Publications
Journals
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2013
2012
2011
2010
2009
2008
2007
2006
S.P. Baskaran#, J. Ravichandran#, P. Shree, V. Thengumthottathil, B.S. Karthikeyan*, A. Samal*, UVREK: Development and analysis of an expression profile knowledgebase of biomolecules induced by ultraviolet radiation exposure, bioRxiv 2024.03.31.587452. [Link to UVREK]
A.K. Sahoo#, N. Chivukula#, S.R. Madgaonkar, K. Ramesh, S.R. Marigoudar, K.V. Sharma, A. Samal*, Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives, bioRxiv 2024.03.27.586984. [Link to sAOPadditives]
M. Mondal#, A. Samal*, F. Münch* & J. Jost*, Bakry-Émery-Ricci curvature: An alternative network geometry measure in the expanding toolbox of graph Ricci curvatures, arXiv.2402.06616 .
P. Sil#, A. Subbaroyan#, S. Kulkarni, O.C. Martin* & A. Samal*, Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph, Briefings in Bioinformatics, 25(3): bbae150 (2024). [GitHub Repository]
S. Mitra#, P. Sil#, A. Subbaroyan#, O.C. Martin* & A. Samal*, Preponderance of generalized chain functions in reconstructed Boolean models of biological networks, Scientific Reports, 14: 6734 (2024).[GitHub Repository]
S. Vijayaraghavan, A. Lakshminarayanan, N. Bhargava, J. Ravichandran, R.P. Vivek-Ananth* & A. Samal*, Machine learning models for prediction of xenobiotic chemicals with high propensity to transfer into human milk, ACS Omega, 9(11): 13006-13016. [GitHub Repository]
A.K. Sahoo#, N. Chivukula#, K. Ramesh, J. Singha, S.R. Marigoudar, K.V. Sharma, A. Samal*, An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity, Science of The Total Environment, 920: 170968 (2024).
J. Kulkarni, S.A. Sahoo, P. Herzyk, V.T. Barvkar, S.A. Kumar, J. Ravichandran, A. Samal, A. Amtmann, M. Borde, P. Suprasanna, A.K. Srivastava, Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.), Plant, Cell & Environment, 47: 961-975 (2024). DOI: 10.1111/pce.14767. [Link to SesuviumKB]
N. Chivukula, K. Ramesh, A. Subbarayon, A.K. Sahoo, G.B. Dhanakoti, J. Ravichandran, A. Samal*, ViCEKb: Vitiligo-linked Chemical Exposome Knowledgebase Science of The Total Environment, 913: 169711 (2024). [Link to Vicekb]
S. Kulkarni, H.K. Pharasi, S. Vijayaraghavan, S. Kumar, A. Chakraborti*, A. Samal*, Investigation of Indian stock markets using topological data analysis and geometry-inspired network measures, arXiv.2311.17016 .
S.P. Baskaran#, A.K. Sahoo#, N. Chivukula, K. Kumar & A. Samal*, Cheminformatics analysis of multi-target structure-activity landscape of environmental chemicals binding to human endocrine receptors, ACS Omega, 8: 49383-49395 (2023). DOI: 10.1021/acsomega.3c07920.
B. Malakar, K. Chauhan, P. Sanyal, S. Naz, H. Kalam, R.P. Vivek-Ananth, L.V. Singh, A. Samal, D. Kumar*, V.K. Nandicoori*, Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence, mBio, 4: e01232-23 (2023).
A.K. Sahoo, R. P. Vivek-Ananth, N. Chivukula, S.V. Rajaram, K. Mohanraj, D. Khare, C. Acharya & A. Samal*, T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility, and the Associated Secreted Proteins, ACS Omega, 8: 34091-34102 (2023). [Link to T9GPred, GitHub Repository]
S. Shee, R.T Veetil, K. Mohanraj, M. Das, N. Malhotra, D. Bandopadhyay, H. Beig, S.Birua, S. Niphadkar, S.N. Nagarajan, V.K. Sinha, C. Thakur, R.S Rajamani, N. Chandra, S. Laxman, M. Singh, A. Samal, A.S.N. Seshasayee & A. Singh*, Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis, eLife, 12: e80218 (2023).
A.K. Sahoo#, S.P. Baskaran#, N. Chivukula, K. Kumar & A. Samal*, Analysis of structure-activity and structure-mechanism relationships among thyroid stimulating hormone receptor binding chemicals by leveraging the ToxCast library, RSC Advances, 13: 23461-23471 (2023).
