Publications

TAS2R38 Polymorphism and Bitter Taste Perception: Implications for Satmaya and Upashaya-Anupshaya Beyond Prakriti

Authors:S. Sharma#, O.A. Sonawane#, R. Jain, A. Sharma, D. Jangir, V. Garisetti, S.P. Baskaran, K. Shreedharala, K.R. Das, A. Samal, S.R. Thrigulla, N.R. Kochar, M. Yadav, D.C. Sharma, S. Chhipa, M. Mukerji*

Year: 2026

Preprint: Research Square rs.3.rs-9278930

Research Area: Natural Product Spaces

Benchmarking Artificial Intelligence Models for Predicting Nuclear Receptor Activity from Tox21 Assays

Authors: N. Chivukula#, J. Karthikeyan#, H. Thangavel#, S.R. Madgaonkar#, A. Samal*

Year: 2026

Preprint: bioRxiv 2026.03.20.713297

GitHub Repository

Research Area: Exposomics / Systems Toxicology

Computational investigation of single herbal drugs in Ayurveda for diabetes and obesity using knowledge graph and network pharmacology

Authors: P. Sil#, R. Tiwari#, V. Garisetti, S.P. Baskaran, F.H. Dhanaseelan, S. Srivastava, A. Samal*

Year: 2026

Preprint: arXiv:2601.21643

Link to SHDKG-DiabetesObesity

Research Area: Natural Product Spaces

A comprehensive resource on chemicals used in aquaculture and their ecotoxicity

Authors: S.R. Madgaonkar, S. Vashishth, N. Chivukula, V. Garisetti, S.R. Marigoudar, K.V. Sharma, A. Samal*

Year: 2026

Preprint: bioRxiv 2026.01.26.701529

Link to ReCAnt

Research Area: Exposomics / Systems Toxicology

DEDuCT 3.0: An enhanced and expanded FAIR-compliant resource and toxicology knowledge graph for endocrine disrupting chemicals

Authors: N. Chivukula, S. Vashishth, P. Kandasamy, S.R. Madgaonkar, A. Samal*

Year: 2026

Preprint: bioRxiv 2026.01.23.701267

Link to DEDuCT

Research Area: Exposomics / Systems Toxicology

TICToK: A comprehensive knowledgebase of tattoo ink chemicals and investigation of their associated toxicities and regulations

Authors: N. Chivukula, S.R. Madgaonkar, S.R. Marigoudar, K.V. Sharma, V. Kishore, A.V. Singh*, A. Samal*

Year: 2025

Preprint: bioRxiv 2025.08.02.668261

Link to TICToK

Research Area: Exposomics / Systems Toxicology

Sec and Tat mediated secretion safeguards Mycobacterium tuberculosis membrane homeostasis

Authors: P. Sanyal#, J. Uppada#, S. Sinha, Y. Bhat, S. Khan, S.V. Rajaram, E.V. Arokiyaraj, G.D. Jhingan, N. Agarwal, A. Samal*, V.K. Nandicoori*

Journal: Molecular & Cellular Proteomics, 101555 (2026)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Node persistence from topological data analysis reveals changes in brain functional connectivity

Authors: M. Mondal, Y. Yadav, J. Jost*, A. Samal*

Journal: Patterns, 7: 101427 (2026)

GitHub Repository

Research Area: Geometry and Topology based methods

A systematic evaluation of simple threshold-based Boolean rules for modeling gene regulatory networks

Authors: P. Sil, O.C. Martin*, A. Samal*

Journal: Journal of Statistical Mechanics: Theory and Experiment, 2026(2): 023502 (2026)

GitHub Repository

Research Area: Boolean Modelling of GRNs

Integrative network-based construction of ecologically relevant computational adverse outcome pathways for organic mercury-induced toxicity

Authors: S.R. Madgaonkar, N. Chivukula, V. Garisetti, S.R. Marigoudar, K.V. Sharma, A. Samal*

Journal: Environmental Toxicology and Chemistry, 45: 731-747 (2026)

Research Area: Exposomics / Systems Toxicology

Network toxicology focused investigation on the impacts of inorganic arsenic and cadmium on human and ecosystem health

Authors: N. Chivukula#, S.R. Madgaonkar#, K. Ramesh, S. Mangot, P. Karthikeyan, S.R. Marigoudar, K.V. Sharma, A. Samal*

