.png){kind=icon}
Complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment
Teh, B.S., Hii, Y.S., Hinks, J., Abdul-Wahab, M.F. and Swarup, S., 2023. Complete genome sequence of Methylomonas sp. UP202 isolated from an urban waterway sediment. Microbiology Resource Announcements, pp.e00633-23.
Volatile methyl jasmonate from roots triggers host-beneficial soil microbiome biofilms
Kulkarni, O.S., Mazumder, M., Kini, S., Hill, E.D., Aow, J.S.B., Phua, S.M.L., Elejalde, U., Kjelleberg, S. and Swarup, S., 2023. Volatile methyl jasmonate from roots triggers host-beneficial soil microbiome biofilms. Nature Chemical Biology, pp.1-11.
Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective
Verrone, V., Gupta, A., Laloo, A.E., Dubey, R.K., Hamid, N.A.A. and Swarup, S., 2023. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. Science of The Total Environment, p.167757.
Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes
Mukherjee, A., Tikariha, H., Bandla, A., Pavagadhi, S. and Swarup, S., 2023. Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes. Msystems, 8(4), pp.e00387-23.
Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation
Bandla, A., Mukhopadhyay, S., Mishra, S., Sudarshan, A.S. and Swarup, S., 2023. Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation. Scientific Data, 10(1), p.373.
Penicillium citrinum Provides Transkingdom Growth Benefits in Choy Sum (Brassica rapa var. parachinensis)
Gu, K., Chen, C.Y., Selvaraj, P., Pavagadhi, S., Yeap, Y.T., Swarup, S., Zheng, W. and Naqvi, N.I., 2023. Penicillium citrinum Provides Transkingdom Growth Benefits in Choy Sum (Brassica rapa var. parachinensis). Journal of Fungi, 9(4), p.420.
High but variable CH4 emissions post-fire is associated with stochastic recruitment and assembly of methanogens
Bandla, A., Akhtar, H., Lupascu, M., Sukri, R.S. and Swarup, S., 2023. High but variable CH4 emissions post-fire is associated with stochastic recruitment and assembly of methanogens (No. EGU23-6930). Copernicus Meetings.
Assessing the effect of water table level on carbon dioxide and methane exchange from a tropical peatland mesocosm experiment using automated soil flux chambers
Lupascu, M., Taillardat, P., Sasmito, S., Moore, J., Tarigan, S., Taufik, M., ... & Swarup, S. (2023). Assessing the effect of water table level on carbon dioxide and methane exchange from a tropical peatland mesocosm experiment using automated soil flux chambers (No. EGU23-14224). Copernicus Meetings.
High methane flux in a tropical peatland post-fire is linked to homogenous selection of diverse methanogenic archaea
Verrone, V., Gupta, A., Laloo, A.E., Dubey, R.K., Hamid, N.A.A. and Swarup, S., 2023. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. Science of The Total Environment, p.167757.
A field study on using soybean waste-derived superabsorbent hydrogel to enhance growth of vegetables
Zhu, J., Tan, W. K., Song, X., Zhang, Z., Gao, Z., Wen, Y., Omg C.N., Swarup, S & Li, J. (2022). Synthesis and Characterization of Okara-Poly (acrylic acid) Superabsorbent Hydrogels for Enhancing Vegetable Growth through Improving Water Holding and Retention Properties of Soils. ACS Food Science & Technology
Microbiome Engineering for Next‐Generation Precision Agriculture
Abdul‐Wahab, M.F., Pavagadhi, S., Tikariha, H. and Swarup, S., 2022. Microbiome Engineering for Next‐Generation Precision Agriculture. Principles in Microbiome Engineering, pp.137-153.
Synthesis and characterization of okara-poly (acrylic acid) superabsorbent hydrogels for enhancing vegetable growth through improving water holding and retention properties of …
Zhu, J., Tan, W.K., Song, X., Zhang, Z., Gao, Z., Wen, Y., Ong, C.N., Swarup, S. and Li, J., 2022. Synthesis and characterization of okara-poly (acrylic acid) superabsorbent hydrogels for enhancing vegetable growth through improving water holding and retention properties of soils. ACS Food Science & Technology, 3(4), pp.553-561.
Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria
Mohanty, B., Majedi, S.M., Pavagadhi, S., Te, S.H., Boo, C.Y., Gin, K.Y.H. and Swarup, S., 2022. Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria. Metabolites, 12(5), p.406.
Urban soil microbiome functions and their linkages with ecosystem services
Ooi, Q.E., Nguyen, C.T.T., Laloo, A., Bandla, A. and Swarup, S., 2022. Urban soil microbiome functions and their linkages with ecosystem services. In Soils in Urban Ecosystem (pp. 47-63). Singapore: Springer Singapore.
Evaluating the effects of environmental perturbations in bloom forming cyanobacteria through untargeted metabolomics
Pavagadhi, S., Benke, P. I., Majedi, S. M., Umashankar, S., Yeap, Y. T., & Swarup, S. (2022). Evaluating the effects of environmental perturbations in bloom forming cyanobacteria through untargeted metabolomics. In Applied Environmental Metabolomics (pp. 231-244). Academic Press.
Fire-mediated disturbances affects microbiome composition and assembly processes in tropical peatlands
Akhtar, H., Bandla, A., Lupascu, M., Sukri, R. and Swarup, S., 2021, December. Fire-mediated disturbances affects microbiome composition and assembly processes in tropical peatlands. In AGU Fall Meeting Abstracts (Vol. 2021, pp. B54E-05).