I. Muralitharan#, A.K. Sahoo#, P.D. Augusthian & A. Samal*, Computational prediction of phytochemical inhibitors against the cap-binding domain of Rift Valley fever virus, Molecular Diversity (2023) DOI: 10.1007/s11030-023-10702-x.
Y. Yadav, P. Elumalai, N. Williams, J. Jost & A. Samal*, Discrete Ricci curvatures capture age-related changes in human brain functional connectivity networks, Frontiers in Aging Neuroscience, 15: 1120846 (2023).
A. Subbaroyan, P. Sil, O.C. Martin* & A. Samal*, Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks, Briefings in Bioinformatics, bbad160 (2023). [GitHub Repository]
A. Natarajan#, N. Chivukula#, G.B. Dhanakoti, A.K. Sahoo, J. Ravichandran* & A. Samal*, EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase, Computational Biology and Chemistry, 104: 107866 (2023). [Link to EPEK, GitHub Repository]
R. P. Vivek-Ananth, K. Mohanraj, A.K. Sahoo & A. Samal*, IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants, ACS Omega, 8: 8827-8845 (2023). [Link to IMPPAT 2.0]
R. P. Vivek-Ananth#, A.K. Sahoo#, S.P. Baskaran#, J. Ravichandran & A. Samal*, Identification of activity cliffs in structure-activity landscape of androgen receptor binding chemicals, Science of the Total Environment, 873: 162263 (2023).
R. P. Vivek-Ananth, A.K. Sahoo, S.P. Baskaran & A. Samal*, Scaffold and structural diversity of the secondary metabolite space of medicinal fungi, ACS Omega, 8: 3102-3113 (2023).
A.K. Sahoo, P.D. Augusthian, I. Muralitharan, R. P. Vivek-Ananth, K. Kumar, G. Kumar, G. Ranganathan & A. Samal*, In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs, Molecular Diversity, 27: 2169–2184 (2023).
The Hindu SCI-TECH: Medicinal fungi may be suitable for identifying novel drugs
Y. Yadav#, A. Subbaroyan#, O.C. Martin* & A. Samal*, Relative importance of composition structures and biologically meaningful logics in bipartite Boolean models of gene regulation, Scientific Reports, 12: 18156 (2022). [GitHub Repository]
P. Elumalai#, Y. Yadav#, N. Williams*, E. Saucan, J. Jost & A. Samal*, Graph Ricci Curvatures Reveal Atypical Functional Connectivity in Autism Spectrum Disorder, Scientific Reports, 12: 8295 (2022). [GitHub Repository]
A. Subbaroyan, O.C. Martin* & A. Samal*, Minimum complexity drives regulatory logic in Boolean models of living systems, PNAS Nexus, 1(1): pgac017 (2022). [GitHub Repository]
IIT Madras Shaastra Magazine: Nature likes it simple! A new study underlines biology's preference for minimal complexity
A. Subbaroyan, O.C. Martin* & A. Samal*, A preference for Link Operator Functions can drive Boolean biological networks towards critical dynamics, Journal of Biosciences, 47: 17 (2022).
J. Ravichandran, B.S. Karthikeyan & A. Samal*, Investigation of a derived adverse outcome pathway (AOP) network for endocrine-mediated perturbations, Science of the Total Environment, 826: 154112 (2022).
R.P. Vivek-Ananth, A.K. Sahoo, A. Srivastava* & A. Samal*, Virtual screening of phytochemicals from Indian medicinal plants against the endonuclease domain of SFTS virus L polymerase, RSC Advances, 12: 6234-6247 (2022).
Y. Yadav, A. Samal & E. Saucan*, A Poset-Based Approach to Curvature of Hypergraphs, Symmetry, 14(2): 420 (2022).
R.P. Vivek-Ananth, S. Krishnaswamy* & A. Samal*, Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study, Molecular Diversity, 26: 429-442 (2022).
J. Ravichandran#, B.S. Karthikeyan#, J. Jost & A. Samal*, An atlas of fragrance chemicals in children's products, Science of the Total Environment, 818: 151682 (2022). [Link to FCCP]
Indian Chemical Regulation: A database of fragrance chemicals found in children's products reveals information gaps
J. Ravichandran#, B.S. Karthikeyan#, S.R. Aparna & A. Samal*, Network biology approach to human tissue-specific chemical exposome, The Journal of Steroid Biochemistry and Molecular Biology, 214: 105998 (2021). [Link to TExAs]
C. Aguilar, S. Costa, C. Maudet, R.P. Vivek-Ananth, S. Zaldívar-López, J.J. Garrido, A. Samal, M. Mano & A. Eulalio*, Reprogramming of microRNA expression via E2F1 downregulation promotes Salmonella infection both in infected and bystander cells, Nature Communications, 12: 3392 (2021).