Journal: Environmental Toxicology and Chemistry, 45: 468-489 (2026)

Link to HeavyMetalTox

Research Area: Exposomics / Systems Toxicology

Computational prediction of cyclotides from Viola odorata as potential inhibitors against the neuraminidase of Streptococcus pneumoniae

Authors: S. Sankar#, A.K. Sahoo#, S.P. Baskaran, R. Babu, S. Srivastava*, A. Samal*

Journal: Molecular Diversity, 30:991-1002 (2026)

GitHub Repository

Research Area: Natural Product Spaces

sCentInDB: A database of essential oil chemical profiles of Indian medicinal plants

Authors: S.P. Baskaran, G. Ranganathan, A.K. Sahoo, K. Kumar, J. Amaresan, K. Ramesh, R.P. Vivek-Ananth, A. Samal*

Journal: Molecular Diversity, 30:789-807 (2026)

Link to sCentInDB

Research Area: Natural Product Spaces

Application of discrete Ricci curvature in pruning randomly wired neural networks: A case study with chest x-ray classification of COVID-19

Authors: P. Elumalai#, S. Vijayaraghavan#, M. Mondal*, A. Samal*

Journal: Journal of Physics: Complexity, 6: 045017 (2025)

GitHub Repository

Research Area: Geometry and Topology based methods

IMPPAT: A digital phytochemical atlas enabling computational approaches to traditional Indian knowledge-centered herbal drug discovery

Authors: P. Sil, R. Tiwari, S.P. Baskaran, A. Samal*

Journal: International Journal of Ayurveda Research, 6(4): 387–398 (2025)

Research Area: Natural Product Spaces

The Dawn of a New Air Pollutant: Inhalable Microplastics as Emerging Vectors of Hazardous Contaminants and Their Implications for Human Health

Authors: A. Biswas, N. Saini, N. Chivukula, A. Samal, M.R. Jhansari, P. Bhadury, G.K. Darbha*

Journal: Environment International, 205: 109897 (2025)

Research Area: Exposomics / Systems Toxicology

Choices of regulatory logic class modulate the dynamical regime in random Boolean networks

Authors: P. Sil, S. Mitra, O.C. Martin*, A. Samal*

Journal: Chaos, Solitons & Fractals, 195: 116231 (2025)

Research Area: Boolean Modelling of GRNs

UVREK: Development and analysis of an expression profile knowledgebase of biomolecules induced by ultraviolet radiation exposure

Authors: S.P. Baskaran#, J. Ravichandran#, P. Shree, V. Thengumthottathil, B.S. Karthikeyan*, A. Samal*

Journal: ACS Omega, 10(2): 1927–1942 (2025)

Link to UVREK | GitHub Repository

Research Area: Exposomics / Systems Toxicology

Network-based investigation of petroleum hydrocarbons-induced ecotoxicological effects and their risk assessment

Authors: A.K. Sahoo#, S.R. Madgaonkar#, N. Chivukula, P. Karthikeyan, K. Ramesh, S.R. Marigoudar, K.V. Sharma, A. Samal*

Journal: Environment International, 194: 109163 (2024)

Research Area: Exposomics / Systems Toxicology

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Authors: A.K. Sahoo#, N. Chivukula#, S.R. Madgaonkar, K. Ramesh, S.R. Marigoudar, K.V. Sharma, A. Samal*

Journal: Archives of Toxicology, 98: 3299–3321 (2024)

Link to sAOPadditives

Research Area: Exposomics / Systems Toxicology

Investigation of Indian stock markets using topological data analysis and geometry-inspired network measures

Authors: S. Kulkarni, H.K. Pharasi, S. Vijayaraghavan, S. Kumar, A. Chakraborti*, A. Samal*

Journal: Physica A, 643: 129785 (2024)

Research Area: Geometry and Topology based methods

Bakry-Émery-Ricci curvature: An alternative network geometry measure in the expanding toolbox of graph Ricci curvatures

Authors: M. Mondal, A. Samal*, F. Münch*, J. Jost*

Journal: Journal of Complex Networks, 12(3): cnae019 (2024)

GitHub Repository

Research Area: Geometry and Topology based methods

Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph

Authors: P. Sil#, A. Subbaroyan#, S. Kulkarni, O.C. Martin*, A. Samal*

Journal: Briefings in Bioinformatics, 25(3): bbae150 (2024)