Hybrid genome assembly for predicting functional potential of a novel Streptomyces strain as plant biomass valorisation agent
Tikariha, H., Pavagadhi, S., Mayalagu, S., Poh, M.C.H. and Swarup, S., 2021. Hybrid genome assembly for predicting functional potential of a novel Streptomyces strain as plant biomass valorisation agent. Indian Journal of Microbiology, 61(3), pp.283-290.
Multi-USV Adaptive Exploration Using Kernel Information and Residual Variance
Mishra, R., Koay, T.B., Chitre, M. and Swarup, S., 2021. Multi-USV Adaptive Exploration Using Kernel Information and Residual Variance. Frontiers in Robotics and AI, 8, p.572243.
Root exudates compounds and microbial community composition regulates CH4 dynamics in fire degraded tropical peatland
Lupascu, M., Akhtar, H., Bandla, A., Sukri, R.S. and Swarup, S., 2021, April. Root exudates compounds and microbial community composition regulates CH4 dynamics in fire degraded tropical peatland. In EGU General Assembly Conference Abstracts (pp. EGU21-10461).
A novel signaling pathway required for Arabidopsis endodermal root organization shapes the rhizosphere microbiome
Durr, J., Reyt, G., Spaepen, S., Hilton, S., Meehan, C., Qi, W., Kamiya, T., Flis, P., Dickinson, H.G., Feher, A. and Shivshankar, U., 2021. A novel signaling pathway required for Arabidopsis endodermal root organization shapes the rhizosphere microbiome. Plant and Cell Physiology, 62(2), pp.248-261.
Significant sedge-mediated methane emissions from degraded tropical peatlands
Akhtar, H., Lupascu, M., Sukri, R.S., Smith, T.E., Cobb, A.R. and Swarup, S., 2020. Significant sedge-mediated methane emissions from degraded tropical peatlands. Environmental Research Letters, 16(1), p.014002.
Freshwater sediment microbial communities are not resilient to disturbance from agricultural land runoff
Beattie, R.E., Bandla, A., Swarup, S. and Hristova, K.R., 2020. Freshwater sediment microbial communities are not resilient to disturbance from agricultural land runoff. Frontiers in Microbiology, 11, p.539921.
Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem
Saxena, G., Hill, E.D., Marzinelli, E.M., Umashankar, S., Wei, T.J., Yissue, W.W., Steinberg, P.D., Rajal, V.B., Kjelleberg, S., Williams, R.B. and Wuertz, S., 2020. Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem. bioRxiv, pp.2020-09.
910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens
Bandla, A., Pavagadhi, S., Sridhar Sudarshan, A., Poh, M.C.H. and Swarup, S., 2020. 910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens. Scientific Data, 7(1), p.278.
Converting Okara to Superabsorbent Hydrogels as Soil Supplements for Enhancing the Growth of Choy Sum (Brassica sp.) under Water-Limited Conditions
Zhu, J., Tan, W.K., Song, X., Gao, Z., Wen, Y., Ong, C.N., Loh, C.S., Swarup, S. and Li, J., 2020. Converting okara to superabsorbent hydrogels as soil supplements for enhancing the growth of choy sum (Brassica sp.) under water-limited conditions. ACS Sustainable Chemistry & Engineering, 8(25), pp.9425-9433.
Metabolomics for evaluating flavor-associated metabolites in plant-based products
Pavagadhi, S. and Swarup, S., 2020. Metabolomics for evaluating flavor-associated metabolites in plant-based products. Metabolites, 10(5), p.197.
Chemical modification of biomass okara using poly (acrylic acid) through free radical graft polymerization
Zhu, J., Song, X., Tan, W.K., Wen, Y., Gao, Z., Ong, C.N., Loh, C.S., Swarup, S. and Li, J., 2020. Chemical modification of biomass okara using poly (acrylic acid) through free radical graft polymerization. Journal of Agricultural and Food Chemistry, 68(46), pp.13241-13246.
Impact of fire on vegetation, soil microbes and CH4 emission from a degraded tropical peatland
Akhtar, H., Lupascu, M., Kulkarni, O.S., Bandla, A., Sukri, R.S., Cobb, A.R., Smith, T.E. and Swarup, S., 2020, May. Impact of fire on vegetation, soil microbes and CH4 emission from a degraded tropical peatland. In EGU General Assembly Conference Abstracts (p. 12743).
Crosskingdom growth benefits of fungus-derived phytohormones in Choy Sum
Gu, K., Pavagadhi, S., Yeap, Y.T., Chen, C.Y., Swarup, S. and Naqvi, N.I., 2020. Crosskingdom growth benefits of fungus-derived phytohormones in Choy Sum. bioRxiv, pp.2020-02.
Forensic Pedology: From Soil Trace Evidence to Courtroom
Stella, T.W.L., Swarup, S., See Suet Ning, M., Lim, N.Q.B.I., Phua Mun Lin, S., Tan Boon Jay, T. and Ghosh, S., 2020. Forensic Pedology: From Soil Trace Evidence to Courtroom. Soil Analysis: Recent Trends and Applications, pp.305-323.
