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L Aravind

Research Profile

Genes & Molecular Sequences

Phenomena

Evolution, Molecular

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Procedures

Sequence Alignment

Chemicals & Drugs

Anatomy

Eukaryotic Cells

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Computational Biology

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Publications

TOP 3
Miranda S Oakley; Phuong Thao Pham; Vivek Anantharaman; L Aravind; Yamei Gao; Noel Gerald; Leda Lotspeich-Cole; Babita Mahajan; Victoria Majam; Thomas F McCutchan; Sheldon L Morris; Timothy G Myers; Sanjai Kumar
Radiation-induced cellular and molecular alterations in asexual intraerythrocytic Plasmodium falciparum.
Vivek Anantharaman; Lakshminarayan M Iyer; L Aravind
Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing.
Dapeng Zhang; L Aravind
Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment.

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All Publications

2013: Miranda S Oakley; Phuong Thao Pham; Vivek Anantharaman; L Aravind; Yamei Gao; Noel Gerald; Leda Lotspeich-Cole; Babita Mahajan; Victoria Majam; Thomas F McCutchan; Sheldon L Morris; Timothy G Myers; Sanjai Kumar
Radiation-induced cellular and molecular alterations in asexual intraerythrocytic Plasmodium falciparum.
The Journal of infectious diseases 2013;207(1):164-74.
2012: Vivek Anantharaman; Lakshminarayan M Iyer; L Aravind
Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing.
Molecular bioSystems 2012;8(12):3142-65.
2012: Dapeng Zhang; L Aravind
Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment.
Cell cycle (Georgetown, Tex.) 2012;11(20):3861-75.
2012: Dapeng Zhang; Lakshminarayan M Iyer; L Aravind
Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms.
Bioinformatics (Oxford, England) 2012;28(19):2407-11.
2012: Lakshminarayan M Iyer; L Aravind
Insights from the architecture of the bacterial transcription apparatus.
Journal of structural biology 2012;179(3):299-319.
2012: Robson Francisco de Souza; L Aravind
Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions.
Molecular bioSystems 2012;8(6):1661-77.
2012: Chalancon Guilhem; Raja Jothi; Alfonso Martinez-Arias; Charles N J Ravarani; L Aravind; S Balaji; M Madan Babu
Interplay between gene expression noise and regulatory network architecture.
Trends in genetics : TIG 2012;28(5):221-32.
2012: Kira S Makarova; Vivek Anantharaman; L Aravind; Eugene V Koonin
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes.
Biology direct 2012;7():40.
2012: Lakshminarayan M Iyer; L Aravind
ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons.
Biology direct 2012;7():39.
2012: Dapeng Zhang; Vivek Anantharaman; Robson F de Souza; Lakshminarayan M Iyer; L Aravind
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics.
Biology direct 2012;7():18.
2012: L Aravind; Lakshminarayan M Iyer
The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications.
Cell cycle (Georgetown, Tex.) 2012;11(1):119-31.
2011: A Maxwell Burroughs; Lakshminarayan M Iyer; L Aravind
Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system.
Molecular bioSystems 2011;7(7):2261-77.
2011: Dapeng Zhang; Lakshminarayan M Iyer; L Aravind
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems.
Nucleic acids research 2011;39(11):4532-52.
2011: Wang Nguitragool; Abdullah A B Bokhari; Ajay D Pillai; Kempaiah Rayavara; Paresh Sharma; Brad Turpin; L Aravind; Sanjay A Desai
Malaria parasite clag3 genes determine channel-mediated nutrient uptake by infected red blood cells.
Cell 2011;145(5):665-77.
2011: Miranda S Oakley; Vivek Anantharaman; Thiago M Venancio; Hong Zheng; Babita Mahajan; Victoria Majam; Thomas F McCutchan; Timothy G Myers; L Aravind; Sanjai Kumar