GitHub Repository

Research Area: Boolean Modelling of GRNs

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

Authors: S. Mitra#, P. Sil#, A. Subbaroyan#, O.C. Martin*, A. Samal*

Journal: Scientific Reports, 14: 6734 (2024)

GitHub Repository

Research Area: Boolean Modelling of GRNs

Machine learning models for prediction of xenobiotic chemicals with high propensity to transfer into human milk

Authors: S. Vijayaraghavan, A. Lakshminarayanan, N. Bhargava, J. Ravichandran, R.P. Vivek-Ananth*, A. Samal*

Journal: ACS Omega, 9(11): 13006–13016 (2024)

GitHub Repository

Research Area: Exposomics / Systems Toxicology

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Authors: A.K. Sahoo#, N. Chivukula#, K. Ramesh, J. Singha, S.R. Marigoudar, K.V. Sharma, A. Samal*

Journal: Science of The Total Environment, 920: 170968 (2024)

Research Area: Exposomics / Systems Toxicology

Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.)

Authors: 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

Journal: Plant, Cell & Environment, 47: 961–975 (2024)

Link to SesuviumKB

Research Area: Others

ViCEKb: Vitiligo-linked Chemical Exposome Knowledgebase

Authors: N. Chivukula, K. Ramesh, A. Subbaroyan, A.K. Sahoo, G.B. Dhanakoti, J. Ravichandran, A. Samal*

Journal: Science of The Total Environment, 913: 169711 (2024)

Link to ViCEKb

Research Area: Exposomics / Systems Toxicology

Computational prediction of phytochemical inhibitors against the cap-binding domain of Rift Valley fever virus

Authors: I. Muralitharan#, A.K. Sahoo#, P.D. Augusthian, A. Samal*

Journal: Molecular Diversity, 28: 2637-2650 (2024)

Research Area: Natural Product Spaces

Cheminformatics analysis of multi-target structure–activity landscape of environmental chemicals binding to human endocrine receptors

Authors: S.P. Baskaran#, A.K. Sahoo#, N. Chivukula, K. Kumar, A. Samal*

Journal: ACS Omega, 8: 49383–49395 (2023)

Research Area: Exposomics / Systems Toxicology

Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence

Authors: B. Malakar, K. Chauhan, P. Sanyal, S. Naz, H. Kalam, R.P. Vivek-Ananth, L.V. Singh, A. Samal, D. Kumar*, V.K. Nandicoori*

Journal: mBio, 14: e01232-23 (2023)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

T9GPred: A comprehensive computational tool for the prediction of Type 9 secretion system

Authors: A.K. Sahoo, R.P. Vivek-Ananth, N. Chivukula, S.V. Rajaram, K. Mohanraj, D. Khare, C. Acharya, A. Samal*

Journal: ACS Omega, 8: 34091–34102 (2023)

Link to T9GPred | GitHub Repository

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis

Authors: 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. Rajmani, N. Chandra, S. Laxman, M. Singh, A. Samal, A.S.N. Seshasayee, A. Singh*

Journal: eLife, 12: e80218 (2023)

Research Area: Others

Analysis of structure-activity and structure-mechanism relationships among thyroid stimulating hormone receptor binding chemicals

Authors: A.K. Sahoo#, S.P. Baskaran#, N. Chivukula, K. Kumar, A. Samal*

Journal: RSC Advances, 13: 23461–23471 (2023)

Research Area: Exposomics / Systems Toxicology

Discrete Ricci curvatures capture age-related changes in human brain functional connectivity networks

Authors: Y. Yadav, P. Elumalai, N. Williams, J. Jost, A. Samal*

Journal: Frontiers in Aging Neuroscience, 15:1120846 (2023)

GitHub Repository

Research Area: Geometry and Topology based methods

Identification of activity cliffs in structure-activity landscape of androgen receptor binding chemicals

Authors: R.P. Vivek-Ananth#, A.K. Sahoo#, S.P. Baskaran#, J. Ravichandran & A. Samal*

Journal: Science of the Total Environment, 873: 162263 (2023)

Research Area: Exposomics / Systems Toxicology

Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks

Authors: A. Subbaroyan, P. Sil, O.C. Martin* & A. Samal*

Journal: Briefings in Bioinformatics, bbad160 (2023)