Harnessing soil microbiomes for creating healthy and functional urban landscapes
Bandla, A., Pavagadhi, S. and Swarup, S., 2020. Harnessing soil microbiomes for creating healthy and functional urban landscapes. Soil analysis: recent trends and applications, pp.325-338.
1H-NMR-based metabolomics to investigate the effects of Phoenix dactylifera seed extracts in LPS-IFN-γ-induced RAW 264.7 cells
Abdul-Hamid, N.A., Abas, F., Ismail, I.S., Tham, C.L., Maulidiani, M., Mediani, A., Swarup, S. and Umashankar, S., 2019. 1H-NMR-based metabolomics to investigate the effects of Phoenix dactylifera seed extracts in LPS-IFN-γ-induced RAW 264.7 cells. Food Research International, 125, p.108565.
Resource partitioning strategies during toxin production in Microcystis aeruginosa revealed by integrative omics analysis
Pan, D., Pavagadhi, S., Umashankar, S., Rai, A., Benke, P.I., Rai, M., Saxena, G., Gangu, V. and Swarup, S., 2019. Resource partitioning strategies during toxin production in Microcystis aeruginosa revealed by integrative omics analysis. Algal Research, 42, p.101582.
NMR metabolomics for evaluating passage number and harvesting effects on mammalian cell metabolome Abdul-Hamid, N.A., Abas, F., Maulidiani, M., Ismail, I.S., Tham, C.L., Swarup, S. and Umashankar, S., 2019. NMR metabolomics for evaluating passage number and harvesting effects on mammalian cell metabolome. Analytical biochemistry, 576, pp.20-32.
Correction for Keogh et al.,“Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism”
Keogh, D., Lam, L.N., Doyle, L.E., Matysik, A., Pavagadhi, S., Umashankar, S., Low, P.M., Dale, J.L., Song, Y., Ng, S.P. and Boothroyd, C.B., 2019. Correction for Keogh et al.,“Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism”. Mbio, 10(3), pp.10-1128.
Metabolites and biological activities of Phoenix dactylifera L. pulp and seeds: A comparative MS and NMR based metabolomics approach
Abdul-Hamid, N.A., Abas, F., Ismail, I.S., Tham, C.L., Maulidiani, M., Mediani, A., Swarup, S., Umashankar, S. and Zolkeflee, N.K.Z., 2019. Metabolites and biological activities of Phoenix dactylifera L. pulp and seeds: A comparative MS and NMR based metabolomics approach. Phytochemistry Letters, 31, pp.20-32.
Impacts of peat-forest smoke on urban PM2. 5 in the Maritime Continent during 2012–2015: Carbonaceous profiles and indicators
Tham, J., Sarkar, S., Jia, S., Reid, J.S., Mishra, S., Sudiana, I.M., Swarup, S., Ong, C.N. and Liya, E.Y., 2019. Impacts of peat-forest smoke on urban PM2. 5 in the Maritime Continent during 2012–2015: Carbonaceous profiles and indicators. Environmental Pollution, 248, pp.496-505.
Systems biology and multi-omics integration: viewpoints from the metabolomics research community
Pinu, F.R., Beale, D.J., Paten, A.M., Kouremenos, K., Swarup, S., Schirra, H.J. and Wishart, D., 2019. Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Metabolites, 9(4), p.76.
Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables
Pavagadhi, S., Bandla, A., Hong, M.P.C., Umashankar, S., Ting, Y.Y. and Swarup, S., 2019. Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables. bioRxiv, p.604819.
Effects of post-fire vegetation structure on CH4 emissions from a degraded tropical peatland in Brunei.
Akhtar, H., Lupascu, M., Pavagadhi, S.A., Hong, M.P., Bisht, N., Sukri, R.S., Smith, T.E., Cobb, A.R. and Swarup, S., 2019, January. Effects of post-fire vegetation structure on CH4 emissions from a degraded tropical peatland in Brunei. In Geophysical Research Abstracts (Vol. 21).
A framework to address the food, energy and water nexus among indian megacities and their rapidly expanding peripheries
BANDLA, A., SAXENA, G., MISHRA, R. and SWARUP, S., 2019. A framework to address the food, energy and water nexus among indian megacities and their rapidly expanding peripheries. Dialogue Sci. Sci. Soc., 2, p.31.
Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation Birrer, S.C., Dafforn, K.A., Sun, M.Y., Williams, R.B., Potts, J., Scanes, P., Kelaher, B.P., Simpson, S.L., Kjelleberg, S., Swarup, S. and Steinberg, P., 2019. Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation. Environmental Microbiology, 21(1), pp.389-401.
Characterization of plant volatiles reveals distinct metabolic profiles and pathways among 12 Brassicaceae vegetables
Liu, Y., Zhang, H., Umashankar, S., Liang, X., Lee, H.W., Swarup, S. and Ong, C.N., 2018. Characterization of plant volatiles reveals distinct metabolic profiles and pathways among 12 Brassicaceae vegetables. Metabolites, 8(4), p.94.
Informed sampling and adaptive monitoring using sparse Gaussian processes
Mishra, R., Chitre, M. and Swarup, S., 2018, November. Informed sampling and adaptive monitoring using sparse Gaussian processes. In 2018 IEEE/OES Autonomous Underwater Vehicle Workshop (AUV) (pp. 1-5). IEEE.