J. Ravichandran#, B.S. Karthikeyan#, P. Singla, S.R. Aparna & A. Samal*, NeurotoxKb 1.0: compilation, curation and exploration of a knowledgebase of environmental neurotoxicants specific to mammals, Chemosphere, 278: 130387 (2021). [Link to NeurotoxKb]
B.S. Karthikeyan#, J. Ravichandran#*, S.R. Aparna & A. Samal*, ExHuMId: A curated resource and analysis of Exposome of Human Milk across India, Chemosphere, 271: 129583 (2021). [Link to ExHuMId]
Nature India: An online repository of breast milk contaminants
R.P. Vivek-Ananth#, A.K. Sahoo#, K. Kumaravel#, K. Mohanraj & A. Samal*, MeFSAT: A curated natural product database specific to secondary metabolites of medicinal fungi, RSC Advances, 11: 2596-2607 (2021). [Link to MeFSAT]
A. Samal*, S. Kumar, Y. Yadav & A. Chakraborti*, Network-centric indicators for fragility in global financial indices, Frontiers in Physics, 8: 624373 (2021).
A. Samal#*, H.K. Pharasi#, S. J. Ramaia, H. Kannan, E. Saucan, J. Jost & A. Chakraborti*, Network geometry and market instability, Royal Society Open Science, 8: 201734 (2021).
Max Planck Society News: Early warning of market bubbles
ScienceDaily: Its curvature foreshadows the next financial bubble
B.S. Karthikeyan#, J. Ravichandran#*, S.R. Aparna & A. Samal*, DEDuCT 2.0: An updated knowledgebase and an exploratory analysis of the current regulations and guidelines from the perspective of endocrine disrupting chemicals, Chemosphere, 267: 128898 (2021). [Link to DEDuCT 2.0]
ChemicalWatch: Indian team expands database of potential endocrine disrupting chemicals Coverage in:
INCI Beauty: DEDuCT: la base des perturbateurs endocriniens
E. Saucan*, A. Samal & J. Jost, A Simple Differential Geometry for Complex Networks, Network Science, 9(S1): S106-S133 (2021).
M. Eidi, A. Farzam, W. Leal, A. Samal & J. Jost*, Edge-based analysis of networks: Curvatures of graphs and hypergraphs, Theory in Biosciences, 139: 337-348 (2020).
A. Farzam*, A. Samal* & J. Jost*, Degree difference: A simple measure to characterize structural heterogeneity in complex networks, Scientific Reports, 10: 21348 (2020).
R.P. Vivek-Ananth, A. Rana, N. Rajan, H.S. Biswal* & A. Samal*, In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection, Molecules, 25(17): 3822 (2020).
Dinamalar Pattam: தாவரங்களில் கோவிட் 19 மருந்து!
Times of India: NISER study identifies plant compound that may cure Covid
Prameya News: Scientists from NISER, IMSc identify phytochemicals ‘potential drug candidates’ for COVID-19 treatment
I. Roy*, S. Vijayaraghavan, S. J. Ramaia & A. Samal*, Forman-Ricci curvature and Persistent homology of unweighted complex networks, Chaos, Solitons & Fractals, 140: 110260 (2020).
E. Saucan*, A. Samal & J. Jost, A Simple Differential Geometry for Networks and Its Generalizations In: H. Cherifi, S. Gaito, J. Mendes, E. Moro, L. Rocha (Eds) Complex Networks and Their Applications VIII. COMPLEX NETWORKS 2019. Studies in Computational Intelligence, Vol. 881. Springer, Cham.
M.A.C. Horta, N. Thieme, Y. Gao, K.E. Burnum-Johnson, C.D. Nicora, M.A. Gritsenko, M.S. Lipton, K. Mohanraj, L.J. de Assis, L. Lin, C. Tian, G.H. Braus, K.A. Borkovich, M. Schmoll, L.F. Larrondo, A. Samal, G.H. Goldman & J. P. Benz*, Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition in Neurospora crassa, Frontiers in Microbiology, 10: 2317 (2019).