GitHub Repository

Research Area: Boolean Modelling of GRNs

IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants

Authors: R.P. Vivek-Ananth, K. Mohanraj, A.K. Sahoo & A. Samal*

Journal: ACS Omega, 8: 8827-8845 (2023)

GitHub Repository

Research Area: Natural Product Spaces

In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs

Authors: A.K. Sahoo, P.D. Augusthian, I. Muralitharan, R.P. Vivek-Ananth, K. Kumar, G. Kumar, G. Ranganathan & A. Samal*

Journal: Molecular Diversity, 27: 2169–2184 (2023)

Research Area: Others

Scaffold and structural diversity of the secondary metabolite space of medicinal fungi

Authors: R.P. Vivek-Ananth, A.K. Sahoo, S.P. Baskaran & A. Samal*

Journal: ACS Omega, 8: 3102-3113 (2023)

Research Area: Natural Product Spaces

EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase

Authors: A. Natarajan#, N. Chivukula#, G.B. Dhanakoti, A.K. Sahoo, J. Ravichandran* & A. Samal*

Journal: Computational Biology and Chemistry, 104: 107866 (2023)

GitHub Repository

Research Area: Others

Relative importance of composition structures and biologically meaningful logics in bipartite Boolean models of gene regulation

Authors: Y. Yadav#, A. Subbaroyan#, O.C. Martin*, A. Samal*

Journal: Scientific Reports, 12: 18156 (2022)

GitHub Repository

Research Area: Boolean Modelling of GRNs

Graph Ricci Curvatures Reveal Atypical Functional Connectivity in Autism Spectrum Disorder

Authors: P. Elumalai#, Y. Yadav#, N. Williams*, E. Saucan, J. Jost, A. Samal*

Journal: Scientific Reports, 12: 8295 (2022)

GitHub Repository

Research Area: Geometry and Topology based methods

Minimum complexity drives regulatory logic in Boolean models of living systems

Authors: A. Subbaroyan, O.C. Martin*, A. Samal*

Journal: PNAS Nexus, 1(1): pgac017 (2022)

GitHub Repository

Research Area: Boolean Modelling of GRNs

A preference for Link Operator Functions can drive Boolean biological networks towards critical dynamics

Authors: A. Subbaroyan, O.C. Martin*, A. Samal*

Journal: Journal of Biosciences, 47: 17 (2022)

GitHub Repository

Research Area: Boolean Modelling of GRNs

Investigation of a derived adverse outcome pathway (AOP) network for endocrine-mediated perturbations

Authors: J. Ravichandran, B.S. Karthikeyan, A. Samal*

Journal: Science of the Total Environment, 826: 154112 (2022)

Research Area: Exposomics / Systems Toxicology

Virtual screening of phytochemicals from Indian medicinal plants against the endonuclease domain of SFTS virus L polymerase

Authors: R.P. Vivek-Ananth, A.K. Sahoo, A. Srivastava*, A. Samal*

Journal: RSC Advances, 12: 6234–6247 (2022)

Research Area: Natural Product Spaces

A Poset-Based Approach to Curvature of Hypergraphs

Authors: Y. Yadav, A. Samal, E. Saucan*

Journal: Symmetry, 14(2): 420 (2022)

GitHub Repository

Research Area: Geometry and Topology based methods

Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study

Authors: R.P. Vivek-Ananth, S. Krishnaswamy*, A. Samal*

Journal: Molecular Diversity, 26: 429–442 (2022)

Research Area: Natural Product Spaces

An atlas of fragrance chemicals in children's products

Authors: J. Ravichandran#, B.S. Karthikeyan#, J. Jost, A. Samal*

Journal: Science of the Total Environment, 818: 151682 (2022)

Link to FCCP Database

Research Area: Exposomics / Systems Toxicology

Network biology approach to human tissue-specific chemical exposome, The Journal of Steroid Biochemistry and Molecular Biology

Authors: J. Ravichandran#, B.S. Karthikeyan#, S.R. Aparna, A. Samal*

Journal: The Journal of Steroid Biochemistry and Molecular Biology, 214: 105998 (2021)

Link to TExAs

Research Area: Exposomics / Systems Toxicology

Reprogramming of microRNA expression via E2F1 downregulation promotes Salmonella infection

Authors: C. Aguilar, S. Costa, C. Maudet, R.P. Vivek-Ananth, S. Zaldívar-López, J.J. Garrido, A. Samal, M. Mano, A. Eulalio*