Molecular correlates of experimental cerebral malaria detectable in whole blood.
Infection and immunity 2011;79(3):1244-53.
2011: Kira S Makarova; Yuri I Wolf; L Aravind; Eugene V Koonin
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems.
Biology direct 2011;6():38.
2010: Lakshminarayan M Iyer; Abhiman Saraswathi; Robson F de Souza; L Aravind
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase.
Nucleic acids research 2010;38(16):5261-79.
2010: Thiago M Venancio; Santhanam Balaji; S Geetha; L Aravind
Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions.
Molecular bioSystems 2010;6(8):1475-91.
2010: Robson F de Souza; L Aravind
UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes.
Bioinformatics (Oxford, England) 2010;26(12):1477-80.
2010: S A Muljo; C Kanellopoulou; L Aravind
MicroRNA targeting in mammalian genomes: genes and mechanisms.
Wiley interdisciplinary reviews. Systems biology and medicine 2010;2(2):148-61.
2010: Thiago M Venancio; L Aravind
CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes.
Bioinformatics (Oxford, England) 2010;26(2):149-52.
2010: L Aravind; Robson F de Souza; Lakshminarayan M Iyer
Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis.
Biology direct 2010;5():48.
2010: Vivek Anantharaman; Lakshminarayan M Iyer; L Aravind
Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains.
Biology direct 2010;5():43.
2010: Vivek Anantharaman; Dapeng Zhang; L Aravind
OST-HTH: a novel predicted RNA-binding domain.
Biology direct 2010;5():13.
2010: Vivek Anantharaman; L Aravind
Novel eukaryotic enzymes modifying cell-surface biopolymers.
Biology direct 2010;5():1.
2010: Thiago M Venancio; S Balaji; L Aravind
High-confidence mapping of chemical compounds and protein complexes reveals novel aspects of chemical stress response in yeast.
Molecular bioSystems 2010;6(1):175-81.
2009: Lakshminarayan M Iyer; Abhiman Saraswathi; A Maxwell Burroughs; L Aravind
Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins.
Molecular bioSystems 2009;5(12):1636-60.
2009: L Aravind; Vivek Anantharaman; Thiago M Venancio
Apprehending multicellularity: regulatory networks, genomics, and evolution.
Birth defects research. Part C, Embryo today : reviews 2009;87(2):143-64.
2009: Lakshminarayan M Iyer; Mamta Tahiliani; Anjana Rao; L Aravind
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
Cell cycle (Georgetown, Tex.) 2009;8(11):1698-710.
2009: A Maxwell Burroughs; Lakshminarayan M Iyer; L Aravind
Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation.
Proteins 2009;75(4):895-910.
2009: Miranda S Oakley; Victoria Majam; Babita Mahajan; Noel Gerald; Vivek Anantharaman; Jerrold M Ward; Lawrence J Faucette; Thomas F McCutchan; Hong Zheng; Masaki Terabe; Jay A Berzofsky; L Aravind; Sanjai Kumar
Pathogenic roles of CD14, galectin-3, and OX40 during experimental cerebral malaria in mice.
PloS one 2009;4(8):e6793.
2009: Robson F De Souza; Lakshminarayan M Iyer; L Aravind
The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains.
Biology direct 2009;4():25; discussion 25.
2009: Thiago M Venancio; Santhanam Balaji; Lakshminarayan M Iyer; L Aravind
Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions.
Genome biology 2009;10(3):R33.
2008: Babita Mahajan; Angamuthu Selvapandiyan; Noel J Gerald; Victoria Majam; Hong Zheng; Thilan Wickramarachchi; Jawahar Tiwari; Hisashi Fujioka; J Kathleen Moch; Nirbhay Kumar; L Aravind; Hira L Nakhasi; Sanjai Kumar
Centrins, cell cycle regulation proteins in human malaria parasite Plasmodium falciparum.
The Journal of biological chemistry 2008;283(46):31871-83.
2008: Miranda S Oakley; Thomas F McCutchan; Vivek Anantharaman; Jerrold M Ward; Laurence Faucette; Cindy Erexson; Babita Mahajan; Hong Zheng; Victoria Majam; L Aravind; Sanjai Kumar