Metabolomic profiles of tropical Chlorella and Parachlorella species in response to physiological changes during exponential and stationary growth phase
Vello, V., Umashankar, S., Phang, S.M., Chu, W.L., Lim, P.E., Nazia, A.M., Liew, K.E., Swarup, S. and Chew, F.T., 2018. Metabolomic profiles of tropical Chlorella and Parachlorella species in response to physiological changes during exponential and stationary growth phase. Algal research, 35, pp.61-75.
Keystone species in pregnancy gingivitis: a snapshot of oral microbiome during pregnancy and postpartum period
Balan, P., Chong, Y.S., Umashankar, S., Swarup, S., Loke, W.M., Lopez, V., He, H.G. and Seneviratne, C.J., 2018. Keystone species in pregnancy gingivitis: a snapshot of oral microbiome during pregnancy and postpartum period. Frontiers in microbiology, 9, p.2360.
Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway
Saxena, G., Mitra, S., Marzinelli, E.M., Xie, C., Wei, T.J., Steinberg, P.D., Williams, R.B., Kjelleberg, S., Lauro, F.M. and Swarup, S., 2018. Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway. Msystems, 3(3), pp.10-1128.
Online informative path planning using sparse Gaussian processes
Mishra, R., Chitre, M. and Swarup, S., 2018, May. Online informative path planning using sparse Gaussian processes. In 2018 OCEANS-MTS/IEEE Kobe Techno-Oceans (OTO) (pp. 1-5). IEEE.
Extracellular electron transfer powers Enterococcus faecalis biofilm metabolism
Keogh, D., Lam, L.N., Doyle, L.E., Matysik, A., Pavagadhi, S., Umashankar, S., Low, P.M., Dale, J.L., Song, Y., Ng, S.P. and Boothroyd, C.B., 2018. Extracellular electron transfer powers Enterococcus faecalis biofilm metabolism. MBio, 9(2), pp.e00626-17.
Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation Kelaher, B.P., Birrer, S.C., Dafforn, K.A., Sun, M.Y., Potts, J., Scanes, P., Simpson, S.L., Kjelleberg, S., Swarup, S., Steinberg, P. and Johnston, E.L., 2018. Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation.
The draft genome of tropical fruit durian (Durio zibethinus)
Teh, B.T., Lim, K., Yong, C.H., Ng, C.C.Y., Rao, S.R., Rajasegaran, V., Lim, W.K., Ong, C.K., Chan, K., Cheng, V.K.Y. and Soh, P.S., 2017. The draft genome of tropical fruit durian (Durio zibethinus). Nature genetics, 49(11), pp.1633-1641.
Correction to ‘Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels’
Chua, S.L., Ding, Y., Liu, Y., Cai, Z., Zhou, J., Swarup, S., Drautz-Moses, D.I., Schuster, S.C., Kjelleberg, S., Givskov, M. and Yang, L., 2017. Correction to ‘Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels’. Open Biology, 7(9), p.170197.
Metabolomics of Microbial Biofilms: Current Status and Future Directions
Suriyanarayanan, T., Seneviratne, C.J., Ng, W.L., Pavagadhi, S. and Swarup, S., 2017. Metabolomics of Microbial Biofilms: Current Status and Future Directions. Microbial Biofilms, pp.163-192.
Drug Targeting of the Human Microbiome
Ling, H., Foo, J.L., Saxena, G., Swarup, S. and Chang, M.W., 2017. Drug Targeting of the Human Microbiome. Systems Biology, 6, pp.191-214.
Transcriptomics analysis reveals putative genes involved in biofilm formation and biofilm-associated drug resistance of Enterococcus faecalis
Seneviratne, C.J., Suriyanarayanan, T., Swarup, S., Chia, K.H.B., Nagarajan, N. and Zhang, C., 2017. Transcriptomics analysis reveals putative genes involved in biofilm formation and biofilm-associated drug resistance of Enterococcus faecalis. Journal of endodontics, 43(6), pp.949-955.
Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels
Chua, S.L., Ding, Y., Liu, Y., Cai, Z., Zhou, J., Swarup, S., Drautz-Moses, D.I., Schuster, S.C., Kjelleberg, S., Givskov, M. and Yang, L., 2016. Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open biology, 6(11), p.160162.
Flagellin FliC Phosphorylation Affects Type 2 Protease Secretion and Biofilm Dispersal in Pseudomonas aeruginosa PAO1
Suriyanarayanan, T., Periasamy, S., Lin, M.H., Ishihama, Y. and Swarup, S., 2016. Flagellin FliC phosphorylation affects type 2 protease secretion and biofilm dispersal in Pseudomonas aeruginosa PAO1. PLoS One, 11(10), p.e0164155.
Coordinate regulation of metabolite glycosylation and stress hormone biosynthesis by TT8 in Arabidopsis
Rai, A., Umashankar, S., Rai, M., Kiat, L.B., Bing, J.A.S. and Swarup, S., 2016. Coordinate regulation of metabolite glycosylation and stress hormone biosynthesis by TT8 in Arabidopsis. Plant Physiology, 171(4), pp.2499-2515.
Microbial biofilms as one of the key elements in modulating ecohydrological processes in both natural and urban water corridors
Fazi, S., Bandla, A., Pizzetti, I. and Swarup, S., 2016. Microbial biofilms as one of the key elements in modulating ecohydrological processes in both natural and urban water corridors. Ecohydrology & Hydrobiology, 16(1), pp.33-38.
Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels
Drautz-Moses, D.I., Schuster, S.C., Kjelleberg, S., Givskov, M., Yang, L., Chua, S.L., Ding, Y., Liu, Y., Cai, Z., Zhou, J. and Swarup, S., 2016. Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels.
RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere
Mynampati, K.C., Lee, Y.J., Wijdeveld, A., Reuben, S., Samavedham, L., Kjelleberg, S. and Swarup, S., 2015. RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere. Environmental Pollution, 207, pp.205-210.
A fungal monooxygenase-derived jasmonate attenuates host innate immunity
Patkar, R.N., Benke, P.I., Qu, Z., Constance Chen, Y.Y., Yang, F., Swarup, S. and Naqvi, N.I., 2015. A fungal monooxygenase-derived jasmonate attenuates host innate immunity. Nature chemical biology, 11(9), pp.733-740.
Global Regulator MorA Affects Virulence-Associated Protease Secretion in Pseudomonas aeruginosa PAO1 Ravichandran, A., Ramachandran, M., Suriyanarayanan, T., Wong, C.C. and Swarup, S., 2015. Global regulator MorA affects virulence-associated protease secretion in Pseudomonas aeruginosa PAO1. PLoS One, 10(4), p.e0123805.
Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity Saxena, G., Marzinelli, E.M., Naing, N.N., He, Z., Liang, Y., Tom, L., Mitra, S., Ping, H., Joshi, U.M., Reuben, S. and Mynampati, K.C., 2015. Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environmental science & technology, 49(3), pp.1462-1471.
Global regulator morA affects virulence-associated protease secretion in pseudomonas aeruginosa PAO1 Swarup, S., Ravichandran, A., Ramachandran, M., Suriyanarayanan, T. and Wong, C.C., 2015. Global regulator morA affects virulence-associated protease secretion in pseudomonas aeruginosa PAO1.
A mass spectrometry-based unique fragment approach for the identification of microcystins
Benke, P.I., Kumar, M.V., Pan, D. and Swarup, S., 2015. A mass spectrometry-based unique fragment approach for the identification of microcystins. Analyst, 140(4), pp.1198-1206.
Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic …
Reuben, S., Banas, K., Banas, A. and Swarup, S., 2014. Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms. Water research, 64, pp.123-133.
Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands
Mishra, S., Lee, W.A., Hooijer, A., Reuben, S., Sudiana, I.M., Idris, A. and Swarup, S., 2014. Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands. Biogeosciences, 11(7), pp.1727-1741.
A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in …
Reuben, S., Rai, A., Pillai, B.V., Rodrigues, A. and Swarup, S., 2013. A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in Arabidopsis. Journal of experimental botany, 64(16), pp.5183-5194.
Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands.
Mishra, S., Lee, W.A., Hooijer, A., Reuben, S., Sudiana, I.M., Idris, A. and Swarup, S., 2013. Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands. Biogeosciences Discussions, 10(8).
Bacterial tethering analysis reveals a “run-reverse-turn” mechanism for Pseudomonas species motility
Qian, C., Wong, C.C., Swarup, S. and Chiam, K.H., 2013. Bacterial tethering analysis reveals a “run-reverse-turn” mechanism for Pseudomonas species motility. Applied and environmental microbiology, 79(15), pp.4734-4743.
Bioinformatics and molecular biology for the quantification of closely related bacteria
Nagarajan, K., Loh, K.C. and Swarup, S., 2013. Bioinformatics and molecular biology for the quantification of closely related bacteria. Applied microbiology and biotechnology, 97, pp.6489-6502.
Enhancement of Plant–Microbe Interactions using Rhizosphere Metabolomics‐Driven Approach and its Application in the Removal of Polychlorinated Biphenyls
Lee, Y.J., Narasimhan, K. and Swarup, S., 2013. Enhancement of Plant–Microbe Interactions using Rhizosphere Metabolomics‐Driven Approach and its Application in the Removal of Polychlorinated Biphenyls. Molecular Microbial Ecology of the Rhizosphere, 1, pp.1191-1198.
Use of Rhizosphere Metabolomics to Investigate Exudation of Phenolics by Arabidopsis Roots
Lee, Y.J., Rai, A., Reuben, S., Nesati, V., Almeida, R. and Swarup, S., 2013, April. Use of Rhizosphere Metabolomics to Investigate Exudation of Phenolics by Arabidopsis Roots. In EGU General Assembly Conference Abstracts (pp. EGU2013-7546).
Understanding aquatic rhizosphere processes through metabolomics and metagenomics approach
Lee, Y.J., Mynampati, K., Drautz, D., Arumugam, K., Williams, R., Schuster, S., Kjelleberg, S. and Swarup, S., 2013, April. Understanding aquatic rhizosphere processes through metabolomics and metagenomics approach. In EGU General Assembly Conference Abstracts (pp. EGU2013-7810).
Plant metabolomics: from experimental design to knowledge extraction
Rai, A., Umashankar, S. and Swarup, S., 2013. Plant metabolomics: from experimental design to knowledge extraction. Legume Genomics: Methods and Protocols, pp.279-312.
Bacterial diversity on different surfaces in urban freshwater
Reuben, S., Chua, C.L.N., Fam, K.D., Thian, Z.Y.A., Kang, M.K. and Swarup, S., 2012. Bacterial diversity on different surfaces in urban freshwater. Water Science and Technology, 65(10), pp.1869-1874.
Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis
Zhang, W.C., Shyh-Chang, N., Yang, H., Rai, A., Umashankar, S., Ma, S., Soh, B.S., Sun, L.L., Tai, B.C., Nga, M.E. and Bhakoo, K.K., 2012. Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis. Cell, 148(1), pp.259-272.
Bacterial diversity on different surfaces in urban freshwater
Swarup, S., Reuben, S., Chua, C.L.N., Fam, K.D., Thian, Z.Y.A. and Kang, M.K., 2012. Bacterial diversity on different surfaces in urban freshwater.
datPAV—an online processing, analysis and visualization tool for exploratory investigation of experimental data
Biswas, A., Rao, R., Umashankar, S., Mynampati, K.C., Reuben, S., Parab, G. and Swarup, S., 2011. datPAV—an online processing, analysis and visualization tool for exploratory investigation of experimental data. Bioinformatics, 27(11), pp.1585-1586.
Swimming Motility of Monotrichous Pseuomonas Aeruginosa
Qian, C., Wong, C.C., Swarup, S. and Chiam, K.H., 2011. Swimming Motility of Monotrichous Pseuomonas Aeruginosa. Biophysical Journal, 100(3), pp.306a-307a.
Quorum sensing modulation of a putative glycosyltransferase gene cluster essential for Xanthomonas campestris biofilm formation
Tao, F., Swarup, S. and Zhang, L.H., 2010. Quorum sensing modulation of a putative glycosyltransferase gene cluster essential for Xanthomonas campestris biofilm formation. Environmental microbiology, 12(12), pp.3159-3170.
MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation
Biswas, A., Mynampati, K.C., Umashankar, S., Reuben, S., Parab, G., Rao, R., Kannan, V.S. and Swarup, S., 2010. MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation. Bioinformatics, 26(20), pp.2639-2640.
Synthesis and in vitro antiproliferative activity of diphenyl (sulphonylpiperidin-4-yl) methanol derivatives
Benaka Prasad, S.B., Vinaya, K., Ananda Kumar, C.S., Swarup, S. and Rangappa, K.S., 2010. Synthesis and in vitro antiproliferative activity of diphenyl (sulphonylpiperidin-4-yl) methanol derivatives. Medicinal chemistry research, 19, pp.220-235.
The Cyclic Nucleotide Monophosphate Domain of Xanthomonas campestris Global Regulator Clp Defines a New Class of Cyclic Di-GMP Effectors
Tao, F., He, Y.W., Wu, D.H., Swarup, S. and Zhang, L.H., 2010. The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors. Journal of bacteriology, 192(4), pp.1020-1029.
Synthesis of novel 6-fluoro-3-(4-piperidinyl)-1, 2-benzisoxazole derivatives as antiproliferative agents: A structure–activity relationship study
Benaka Prasad, S.B., Vinaya, K., Ananda Kumar, C.S., Swarup, S. and Rangappa, K.S., 2009. Synthesis of novel 6-fluoro-3-(4-piperidinyl)-1, 2-benzisoxazole derivatives as antiproliferative agents: A structure–activity relationship study. Investigational new drugs, 27, pp.534-542.
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species
Ravichandran, A., Sugiyama, N., Tomita, M., Swarup, S. and Ishihama, Y., 2009. Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species. Proteomics, 9(10), pp.2764-2775.
Synthesis and antiproliferative activity of substituted diazaspiro hydantoins: a structure–activity relationship study
CS, A.K., Prasad, S.B., Vinaya, K., Chandrappa, S., Thimmegowda, N.R., Ranganatha, S.R., Swarup, S. and Rangappa, K.S., 2009. Synthesis and antiproliferative activity of substituted diazaspiro hydantoins: a structure–activity relationship study. Investigational new drugs, 27, pp.131-139.
Synthesis and in vitro antiproliferative activity of novel 1-benzhydrylpiperazine derivatives against human cancer cell lines
Kumar, C.A., Prasad, S.B., Vinaya, K., Chandrappa, S., Thimmegowda, N.R., Kumar, Y.S., Swarup, S. and Rangappa, K.S., 2009. Synthesis and in vitro antiproliferative activity of novel 1-benzhydrylpiperazine derivatives against human cancer cell lines. European journal of medicinal chemistry, 44(3), pp.1223-1229.
Data-driven optimization of metabolomics methods using rat liver samples
Parab, G.S., Rao, R., Lakshminarayanan, S., Bing, Y.V., Moochhala, S.M. and Swarup, S., 2009. Data-driven optimization of metabolomics methods using rat liver samples. Analytical chemistry, 81(4), pp.1315-1323.
Combining genomics and metabolomics approaches to aid discovery and production of small molecules as therapeutics
Prasanna, S.S., Reuben, S., Benaka Prasad, S.B., Rangappa, K.S. and Swarup, S., 2009. Combining genomics and metabolomics approaches to aid discovery and production of small molecules as therapeutics. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY (Vol. 238). Amer Chemical Soc.
Synthesis and in vitro antiproliferative activity of diphenyl (piperidin-4-yl) thioamide methanol derivatives Benaka Prasad, S.B., Vinaya, M.K., Ananda Kumar, C.K., Swarup, S. and Rangappa, K.S., 2008. Synthesis and in vitro antiproliferative activity of diphenyl (piperidin-4-yl) thioamide methanol derivatives. Letters in Drug Design & Discovery, 5(7), pp.454-461.
