A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic ma... more A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic marine sediment sample, is reported.
The novel pinkish-orange pigmented, Gram-negative-staining, half-moon-shaped, non-motile, strictl... more The novel pinkish-orange pigmented, Gram-negative-staining, half-moon-shaped, non-motile, strictly aerobic, designated strains AK24 T and AK26, were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C 15:0 (41.5 %), anteiso-C 15:0 (9.7 %), iso-C 17:0 3OH (9.6 %), iso-C 17:1 ω9c (10.2 %) and C 16:1 ω7c /C 16:1 ω6c /iso-C 15:0 2OH (summed feature 3) (14.4 %). The strains contained MK-7 as the major respiratory quinone and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24 T showed that it is closely related to Aquiflexum balticum with pair-wise sequence similarity of 91.6% and next with Fontibacter ferrireducens, Beliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2% pair-wise sequence similarity respectively) and with rest of the family members is between 88.6-91.0% pair-wise sequence similarity. MALDI-TOF assay reported no significant similarities for AK24 T and AK26. MALDI MSP dendrogram shows close similarity between the two strains, AK24 T and AK26, while maintaining a distance from their phylogenetic neighbors. The genome of AK24 T shows the presence of heavy metal tolerance genes, including the genes providing resistance against arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes were also found in the genome. We also found two lantibiotics producing genes, LanR and LasB, in the genome of AK24 T. Strains AK24 T and AK26 are very close to each other with 99.5% pair-wise sequence similarity. Phylogenetic analysis indicated that strains AK24 T and AK26 were members of the family Cyclobacteriaceae and clustered with the genus Mariniradius and together with other genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella. DNA-DNA hybridization between strains AK24 T and AK26 showed a relatedness of 82% and rep-PCR banding patterns were nearly similar. Based on data from the current polyphasic study, it is proposed that the new isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24 T (= JCM 18822 T = MTCC 11627 T).
Grimontia indica strain AK16 T sp. nov. is the type strain of G. indica sp. nov. a new species wi... more Grimontia indica strain AK16 T sp. nov. is the type strain of G. indica sp. nov. a new species within the genus Grimontia. This strain, whose genome is described here, was isolated from seawater sample collected from southeast coast of Palk Bay, India. G. indica AK16 T is a Gram-negative, facultative aerobic rod shaped bacterium. There are only two other strains in the genus Grimontia one of which, Grimontia hollisae CIP 101886 T , is a reported human pathogen isolated from human stool sample while the other, 'Grimontia marina IMCC5001 T ', was isolated from a seawater sample. As compared to the pathogenic strain Grimontia hollisae CIP 101886 T , the strain AK16 T lacks some genes for pathogenesis like the accessory colonization factors AcfA and AcfD, which are required for the colonization of the bacterium in the host body. While it carries some pathogenesis genes like OmpU, which are related to pathogenesis of Vibrio strains. This suggests that the life cycle of AK16 T may include some pathogenic interactions with marine animal(s), or it may be an opportunistic pathogen. Study of the Grimontia genus is important because of the severe pathogenic traits exhibited by a member of the genus with only three species reported in total. The study will provide some vital information which may be useful in future clinical studies on the genus.
We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air collec... more We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air collected at an altitude ranging from 27 to 30 km above the city of Hyderabad, in India. This genome sequence will contribute to the objective of determining the microbial diversity of the upper atmosphere.
2011 3rd Conference on Data Mining and Optimization (DMO), 2011
In this paper we introduce a novel and efficient approach to detect topics in a large corpus of r... more In this paper we introduce a novel and efficient approach to detect topics in a large corpus of research papers. With rapidly growing size of academic literature, the problem of topic detection has become a very challenging task. We present a unique approach that uses closed frequent keyword-set to form topics. Our approach also provides a natural method to cluster the research papers into hierarchical, overlapping clusters using topic as similarity measure. To rank the research papers in the topic cluster, we devise a modified PageRank algorithm that assigns an authoritative score to each research paper by considering the sub-graph in which the research paper appears. We test our algorithms on the DBLP dataset and experimentally show that our algorithms are fast, effective and scalable.