Host biomarkers and biological pathways that are associated with the expression of experimental cerebral malaria in mice.
Infection and immunity 2008;76(10):4518-29.
2008: Santhanam Balaji; Lakshminarayan M Iyer; M Madan Babu; L Aravind
Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?
Trends in genetics : TIG 2008;24(7):319-23.
2008: Vivek Anantharaman; L Aravind
Analysis of DBC1 and its homologs suggests a potential mechanism for regulation of sirtuin domain deacetylases by NAD metabolites.
Cell cycle (Georgetown, Tex.) 2008;7(10):1467-72.
2008: A Maxwell Burroughs; Marcie Jaffee; Lakshminarayan M Iyer; L Aravind
Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.
Journal of structural biology 2008;162(2):205-18.
2008: Abhiman Saraswathi; Lakshminarayan M Iyer; L Aravind
BEN: a novel domain in chromatin factors and DNA viral proteins.
Bioinformatics (Oxford, England) 2008;24(4):458-61.
2008: Lakshminarayan M Iyer; A M Burroughs; L Aravind
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.
Biology direct 2008;3():45.
2008: Lakshminarayan M Iyer; Abhiman Saraswathi; L Aravind
A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases.
Biology direct 2008;3():39.
2008: Teresa M Przytycka; Raja Jothi; L Aravind; David Lipman
Differences in evolutionary pressure acting within highly conserved ortholog groups.
BMC evolutionary biology 2008;8():208.
2008: Lakshminarayan M Iyer; Abhiman Saraswathi; L Aravind
MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.
Biology direct 2008;3():8.
2008: Ezra Peisach; Liangbing Wang; A Maxwell Burroughs; L Aravind; Debra Dunaway-Mariano; Karen N Allen
The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function.
Proteins 2008;70(1):197-207.
2007: Lakshminarayan M Iyer; Vivek Anantharaman; L Aravind
The DOMON domains are involved in heme and sugar recognition.
Bioinformatics (Oxford, England) 2007;23(20):2660-4.
2007: L Aravind; Lakshminarayan M Iyer; Carl Wu
Domain architectures of the Scm3p protein provide insights into centromere function and evolution.
Cell cycle (Georgetown, Tex.) 2007;6(20):2511-5.
2007: Santhanam Balaji; M Madan Babu; L Aravind
Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli.
Journal of molecular biology 2007;372(4):1108-22.
2007: Santhanam Balaji; L Aravind
The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks.
BioEssays : news and reviews in molecular, cellular and developmental biology 2007;29(7):625-9.
2007: Miranda S M Oakley; Sanjai Kumar; Vivek Anantharaman; Hong Zheng; Babita Mahajan; J David Haynes; J Kathleen Moch; Rick Fairhurst; Thomas F McCutchan; L Aravind
Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites.
Infection and immunity 2007;75(4):2012-25.
2007: M Madan Babu; Santhanam Balaji; L Aravind
General trends in the evolution of prokaryotic transcriptional regulatory networks.
Genome dynamics 2007;3():66-80.
2007: A Maxwell Burroughs; Lakshminarayan M Iyer; L Aravind
Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems.
Genome dynamics 2007;3():48-65.
2007: L Aravind
Opening Pandora's Box: making biological discoveries through computational data exploration.
Biology direct 2007;2():29.
2007: Santhanam Balaji; L Aravind
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins.
Nucleic acids research 2007;35(17):5658-71.
2007: Vivek Anantharaman; Lakshminarayan M Iyer; Santhanam Balaji; L Aravind
Adhesion molecules and other secreted host-interaction determinants in Apicomplexa: insights from comparative genomics.
International review of cytology 2007;262():1-74.
2007: A Maxwell Burroughs; S Balaji; Lakshminarayan M Iyer; L Aravind
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
Biology direct 2007;2():18.
2007: Vivek Anantharaman; Lakshminarayan M Iyer; L Aravind