B.S. Karthikeyan#, J. Ravichandran#*, K. Mohanraj, R.P. Vivek-Ananth & A. Samal*, A curated knowledgebase on endocrine disrupting chemicals and their biological systems-level perturbations, Science of the Total Environment, 692: 281-296 (2019). [Link to DEDuCT]
Hindustan Times: Now, a database of harmful chemicals in everyday items
India Science Wire: Indian scientists develop database of everyday chemicals harmful to human health
ChemicalWatch: Indian team identifies hundreds of potential EDCs from literature
European Trade Union Institute: New online database for identifying endocrine disruptors
c&en: Database of endocrine disruptors focuses on experimental evidence
H. Kannan, E. Saucan, I. Roy* & A. Samal*, Persistent homology of unweighted complex networks via discrete Morse theory, Scientific Reports 9: 13817 (2019).
C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal & M. Giacca*, Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation, Cell Reports, 27(9): 2759-2771 (2019).
E. Saucan, R.P. Sreejith, R.P. Vivek-Ananth, J. Jost & A. Samal*, Discrete Ricci curvatures for directed networks, Chaos, Solitons & Fractals, 118: 347-360 (2019).
E. Saucan, A. Samal , M. Weber & J. Jost*, Discrete curvatures and network analysis, MATCH Communications in Mathematical and in Computer Chemistry, 80(3): 605-622 (2018).
A. Samal#, R.P. Sreejith#, J. Gu, S. Liu, E. Saucan* & J. Jost*, Comparative analysis of two discretizations of Ricci curvature for complex networks, Scientific Reports 8: 8650 (2018).
Max Planck Society News: Meaningful relationships - mathematical insights into the geometry of complex networks
IDW News: Meaningful relationships - mathematical insights into the geometry of complex networks
Nature India: How geometry helps understand networks better
R.P. Vivek-Ananth, K. Mohanraj, M. Vandanashree, A. Jhingran, J.P. Craig & A. Samal*, Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species, Scientific Reports 8: 6617 (2018). [Link to ASPERTOME]
K. Mohanraj#, B.S. Karthikeyan#, R.P. Vivek-Ananth#, R.P. Bharath Chand, S.R. Aparna, P. Mangalapandi & A. Samal*, IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry and Therapeutics, Scientific Reports 8: 4329 (2018). [Link to IMPPAT]
Hindustan Times: Indian plants may hold gateway to new drugs
Nature India: Phytochemical database raises hopes for herbal drugs
The Hindu: A knowledge hub for medicinal plants
India Science Wire: New database on Indian medicinal plants may ease drug discovery
Down to Earth: New database finds 960 new ‘druggable’ components in Indian medicinal plants
Researchstash: New database on Indian medicinal plants may ease drug discovery
Biotech News: New database on Indian medicinal plants may ease drug discovery
Biovoice News: Fresh database on Indian medicinal plants may ease drug discovery
Dinamalar Pattam: 1742 தாவரங்களில் இருந்து மருந்து!
தி இந்து: இந்திய மூலிகைகளுக்குக் கிடைக்குமா அங்கீகாரம்?
S. Venkatesan#, R.P. Vivek-Ananth#, R.P. Sreejith, P. Mangalapandi, A.A. Hassanali* & A. Samal*, Network approach towards understanding the crazing in glassy amorphous polymers, Journal of Statistical Mechanics: Theory and Experiment 043305 (2018).
A. Samal* & O.C. Martin*, Haldane, Waddington and recombinant inbred lines: extension of their work to any number of genes, Journal of Genetics, 96(5): 795-800 (2017).
A. Samal, J.P. Craig, S.T. Coradetti#, J.P. Benz#, J.A. Eddy, N.D. Price* & N.L. Glass*, Network Reconstruction And Systems Analysis Of Plant Cell Wall Deconstruction By Neurospora crassa, Biotechnology for Biofuels, 10: 225 (2017).
R.P. Sreejith, J. Jost, E. Saucan & A. Samal*, Systematic evaluation of a new combinatorial curvature for complex networks, Chaos, Solitons & Fractals, 101: 50-67 (2017).
R.P. Vivek-Ananth & A. Samal*, Advances in the integration of transcriptional regulatory information into genome-scale metabolic models, Biosystems 147: 1-10 (2016).
R.P. Sreejith, K. Mohanraj, J. Jost, E. Saucan & A. Samal*, Forman curvature for complex networks, Journal of Statistical Mechanics: Theory and Experiment 063206 (2016).
G.D. Jhingan#, S. Kumari#, S.V. Jamwal, H. Kalam, D. Arora, N. Jain, L. KrishnaKumaar, A. Samal, K.V.S. Rao, D. Kumar & V.K. Nandicoori*, Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns, Journal of Biological Chemistry 291: 14257-14273 (2016).