Journal: Nature Communications, 12: 3392 (2021)

Research Area: Others

NeurotoxKb 1.0: compilation, curation and exploration of a knowledgebase of environmental neurotoxicants

Authors: J. Ravichandran#, B.S. Karthikeyan#, P. Singla, S.R. Aparna, A. Samal*

Journal: Chemosphere, 278: 130387 (2021)

Link to NeurotoxKb

Research Area: Exposomics / Systems Toxicology

ExHuMId: A curated resource and analysis of Exposome of Human Milk across India

Authors: B.S. Karthikeyan#, J. Ravichandran#*, S.R. Aparna, A. Samal*

Journal: Chemosphere, 271: 129583 (2021)

Link to ExHuMId

Research Area: Exposomics / Systems Toxicology

MeFSAT: A curated natural product database specific to secondary metabolites of medicinal fungi

Authors: R.P. Vivek-Ananth#, A.K. Sahoo#, K. Kumaravel#, K. Mohanraj, A. Samal*

Journal: RSC Advances, 11: 2596–2607 (2021)

Link to MeFSAT

Research Area: Natural Product Spaces

Network-centric indicators for fragility in global financial indices

Authors: A. Samal*, S. Kumar, Y. Yadav, A. Chakraborti*

Journal: Frontiers in Physics, 8: 624373 (2021)

GitHub Repository

Research Area: Geometry and Topology based methods

Network geometry and market instability

Authors: A. Samal*, H.K. Pharasi#, S.J. Ramaia, H. Kannan, E. Saucan, J. Jost, A. Chakraborti*

Journal: Royal Society Open Science, 8: 201734 (2021)

GitHub Repository 1 | GitHub Repository 2

Research Area: Geometry and Topology based methods

A Simple Differential Geometry for Complex Networks

Authors: E. Saucan*, A. Samal, J. Jost

Journal: Network Science, 9(S1): S106–S133 (2021)

Research Area: Geometry and Topology based methods

DEDuCT 2.0: An updated knowledgebase and an exploratory analysis of the current regulations and guidelines from the perspective of endocrine disrupting chemicals

Authors: B.S. Karthikeyan#, J. Ravichandran#*, S.R. Aparna & A. Samal*

Journal: Chemosphere, 267: 128898 (2021)

Link to DEDuCT 2.0

Research Area: Exposomics / Systems Toxicology

Edge-based analysis of networks: Curvatures of graphs and hypergraphs

Authors: M. Eidi, A. Farzam, W. Leal, A. Samal, J. Jost*

Journal: Theory in Biosciences, 139: 337–348 (2020)

Research Area: Geometry and Topology based methods

Degree difference: A simple measure to characterize structural heterogeneity in complex networks

Authors: A. Farzam*, A. Samal*, J. Jost*

Journal: Scientific Reports, 10: 21348 (2020)

Research Area: Geometry and Topology based methods

In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection

Authors: R.P. Vivek-Ananth, A. Rana, N. Rajan, H.S. Biswal*, A. Samal*

Journal: Molecules, 25(17): 3822 (2020)

Research Area: Natural Product Spaces

Forman-Ricci curvature and persistent homology of unweighted complex networks

Authors: I. Roy*, S. Vijayaraghavan, S.J. Ramaia, A. Samal*

Journal: Chaos, Solitons & Fractals, 140: 110260 (2020)

Research Area: Geometry and Topology based methods

A Simple Differential Geometry for Networks and Its Generalizations

Authors: E. Saucan*, A. Samal, J. Jost

In: Complex Networks and Their Applications VIII, Springer (2019)

Research Area: Geometry and Topology based methods

Broad substrate-specific phosphorylation events are associated with the initial stage of plant cell wall recognition in Neurospora crassa

Authors: 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*

Journal: Frontiers in Microbiology, 10: 2317 (2019)

Research Area: Others

A curated knowledgebase on endocrine disrupting chemicals and their biological systems-level perturbations

Authors: B.S. Karthikeyan#, J. Ravichandran#*, K. Mohanraj, R.P. Vivek-Ananth, A. Samal*

Journal: Science of the Total Environment, 692: 281–296 (2019)