Comparative genomics of protists: new insights into the evolution of eukaryotic signal transduction and gene regulation.
Annual review of microbiology 2007;61():453-75.
2007: A Maxwell Burroughs; S Balaji; Lakshminarayan M Iyer; L Aravind
A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.
Biology direct 2007;2():4.
2006: M Madan Babu; Santhanam Balaji; Lakshminarayan M Iyer; L Aravind
Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation.
Cell cycle (Georgetown, Tex.) 2006;5(20):2354-63.
2006: A Maxwell Burroughs; Karen N Allen; Debra Dunaway-Mariano; L Aravind
Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes.
Journal of molecular biology 2006;361(5):1003-34.
2006: Santhanam Balaji; M Madan Babu; Lakshminarayan M Iyer; Nicholas M Luscombe; L Aravind
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
Journal of molecular biology 2006;360(1):213-27.
2006: Santhanam Balaji; Lakshminarayan M Iyer; L Aravind; M Madan Babu
Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.
Journal of molecular biology 2006;360(1):204-12.
2006: L Aravind; Lakshminarayan M Iyer; Eugene V Koonin
Comparative genomics and structural biology of the molecular innovations of eukaryotes.
Current opinion in structural biology 2006;16(3):409-19.
2006: M Madan Babu; Sarah A Teichmann; L Aravind
Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
Journal of molecular biology 2006;358(2):614-33.
2006: Lakshminarayan M Iyer; M Madan Babu; L Aravind
The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA.
Cell cycle (Georgetown, Tex.) 2006;5(7):775-82.
2006: M Madan Babu; M Leena Priya; A Tamil Selvan; Martin Madera; Julian Gough; L Aravind; Krishnan Sankaran
A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins.
Journal of bacteriology 2006;188(8):2761-73.
2006: Lakshminarayan M Iyer; S Balaji; Eugene V Koonin; L Aravind
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.
Virus research 2006;117(1):156-84.
2006: Vivek Anantharaman; L Aravind
Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase.
Journal of molecular biology 2006;356(3):823-42.
2006: Lakshminarayan M Iyer; A Maxwell Burroughs; L Aravind
The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism.
Bioinformatics (Oxford, England) 2006;22(3):257-63.
2006: M Madan Babu; Lakshminarayan M Iyer; Santhanam Balaji; L Aravind
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
Nucleic acids research 2006;34(22):6505-20.
2006: Vivek Anantharaman; L Aravind
The NYN domains: novel predicted RNAses with a PIN domain-like fold.
RNA biology 2006;3(1):18-27.
2006: Vivek Anantharaman; S Balaji; L Aravind
The signaling helix: a common functional theme in diverse signaling proteins.
Biology direct 2006;1():25.
2006: Lakshminarayan M Iyer; A Maxwell Burroughs; L Aravind
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.
Genome biology 2006;7(7):R60.
2006: M Madan Babu; L Aravind
Adaptive evolution by optimizing expression levels in different environments.
Trends in microbiology 2006;14(1):11-4.
2005: Karl Boynton Seydel; Deepak Gaur; L Aravind; G. SUBRAMANIAN; Louis H Miller
Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains.
Experimental parasitology 2005;110(4):389-93.
2005: Vivek Anantharaman; L Aravind
MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems.
Bioinformatics (Oxford, England) 2005;21(12):2805-11.
2005: L Aravind; Vivek Anantharaman; Santhanam Balaji; M Madan Babu; Lakshminarayan M Iyer
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
FEMS microbiology reviews 2005;29(2):231-62.
2005: Santhanam Balaji; M Madan Babu; Lakshminarayan M Iyer; L Aravind
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.
Nucleic acids research 2005;33(13):3994-4006.
2005: Lakshminarayan M Iyer; Eugene V Koonin; Detlef D Leipe; L Aravind
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.