Berberine targets assembly of Escherichia coli cell division protein FtsZ
Domadia, P.N., Bhunia, A., Sivaraman, J., Swarup, S. and Dasgupta, D., 2008. Berberine targets assembly of Escherichia coli cell division protein FtsZ. Biochemistry, 47(10), pp.3225-3234.
Rhizosphere metabolomics: methods and applications
Reuben, S., Bhinu, V.S. and Swarup, S., 2008. Rhizosphere metabolomics: methods and applications. In Secondary metabolites in soil ecology (pp. 37-68). Berlin, Heidelberg: Springer Berlin Heidelberg.
Inhibition of bacterial cell division protein FtsZ by cinnamaldehyde
Domadia, P., Swarup, S., Bhunia, A., Sivaraman, J. and Dasgupta, D., 2007. Inhibition of bacterial cell division protein FtsZ by cinnamaldehyde. Biochemical pharmacology, 74(6), pp.831-840.
Structure of two genes encoding parallel prothrombin activators in Tropidechis carinatus snake: gene duplication and recruitment of factor X gene to the venom gland
Reza, M.A., Swarup, S. and Kini, R.M., 2007. Structure of two genes encoding parallel prothrombin activators in Tropidechis carinatus snake: gene duplication and recruitment of factor X gene to the venom gland. Journal of Thrombosis and Haemostasis, 5(1), pp.117-126.
Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake)
Reza, M.A., Le, T.M., Swarup, S. and Kini, R.M., 2006. Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake). Journal of Thrombosis and Haemostasis, 4(6), pp.1346-1353.
Gene structures of trocarin D and coagulation factor X, two functionally diverse prothrombin activators from Australian rough scaled snake
Reza, M.A., Swarup, S. and Kini, R.M., 2006. Gene structures of trocarin D and coagulation factor X, two functionally diverse prothrombin activators from Australian rough scaled snake. Pathophysiology of haemostasis and thrombosis, 34(4-5), pp.205-208.
Extracting information for meaningful function inference through text-mining
Eisenhaber, F., Pan, H., Zuo, L., Kanagasabai, R., Zhang, Z., Choudhary, V., Mohanty, B., Tan, S.L., Krishnan, S.P.T., Veladandi, P.S. and Meka, A., 2006. Extracting information for meaningful function inference through text-mining. Discovering biomolecular mechanisms with computational biology, pp.57-73.
Molecular biology of plant natural products
Reuben, S., Cseke, L.J., Bhinu, V.S., Narasimhan, K., Jeyakumar, M., Swarup, S., Kirakosyan, A., Kaufman, P.B., Warber, S.L., Duke, J.A. and Brielmann, H.L., 2006. Molecular biology of plant natural products. Natural Products from Plants, LJ Cseke, A. Kirakosyan, PB Kaufman, SL Warber, JA Duke, and HL Brielmann, eds (Boca Raton: CRC Press/Taylor & Francis), pp.165-202.
Plant natural products in the rhizosphere
Bhinu, V.S., Narasimhan, K. and Swarup, S., 2006. Plant natural products in the rhizosphere. Natural products from plants. CRC Press, Boca Raton, FL, pp.143-164.
Metabolomics and its role in understanding cellular responses in plants
Bhalla, R., Narasimhan, K. and Swarup, S., 2005. Metabolomics and its role in understanding cellular responses in plants. Plant cell reports, 24, pp.562-571.
Microfluidic chips for viral RNA extraction & detection
Yobas, L., Hui, W., Ji, H., Chen, Y., Liw, S.S.I., Li, J., Chong, C.S., Ling, X., Heng, C.K., Lye, H.J. and Bte, S.R., 2005, October. Microfluidic chips for viral RNA extraction & detection. In SENSORS, 2005 IEEE (pp. 4-pp). IEEE.
Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species
Mohanty, B., Krishnan, S.P.T., Swarup, S. and Bajic, V.B., 2005. Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species. Annals of Botany, 96(4), pp.669-681.
Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists
Bajic, V.B., Veronika, M., Veladandi, P.S., Meka, A., Heng, M.W., Rajaraman, K., Pan, H. and Swarup, S., 2005. Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. Plant physiology, 138(4), pp.1914-1925.
Characterization of copABCD operon from a copper-sensitive Pseudomonas putida strain
Adaikkalam, V. and Swarup, S., 2005. Characterization of copABCD operon from a copper-sensitive Pseudomonas putida strain. Canadian journal of microbiology, 51(3), pp.209-216.
Two parallel prothrombin activator systems in Australian rough-scaled snake, Tropidechis carinatus
Reza, M.A., Swarup, S. and Kini, M.R., 2005. Two parallel prothrombin activator systems in Australian rough-scaled snake, Tropidechis carinatus. Thrombosis and haemostasis, 93(01), pp.40-47.
Gene duplication of coagulation factor V and origin of venom prothrombin activator in Pseudonaja textilis snake Le, T.N.M., Reza, M.A., Swarup, S. and Kini, R.M., 2005. Gene duplication of coagulation factor V and origin of venom prothrombin activator in Pseudonaja textilis snake. Thrombosis and haemostasis, 93(03), pp.420-429.
