Declercq M, Treps L, Geldhof V, Conchinha NV, Rooij LD, Abhishek Subramanian, Feyeux M, Cotinat M, Boeckx B, Vinckier S, Dupont L, Vermeulen F, Boon M, Proesmans M, Libbrecht L, Pirenne J, Monbaliu D, Jochmans I, Dewerchin M, Eelen G, Roskams T, Verleden S, Lambrechts D, Carmeliet P, Witters P (2024), "Single cell RNA sequencing of cystic fibrosis liver disease explants revealed alternative complement activation", Liver International, 44 (9), 2382-2395, DOI: 10.1111/liv.15963
Laura de Rooij, Lisa Becker, Laure-Anne Teuwen, Bram Boeckx, Sander Jansen, Simon Feys, Stijn Verleden, Laurens Liesenborghs, Sasha Libbrecht, Tina Van Buyten, Gino Philips, Abhishek Subramanian, Sebastien Dumas, Elda Meta, Mila Borri, Liliana Sokol, Amelie Dendooven, Anh-Co Truong, Jan Gunst, Pierre Van Mol, Katerina Rohlenova, Robbert Boudewijns, Vincent Geldhof, Stefan Vinckier, Jacob Amersfoort, Wim Wuyts, Dirk Van Raemdonck, Werner Jacobs, Laurens Ceulemans, Birgit Weynand, Bernard Thienpont, Martin Lammens, Guy Eelen, Mieke Dewerchin, Luc Schoonjans, Jo van Dorpe, Els Wauters, Massimiliano Mazzone, Johan Neyts, Joost Wauters, Diether Lambrechts, and Peter Carmeliet (2022), “The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single cell resolution”, Cardiovascular Research, 119 (2), 520-535, DOI: 10.1093/cvr/cvac139
Abhishek Subramanian, Pooya Zakeri, Mira Mousa, Halima Alnaqbi, Fatima Yousif Alshamsi, Leo Bettoni, Ernesto Damiani, Habiba Al Safar, Yvan Saeys and Peter Carmeliet, (2022), “Angiogenesis goes computational – the future way forward to discover new angiogenic targets?”, Computational and Structural Biotechnology Journal, 20, 5235-5255, DOI: 10.1016/j.csbj.2022.09.019
Abhishek Subramanian, Lisa M. Becker, Peter Carmeliet (2021), “Endothelial metabolism going single”, Nature Metabolism, 3, 593-594, DOI: 10.1038/s42255-021-00399-3
Federico Taverna, Jermaine Goveia, Tobias K Karakach, Shawez Khan, Katerina Rohlenova, Lucas Treps, Abhishek Subramanian, Luc Schoonjans, Mieke Dewerchin, Guy Eelen, Peter Carmeliet (2020), “BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization”, Nucleic Acids Research, 48 (W1), W385–W394, DOI: 10.1093/nar/gkaa332
Katerina Rohlenova #, Jermaine Goveia #, Melissa García-Caballero #, Abhishek Subramanian #, Joanna Kalucka, Lucas Treps, Kim D Falkenberg, Laura PMH de Rooij, Yingfeng Zheng, Lin Lin, Liliana Sokol, Laure-Anne Teuwen, Vincent Geldhof, Federico Taverna, Andreas Pircher, Lena- Christin Conradi, Shawez Khan, Steve Stegen, Dena Panovska, Frederik De Smet, Frank JT Staal, Rene J Mclaughlin, Stefan Vinckier, Tine Van Bergen, Nadine Ectors, Patrik De Haes, Jian Wang, Lars Bolund, Luc Schoonjans, Tobias K Karakach, Huanming Yang, Geert Carmeliet, Yizhi Liu, Bernard Thienpont, Mieke Dewerchin, Guy Eelen, Xuri Li, Yonglun Luo, Peter Carmeliet (2020), “Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis”, Cell Metabolism, 31(4), 862-877 e14, DOI: 10.1016/j.cmet.2020.03.009 #equal contribution as first author
Abhishek Subramanian, Ram Rup Sarkar (2018), “Perspectives on Leishmania species and stage- specific adaptive mechanisms”, Trends in Parasitology, 34(12), 1068-1081, DOI: 10.1016/j.pt.2018.09.004