In this paper we introduce a novel and efficient approach to detect and rank topics in a large co... more In this paper we introduce a novel and efficient approach to detect and rank topics in a large corpus of research papers. With rapidly growing size of academic literature, the problem of topic detection and topic ranking has become a challenging task. We present a unique approach that uses closed frequent keywordset to form topics. We devise a modified time independent PageRank algorithm that assigns an authoritative score to each topic by considering the sub-graph in which the topic appears, producing a ranked list of topics. The use of citation network and the introduction of time invariance in the topic ranking algorithm reveal very interesting results. Our approach also provides a clustering technique for the research papers using topics as similarity measure. We extend our algorithms to study various aspects of topic evolution which gives interesting insight into trends in research areas over time. Our algorithms also detect hot topics and landmark topics over the years. We test our algorithms on the DBLP dataset and show that our algorithms are fast, effective and scalable.
2011 3rd Conference on Data Mining and Optimization (DMO), 2011
In this paper we propose an efficient method to rank the research papers from various fields of r... more In this paper we propose an efficient method to rank the research papers from various fields of research published in various conferences over the years. This ranking method is based on citation network. The importance of a research paper is captured well by the peer vote, which in this case is the research paper being cited in other research papers. Using a modified version of the PageRank algorithm, we rank the research papers, assigning each of them an authoritative score. Using the scores of the research papers calculated by above mentioned method, we formulate scores for conferences and authors and rank them as well. We have introduced a new metric in the algorithm which takes into account the time factor in ranking the research papers to reduce the bias against the recent papers which get less time for being studied and consequently cited by the researchers as compared to the older papers. Often a researcher is more interested in finding the top conferences in a particular year rather than the overall conference ranking. Considering the year of publication of the papers, in addition to the paper scores we also calculated the yearwise score of each conference by slight improvisation of the above mentioned algorithm.
A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic ma... more A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic marine sediment sample, is reported.
The novel pinkish-orange pigmented, Gram-negative-staining, half-moon-shaped, non-motile, strictl... more The novel pinkish-orange pigmented, Gram-negative-staining, half-moon-shaped, non-motile, strictly aerobic, designated strains AK24 T and AK26, were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C 15:0 (41.5 %), anteiso-C 15:0 (9.7 %), iso-C 17:0 3OH (9.6 %), iso-C 17:1 ω9c (10.2 %) and C 16:1 ω7c /C 16:1 ω6c /iso-C 15:0 2OH (summed feature 3) (14.4 %). The strains contained MK-7 as the major respiratory quinone and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24 T showed that it is closely related to Aquiflexum balticum with pair-wise sequence similarity of 91.6% and next with Fontibacter ferrireducens, Beliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2% pair-wise sequence similarity respectively) and with rest of the family members is between 88.6-91.0% pair-wise sequence similarity. MALDI-TOF assay reported no significant similarities for AK24 T and AK26. MALDI MSP dendrogram shows close similarity between the two strains, AK24 T and AK26, while maintaining a distance from their phylogenetic neighbors. The genome of AK24 T shows the presence of heavy metal tolerance genes, including the genes providing resistance against arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes were also found in the genome. We also found two lantibiotics producing genes, LanR and LasB, in the genome of AK24 T. Strains AK24 T and AK26 are very close to each other with 99.5% pair-wise sequence similarity. Phylogenetic analysis indicated that strains AK24 T and AK26 were members of the family Cyclobacteriaceae and clustered with the genus Mariniradius and together with other genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella. DNA-DNA hybridization between strains AK24 T and AK26 showed a relatedness of 82% and rep-PCR banding patterns were nearly similar. Based on data from the current polyphasic study, it is proposed that the new isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24 T (= JCM 18822 T = MTCC 11627 T).