J.X. Zhou#, A. Samal#, A.F. d'Hérouël, N.D. Price & S. Huang*, Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development, Biosystems 142: 15-24 (2016).
M. Bardoscia, M. Marsili & A. Samal*, Phenotypic constraints promote latent versatility and carbon efficiency in metabolic networks, Physical Review E 92: 012809 (2015).
A. Samal & O.C. Martin*, Statistical physics methods provide the exact solution to a long-standing problem of genetics, Physical Review Letters, 114: 238101 (2015). – Editors’ suggestion article
Physics Today: Gauging genetic odds after repeated inbreeding
ICTP: A Matter of (in)Breeding
INRA: Lignées recombinantes: quand la physique théorique aide à résoudre un vieux problème de génétique
S. Kumar, M. Vendruscolo, A. Singh, D. Kumar & A. Samal*, Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network, Molecular Biosystems, 11: 930-941 (2015).
A. Samal & O.C. Martin*, Shining fresh light on the evolution of photosynthesis, eLife, 2: e01403 (2013).
A. Henry, F. Monéger, A. Samal* & O.C. Martin*, Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network, Molecular Biosystems, 9(7): 1726-1735 (2013).
S. Singh, A. Samal, V. Giri, S. Krishna, N. Raghuram & S. Jain*, Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks, Physical Review E, 87: 052708 (2013).
Q. Ren*, K.M. Kolwankar, A. Samal & J. Jost, Hopf bifurcation in the evolution of networks driven by spike-timing-dependent plasticity, Physical Review E, 86: 056103 (2012).
A. Samal, A. Wagner* & O.C. Martin*, Environmental versatility promotes modularity in genome-scale metabolic networks, BMC Systems Biology, 5: 135 (2011). - Highly accessed article
A. Samal & O.C. Martin*, Randomizing genome-scale metabolic networks, PLoS ONE, 6(7): e22295 (2011).
D. Perumal, A. Samal, K.R. Sakharkar & M.K. Sakharkar*, Targeting Multiple Targets in Pseudomonas aeruginosa PAO1 using Flux Balance Analysis of a Reconstructed Genome-scale Metabolic Network, Journal of Drug Targeting, 19(1): 1-13 (2011).
K.M. Kolwankar*, Q. Ren, A. Samal & J. Jost, Learning and structure of neuronal networks, Pramana, 77(5): 817-826 (2011).
P.-Y. Bourguignon, A. Samal, F. Képès, J. Jost* & O.C. Martin*, Challenges in experimental data integration within genome-scale metabolic models, Algorithms for Molecular Biology, 5: 20 (2010). - Highly accessed article
D. Perumal, K.R. Sakharkar, T.H. Tang, V.T.K. Chow, C.S. Lim, A. Samal , N. Sugiura & M.K. Sakharkar*, Cloning and Targeted Disruption of Two Lipopolysaccharide Biosynthesis Genes, kdsA and waaG, of Pseudomonas aeruginosa PAO1 by Site-Directed Mutagenesis, Journal of Molecular Microbiology and Biotechnology, 19(1): 169-179 (2010).
Q. Ren, K.M. Kolwankar*, A. Samal & J. Jost, STDP-driven networks and C. elegans neuronal network, Physica A, 389(15): 3900-3914 (2010).
A. Samal, J.F. Matias Rodrigues, J. Jost, O.C. Martin* & A. Wagner*, Genotype networks in metabolic reaction spaces, BMC Systems Biology, 4: 30 (2010). - Highly accessed article
A. Samal & H. Meyer-Ortmanns*, Preferential attachment renders an evolving network of populations robust against crashes, Physica A, 388(8): 1535-1545 (2009).
A. Samal*, Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks, Systems and Synthetic Biology, 2: 83-93 (2008).
A. Samal & S. Jain*, The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response, BMC Systems Biology, 2: 21 (2008). - Highly accessed article
S. Singh, A. Samal, V. Giri, S. Krishna, N. Raghuram & S. Jain*, A universal power law and proportionate change process characterize the evolution of metabolic networks, Eur. Phys. J. B, 57: 75-80 (2007).
A. Samal, S. Singh, V. Giri, S. Krishna, N. Raghuram & S. Jain*, Low degree metabolites explain essential reactions and enhance modularity in biological networks, BMC Bioinformatics, 7: 118 (2006). - Highly accessed article
# Equal Contribution
PhD Thesis
- A. Samal , Study of the structure and dynamics of the complex biological networks, University of Delhi, India (2008).
(Available at Arxiv:0812.5094)