Nucleic acids research 2005;33(12):3875-96.
2004: Ben Mans; Vivek Anantharaman; L Aravind; Eugene V Koonin
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.
Cell cycle (Georgetown, Tex.) 2004;3(12):1612-37.
2004: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.
Cell cycle (Georgetown, Tex.) 2004;3(11):1440-50.
2004: Detlef D Leipe; Eugene V Koonin; L Aravind
STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.
Journal of molecular biology 2004;343(1):1-28.
2004: Vivek Anantharaman; L Aravind
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
Proteins 2004;56(4):795-807.
2004: Vivek Anantharaman; L Aravind
Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability.
BMC genomics 2004;5(1):45.
2004: Lakshminarayan M Iyer; L Aravind; Steven L Coon; David Klein; Eugene V Koonin
Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role?
Trends in genetics : TIG 2004;20(7):292-9.
2004: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer.
Gene 2004;335():73-88.
2004: M Madan Babu; Nicholas M Luscombe; L Aravind; Mark Gerstein; Sarah A Teichmann
Structure and evolution of transcriptional regulatory networks.
Current opinion in structural biology 2004;14(3):283-91.
2004: Lakshminarayan M Iyer; L Aravind
The emergence of catalytic and structural diversity within the beta-clip fold.
Proteins 2004;55(4):977-91.
2004: Lakshminarayan M Iyer; Detlef D Leipe; Eugene V Koonin; L Aravind
Evolutionary history and higher order classification of AAA+ ATPases.
Journal of structural biology 2004;146(1-2):11-31.
2004: Lakshminarayan M Iyer; Kira S Makarova; Eugene V Koonin; L Aravind
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.
Nucleic acids research 2004;32(17):5260-79.
2004: L Aravind; Lakshminarayan M Iyer; Detlef D Leipe; Eugene V Koonin
A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain.
Genome biology 2004;5(5):R30.
2003: Detlef D Leipe; Eugene V Koonin; L Aravind
Evolution and classification of P-loop kinases and related proteins.
Journal of molecular biology 2003;333(4):781-815.
2003: Vivek Anantharaman; L Aravind
Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria.
BMC genomics 2003;4(1):34.
2003: Jianbing Mu; Michael T Ferdig; Xiaorong Feng; Deirdre Joy; Junhui Duan; Tetsuya Furuya; G. SUBRAMANIAN; L Aravind; Roland A Cooper; John C Wootton; Momiao Xiong; Xin-zhuan Su
Multiple transporters associated with malaria parasite responses to chloroquine and quinine.
Molecular microbiology 2003;49(4):977-89.
2003: L Aravind; Lakshminarayan M Iyer
Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit.
Cell cycle (Georgetown, Tex.) 2003;2(4):369-76.
2003: L Aravind; Vivek Anantharaman
HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold.
FEMS microbiology letters 2003;222(1):17-23.
2003: Igor Rogozin; L Aravind; Eugene V Koonin
Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain.
Journal of molecular biology 2003;326(5):1449-61.
2003: L Aravind; Lakshminarayan M Iyer; Eugene V Koonin
Scores of RINGS but no PHDs in ubiquitin signaling.
Cell cycle (Georgetown, Tex.) 2003;2(2):123-6.
2003: Vivek Anantharaman; L Aravind; Eugene V Koonin
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
Current opinion in chemical biology 2003;7(1):12-20.
2003: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.
BMC structural biology 2003;3():1.
2003: Vivek Anantharaman; L Aravind
New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system.
Genome biology 2003;4(12):R81.
2003: L Aravind; Lakshminarayan M Iyer; Vivek Anantharaman
The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.
Genome biology 2003;4(10):R64.
2003: Vladimir A Ponomarev; Kira S Makarova; L Aravind; Eugene V Koonin
Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb.