Link to DEDuCT

Research Area: Exposomics / Systems Toxicology

Persistent homology of unweighted complex networks via discrete Morse theory

Authors: H. Kannan, E. Saucan, I. Roy*, A. Samal*

Journal: Scientific Reports, 9: 13817 (2019)

Research Area: Geometry and Topology based methods

Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation

Authors: 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*

Journal: Cell Reports, 27(9): 2759–2771 (2019)

Research Area: Others

Discrete Ricci curvatures for directed networks

Authors: E. Saucan, R.P. Sreejith, R.P. Vivek-Ananth, J. Jost, A. Samal*

Journal: Chaos, Solitons & Fractals, 118: 347–360 (2019)

Research Area: Geometry and Topology based methods

Discrete curvatures and network analysis

Authors: E. Saucan, A. Samal, M. Weber, J. Jost*

Journal: MATCH Communications in Mathematical and in Computer Chemistry, 80(3): 605–622 (2018)

Research Area: Geometry and Topology based methods

Comparative analysis of two discretizations of Ricci curvature for complex networks

Authors: A. Samal#, R.P. Sreejith#, J. Gu, S. Liu, E. Saucan*, J. Jost*

Journal: Scientific Reports, 8: 8650 (2018)

GitHub Repository 1, GitHub Repository 2

Research Area: Geometry and Topology based methods

Comparative systems analysis of the secretome of Aspergillus fumigatus and other Aspergillus species

Authors: R.P. Vivek-Ananth, K. Mohanraj, M. Vandanashree, A. Jhingran, J.P. Craig, A. Samal*

Journal: Scientific Reports, 8: 6617 (2018)

Link to ASPERTOME

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry and Therapeutics

Authors: K. Mohanraj#, B.S. Karthikeyan#, R.P. Vivek-Ananth#, R.P. Bharath Chand, S.R. Aparna, P. Mangalapandi, A. Samal*

Journal: Scientific Reports, 8: 4329 (2018)

Link to IMPPAT

Research Area: Natural Product Spaces

Network approach towards understanding the crazing in glassy amorphous polymers

Authors: S. Venkatesan#, R.P. Vivek-Ananth#, R.P. Sreejith, P. Mangalapandi, A.A. Hassanali*, A. Samal*

Journal: Journal of Statistical Mechanics: Theory and Experiment, 043305 (2018)

GitHub Repository 1, GitHub Repository 2

Research Area: Geometry and Topology based methods

Haldane, Waddington and recombinant inbred lines: extension of their work to any number of genes

Authors: A. Samal*, O.C. Martin*

Journal: Journal of Genetics, 96(5): 795–800 (2017)

Research Area: Others

Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa

Authors: A. Samal, J.P. Craig, S.T. Coradetti#, J.P. Benz#, J.A. Eddy, N.D. Price*, N.L. Glass*

Journal: Biotechnology for Biofuels, 10: 225 (2017)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Systematic evaluation of a new combinatorial curvature for complex networks

Authors: R.P. Sreejith, J. Jost, E. Saucan, A. Samal*

Journal: Chaos, Solitons & Fractals, 101: 50–67 (2017)

Research Area: Geometry and Topology based methods

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

Authors: R.P. Vivek-Ananth, A. Samal*

Journal: Biosystems, 147: 1–10 (2016)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Forman curvature for complex networks

Authors: R.P. Sreejith, K. Mohanraj, J. Jost, E. Saucan, A. Samal*

Journal: Journal of Statistical Mechanics: Theory and Experiment, 063206 (2016)

GitHub Repository 1 | GitHub Repository 2

Research Area: Geometry and Topology based methods

Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns

Authors: 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*

Journal: Journal of Biological Chemistry, 291: 14257–14273 (2016)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Relative stability of network states in Boolean network models of gene regulation in development

Authors: J.X. Zhou#, A. Samal#, A.F. d'Hérouël, N.D. Price, S. Huang*

Journal: Biosystems, 142: 15–24 (2016)

Research Area: Boolean Modelling of GRNs

Phenotypic constraints promote latent versatility and carbon efficiency in metabolic networks

Authors: M. Bardoscia, M. Marsili, A. Samal*

Journal: Physical Review E, 92: 012809 (2015)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Statistical physics methods provide the exact solution to a long-standing problem of genetics

Authors: A. Samal, O.C. Martin*

Journal: Physical Review Letters, 114: 238101 (2015)