MorA Defines a New Class of Regulators Affecting Flagellar Development and Biofilm Formation in Diverse Pseudomonas Species
Choy, W.K., Zhou, L., Syn, C.K.C., Zhang, L.H. and Swarup, S., 2004. MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. Journal of Bacteriology, 186(21), pp.7221-7228.
A geminivirus AYVV-derived shuttle vector for tobacco BY2 cells
Tamilselvi, D., Anand, G. and Swarup, S., 2004. A geminivirus AYVV-derived shuttle vector for tobacco BY2 cells. Plant cell reports, 23, pp.81-90.
Characterization of Pseudomonas putida genes responsive to nutrient limitation
Syn, C.K., Magnuson, J.K., Kingsley, M.T. and Swarup, S., 2004. Characterization of Pseudomonas putida genes responsive to nutrient limitation. Microbiology, 150(6), pp.1661-1669.
The catalytic subunit of pseutarin C, a group C prothrombin activator from the venom of Pseudonaja textilis, is structurally similar to mammalian blood coagulation factor Xa
Rao, V.S., Swarup, S. and Kini, M.R., 2004. The catalytic subunit of pseutarin C, a group C prothrombin activator from the venom of Pseudonaja textilis, is structurally similar to mammalian blood coagulation factor Xa. Thrombosis and haemostasis, 92(09), pp.509-521.
The nonenzymatic subunit of pseutarin C, a prothrombin activator from eastern brown snake (Pseudonaja textilis) venom, shows structural similarity to mammalian coagulation factor V
Rao, V.S., Swarup, S. and Kini, R.M., 2003. The nonenzymatic subunit of pseutarin C, a prothrombin activator from eastern brown snake (Pseudonaja textilis) venom, shows structural similarity to mammalian coagulation factor V. Blood, 102(4), pp.1347-1354.
Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls
Narasimhan, K., Basheer, C., Bajic, V.B. and Swarup, S., 2003. Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiology, 132(1), pp.146-153.
Molecular characterization of an operon, cueAR, encoding a putative P1-type ATPase and a MerR-type regulatory protein involved in copper homeostasis in Pseudomonas putida
Adaikkalam, V. and Swarup, S., 2002. Molecular characterization of an operon, cueAR, encoding a putative P1-type ATPase and a MerR-type regulatory protein involved in copper homeostasis in Pseudomonas putida. Microbiology, 148(9), pp.2857-2867.
Elucidation of the Flavonoid Catabolism Pathway in Pseudomonas putida PML2 by Comparative Metabolic Profiling
Pillai, B.V. and Swarup, S., 2002. Elucidation of the flavonoid catabolism pathway in Pseudomonas putida PML2 by comparative metabolic profiling. Applied and environmental microbiology, 68(1), pp.143-151.
A differentially expressed bZIP gene is associated with adventitious shoot regeneration in leaf cultures of Paulownia kawakamii
Low, R., Prakash, A., Swarup, S., Goh, C.J. and Kumar, P., 2001. A differentially expressed bZIP gene is associated with adventitious shoot regeneration in leaf cultures of Paulownia kawakamii. Plant cell reports, 20, pp.696-700.
High-frequency direct shoot regeneration and continuous production of rapid-cycling Brassica oleracea in vitro
Cheng, P.K., Lakshmanan, P. and Swarup, S., 2001. High-frequency direct shoot regeneration and continuous production of rapid-cycling Brassica oleracea in vitro. In Vitro Cellular & Developmental Biology-Plant, 37, pp.592-598.
λ Exonuclease-Based Subtractive Hybridization Approach to Isolate Differentially Expressed Genes from Leaf Cultures of Paulownia kawakamii
Low, R.K., Prakash, A.P., Swarup, S., Goh, C.J. and Kumar, P.P., 2001. λ Exonuclease-Based Subtractive Hybridization Approach to Isolate Differentially Expressed Genes from Leaf Cultures of Paulownia kawakamii. Analytical Biochemistry, 295(2), pp.240-247.
The expression of Brostm, a KNOTTED1-like gene, marks the cell type and timing of in vitro shoot induction in Brassica oleracea
Teo, W.L.L., Kumar, P., Goh, C.J. and Swarup, S., 2001. The expression of Brostm, a KNOTTED1-like gene, marks the cell type and timing of in vitro shoot induction in Brassica oleracea. Plant Molecular Biology, 46, pp.567-580.
A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria
Syn, C.K.C. and Swarup, S., 2000. A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Analytical biochemistry, 278(1), pp.86-90.
Three-detergent method for the extraction of RNA from several bacteria
Syn, C.K.C., Teo, W.L. and Swarup, S., 1999. Three-detergent method for the extraction of RNA from several bacteria. Biotechniques, 27(6), pp.1140-1145.
Histological and protein changes during early stages of seed germination in the orchid, Dendrobium crumenatum
Vellupillai, M., Swarup, S. and Jin Goh, C., 1997. Histological and protein changes during early stages of seed germination in the orchid, Dendrobium crumenatum. Journal of Horticultural science, 72(6), pp.941-948.
Determinants of the high‐methionine trait in wild and exotic germplasm may have escaped selection during early cultivation of maize
Swarup, S., Timmermans, M.C., Chaudhuri, S. and Messing, J., 1995. Determinants of the high‐methionine trait in wild and exotic germplasm may have escaped selection during early cultivation of maize. The Plant Journal, 8(3), pp.359-368.