Abhishek Subramanian, Ram Rup Sarkar (2018), “Evolutionary Perspectives of Genotype– Phenotype Factors in Leishmania Metabolism”, Journal of Molecular Evolution, 86(7), 443-456, DOI: 10.1007/s00239-018-9857-5
Swarnendu Banerjee, Abhishek Subramanian, Joydev Chattopadhyay, Ram Rup Sarkar (2017), “Exploring the role of GS–GOGAT cycle in microcystin synthesis and regulation–a model based analysis”, Molecular BioSystems, 13, 2603-2614, DOI: c7mb00342k
Abhishek Subramanian, Ram Rup Sarkar (2017), “Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum”, Scientific Reports, 7(1):10262, DOI: 10.1038/s41598-017-10743-x
Sutanu Nandi, Abhishek Subramanian, Ram Rup Sarkar (2017), “An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux- coupled features”, Molecular BioSystems, 13, 1584 – 1596, DOI: 10.1039/C7MB00234C
Santanu Biswas, Abhishek Subramanian, Ibrahim M. ELMojtaba, Joydev Chattopadhyay, Ram Rup Sarkar (2017), “Optimal combinations of control strategies and cost-effective analysis for visceral leishmaniasis disease transmission”, PLoS ONE, 12(2): e0172465, DOI: 10.1371/journal.pone.0172465
Abhishek Subramanian, Ram Rup Sarkar (2016), “Network structure and enzymatic evolution in Leishmania metabolism: a computational study”, Proceedings of the International Symposium on Mathematical and Computational Biology - BIOMAT 2015., World Scientific, ISBN: 978-981- 3141- 90-2, 1 – 20, 11/2015, DOI:10.1142/9789813141919_0001 (Conference paper)
Abhishek Subramanian, Ram Rup Sarkar (2015), “Dynamics of GLI regulation and a strategy to control cancerous situation: hedgehog signaling pathway revisited”, Journal of Biological Systems, 23: 1550033, DOI: 10.1142/S0218339015500333
Rupa Bhowmick, Abhishek Subramanian, Ram Rup Sarkar (2015), “Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach”, Systems and Synthetic Biology, 9:159–177, DOI: 10.1007%2Fs11693-015-9183-9
Abhishek Subramanian, Jitesh Jhawar, Ram Rup Sarkar (2015), “Dissecting Leishmania infantum energy metabolism - a systems perspective”, PLoS ONE, 10(9): e0137976, DOI: 10.1371/journal.pone.0137976
Abhishek Subramanian, Vidhi Singh, Ram Rup Sarkar (2015), “Understanding Visceral Leishmaniasis Disease Transmission and its Control - A Study Based on Mathematical Modeling”, Mathematics, 3:913-944, DOI: 10.3390/math3030913
Abhishek Subramanian, Ram Rup Sarkar (2015), “Data in support of large scale comparative codon usage analysis in Leishmania and Trypanosomatids”, Data in Brief, 4:269–272, DOI: 10.1016/j.dib.2015.06.003
Abhishek Subramanian, Ram Rup Sarkar (2015), “Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions”, Genomics, 106:232–241, DOI: 10.1016/j.ygeno.2015.05.009
Ram Rup Sarkar, Rupa Bhowmick, Abhishek Subramanian, “Method of Identification of Combinatorial Enzymatic Reaction Targets in Glioblastoma Specific Metabolic Network, - Patent No. 454732, grant date: 26-09-2023
Abhishek Subramanian and Nishant Kumar (2024), “Artificial Intelligence in Bioinformatics”, Chapter 21, 357-374, CRC Press
2. Abhishek Subramanian, Ram Rup Sarkar (2018) Computational Techniques for a Comprehensive Understanding of Different Genotype-Phenotype Factors in Biological Systems and Their Applications. Pp. 113 -139, In: Singh S. (eds) Synthetic Biology. Springer, Singapore. ISBN 978-981-10-8692-2, DOI: 10.1007/978-981-10-8693-9_8