Editors’ Suggestion

Research Area: Others

Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

Authors: S. Kumar, M. Vendruscolo, A. Singh, D. Kumar, A. Samal*

Journal: Molecular Biosystems, 11: 930–941 (2015)

Research Area: Complex Systems / Network Science

Shining fresh light on the evolution of photosynthesis

Authors: A. Samal, O.C. Martin*

Journal: eLife, 2: e01403 (2013)

Research Area: Others

Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network

Authors: A. Henry, F. Monéger, A. Samal*, O.C. Martin*

Journal: Molecular Biosystems, 9(7): 1726–1735 (2013)

Research Area: Boolean Modelling of GRNs

Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks

Authors: S. Singh, A. Samal, V. Giri, S. Krishna, N. Raghuram, S. Jain*

Journal: Physical Review E, 87: 052708 (2013)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Hopf bifurcation in the evolution of networks driven by spike-timing-dependent plasticity

Authors: Q. Ren*, K.M. Kolwankar, A. Samal, J. Jost

Journal: Physical Review E, 86: 056103 (2012)

Research Area: Complex Systems / Network Science

Environmental versatility promotes modularity in genome-scale metabolic networks

Authors: A. Samal, A. Wagner*, O.C. Martin*

Journal: BMC Systems Biology, 5: 135 (2011)

Note: Highly accessed article

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Randomizing genome-scale metabolic networks

Authors: A. Samal, O.C. Martin*

Journal: PLoS ONE, 6(7): e22295 (2011)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Targeting Multiple Targets in Pseudomonas aeruginosa PAO1 using Flux Balance Analysis of a Reconstructed Genome-scale Metabolic Network

Authors: D. Perumal, A. Samal, K.R. Sakharkar, M.K. Sakharkar*

Journal: Journal of Drug Targeting, 19(1): 1–13 (2011)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Learning and structure of neuronal networks

Authors: K.M. Kolwankar*, Q. Ren, A. Samal, J. Jost

Journal: Pramana, 77(5): 817–826 (2011)

Research Area: Complex Systems / Network Science

Challenges in experimental data integration within genome-scale metabolic models

Authors: P.-Y. Bourguignon, A. Samal, F. Képès, J. Jost*, O.C. Martin*

Journal: Algorithms for Molecular Biology, 5: 20 (2010)

Note: Highly accessed article

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Cloning and Targeted Disruption of Two Lipopolysaccharide Biosynthesis Genes, kdsA and waaG, of Pseudomonas aeruginosa PAO1 by Site-Directed Mutagenesis

Authors: D. Perumal, K.R. Sakharkar, T.H. Tang, V.T.K. Chow, C.S. Lim, A. Samal, N. Sugiura, M.K. Sakharkar*

Journal: Journal of Molecular Microbiology and Biotechnology, 19(1): 169–179 (2010)

Research Area: Others

STDP-driven networks and C. elegans neuronal network

Authors: Q. Ren, K.M. Kolwankar*, A. Samal, J. Jost

Journal: Physica A, 389(15): 3900–3914 (2010)

Research Area: Complex Systems / Network Science

Genotype networks in metabolic reaction spaces

Authors: A. Samal, J.F. Matias Rodrigues, J. Jost, O.C. Martin*, A. Wagner*

Journal: BMC Systems Biology, 4: 30 (2010)

Note: Highly accessed article

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Preferential attachment renders an evolving network of populations robust against crashes

Authors: A. Samal, H. Meyer-Ortmanns*

Journal: Physica A, 388(8): 1535–1545 (2009)

Research Area: Complex Systems / Network Science

Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks

Authors: A. Samal*

Journal: Systems and Synthetic Biology, 2: 83–93 (2008)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response

Authors: A. Samal, S. Jain*

Journal: BMC Systems Biology, 2: 21 (2008)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

A universal power law and proportionate change process characterize the evolution of metabolic networks

Authors: S. Singh, A. Samal, V. Giri, S. Krishna, N. Raghuram, S. Jain*

Journal: European Physical Journal B, 57: 75–80 (2007)

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

Low degree metabolites explain essential reactions and enhance modularity in biological networks

Authors: A. Samal, S. Singh, V. Giri, S. Krishna, N. Raghuram, S. Jain*

Journal: BMC Bioinformatics, 7: 118 (2006)

Highly accessed article

Research Area: Systems Modelling of Metabolism and Protein Secretion Systems

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)