Scopus - Elsevier
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Peer review (1 review for 1 publication/grant)

Review activity for Neurocomputing. (1)