Grimontia indica strain AK16 T sp. nov. is the type strain of G. indica sp. nov. a new species wi... more Grimontia indica strain AK16 T sp. nov. is the type strain of G. indica sp. nov. a new species within the genus Grimontia. This strain, whose genome is described here, was isolated from seawater sample collected from southeast coast of Palk Bay, India. G. indica AK16 T is a Gram-negative, facultative aerobic rod shaped bacterium. There are only two other strains in the genus Grimontia one of which, Grimontia hollisae CIP 101886 T , is a reported human pathogen isolated from human stool sample while the other, 'Grimontia marina IMCC5001 T ', was isolated from a seawater sample. As compared to the pathogenic strain Grimontia hollisae CIP 101886 T , the strain AK16 T lacks some genes for pathogenesis like the accessory colonization factors AcfA and AcfD, which are required for the colonization of the bacterium in the host body. While it carries some pathogenesis genes like OmpU, which are related to pathogenesis of Vibrio strains. This suggests that the life cycle of AK16 T may include some pathogenic interactions with marine animal(s), or it may be an opportunistic pathogen. Study of the Grimontia genus is important because of the severe pathogenic traits exhibited by a member of the genus with only three species reported in total. The study will provide some vital information which may be useful in future clinical studies on the genus.
We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air collec... more We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air collected at an altitude ranging from 27 to 30 km above the city of Hyderabad, in India. This genome sequence will contribute to the objective of determining the microbial diversity of the upper atmosphere.
2011 3rd Conference on Data Mining and Optimization (DMO), 2011
In this paper we introduce a novel and efficient approach to detect topics in a large corpus of r... more In this paper we introduce a novel and efficient approach to detect topics in a large corpus of research papers. With rapidly growing size of academic literature, the problem of topic detection has become a very challenging task. We present a unique approach that uses closed frequent keyword-set to form topics. Our approach also provides a natural method to cluster the research papers into hierarchical, overlapping clusters using topic as similarity measure. To rank the research papers in the topic cluster, we devise a modified PageRank algorithm that assigns an authoritative score to each research paper by considering the sub-graph in which the research paper appears. We test our algorithms on the DBLP dataset and experimentally show that our algorithms are fast, effective and scalable.
In this paper we introduce a novel and efficient approach to detect and rank topics in a large co... more In this paper we introduce a novel and efficient approach to detect and rank topics in a large corpus of research papers. With rapidly growing size of academic literature, the problem of topic detection and topic ranking has become a challenging task. We present a unique approach that uses closed frequent keywordset to form topics. We devise a modified time independent PageRank algorithm that assigns an authoritative score to each topic by considering the sub-graph in which the topic appears, producing a ranked list of topics. The use of citation network and the introduction of time invariance in the topic ranking algorithm reveal very interesting results. Our approach also provides a clustering technique for the research papers using topics as similarity measure. We extend our algorithms to study various aspects of topic evolution which gives interesting insight into trends in research areas over time. Our algorithms also detect hot topics and landmark topics over the years. We test our algorithms on the DBLP dataset and show that our algorithms are fast, effective and scalable.
2011 3rd Conference on Data Mining and Optimization (DMO), 2011
In this paper we propose an efficient method to rank the research papers from various fields of r... more In this paper we propose an efficient method to rank the research papers from various fields of research published in various conferences over the years. This ranking method is based on citation network. The importance of a research paper is captured well by the peer vote, which in this case is the research paper being cited in other research papers. Using a modified version of the PageRank algorithm, we rank the research papers, assigning each of them an authoritative score. Using the scores of the research papers calculated by above mentioned method, we formulate scores for conferences and authors and rank them as well. We have introduced a new metric in the algorithm which takes into account the time factor in ranking the research papers to reduce the bias against the recent papers which get less time for being studied and consequently cited by the researchers as compared to the older papers. Often a researcher is more interested in finding the top conferences in a particular year rather than the overall conference ranking. Considering the year of publication of the papers, in addition to the paper scores we also calculated the yearwise score of each conference by slight improvisation of the above mentioned algorithm.
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Papers by Aditya Singh