Journal of molecular microbiology and biotechnology 2003;5(4):225-9.
2003: Vivek Anantharaman; L Aravind
Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes.
Genome biology 2003;4(2):R11.
2003: Lakshminarayan M Iyer; Vivek Anantharaman; L Aravind
Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins.
BMC genomics 2003;4(1):5.
2002: Raja Mazumder; Lakshminarayan M Iyer; Sona Vasudevan; L Aravind
Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.
Nucleic acids research 2002;30(23):5229-43.
2002: Lakshminarayan M Iyer; L Aravind
The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates.
BMC genomics 2002;3(1):33.
2002: Vivek Anantharaman; L Aravind
The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism.
Genome biology 2002;3(11):RESEARCH0061.
2002: L Aravind; Lakshminarayan M Iyer
Intraproteomic networks: new forays into predicting interaction partners.
Genome research 2002;12(8):1156-8.
2002: Kira S Makarova; L Aravind; Eugene V Koonin
SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes.
Trends in biochemical sciences 2002;27(8):384-6.
2002: L Aravind; Lakshminarayan M Iyer
The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities.
Genome biology 2002;3(8):RESEARCH0039.
2002: Olivier Lespinet; Yuri I Wolf; Eugene V Koonin; L Aravind
The role of lineage-specific gene family expansion in the evolution of eukaryotes.
Genome research 2002;12(7):1048-59.
2002: L Aravind; Vivek Anantharaman; Eugene V Koonin
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.
Proteins 2002;48(1):1-14.
2002: L Aravind; Raja Mazumder; Sona Vasudevan; Eugene V Koonin
Trends in protein evolution inferred from sequence and structure analysis.
Current opinion in structural biology 2002;12(3):392-9.
2002: Alexei I Slesarev; Katja V Mezhevaya; Kira S Makarova; Nikolai Polushin; Olga V Shcherbinina; Vera V Shakhova; Galina I Belova; L Aravind; Darren A Natale; Igor Rogozin; Roman L Tatusov; Yuri I Wolf; Karl O Stetter; Andrei Malykh; Eugene V Koonin; Sergei A Kozyavkin
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4644-9.
2002: Eugene V Koonin; L Aravind
Origin and evolution of eukaryotic apoptosis: the bacterial connection.
Cell death and differentiation 2002;9(4):394-404.
2002: Vivek Anantharaman; Eugene V Koonin; L Aravind
Comparative genomics and evolution of proteins involved in RNA metabolism.
Nucleic acids research 2002;30(7):1427-64.
2002: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52.
BMC genomics 2002;3():8.
2002: Detlef D Leipe; Yuri I Wolf; Eugene V Koonin; L Aravind
Classification and evolution of P-loop GTPases and related ATPases.
Journal of molecular biology 2002;317(1):41-72.
2002: L Aravind; Eugene V Koonin
Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins.
Proteins 2002;46(4):355-67.
2002: Vivek Anantharaman; L Aravind
MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases.
FEMS microbiology letters 2002;207(1):55-61.
2002: Kira S Makarova; L Aravind; Nick V Grishin; Igor Rogozin; Eugene V Koonin
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Nucleic acids research 2002;30(2):482-96.
2002: Vivek Anantharaman; L Aravind
The GOLD domain, a novel protein module involved in Golgi function and secretion.
Genome biology 2002;3(5):research0023.
2002: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
Genome biology 2002;3(3):RESEARCH0012.
2002: Vivek Anantharaman; Eugene V Koonin; L Aravind
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.
Journal of molecular microbiology and biotechnology 2002;4(1):71-5.
2001: Lakshminarayan M Iyer; L Aravind; Eugene V Koonin
Common origin of four diverse families of large eukaryotic DNA viruses.
Journal of virology 2001;75(23):11720-34.
2001: Vivek Anantharaman; L Aravind
The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors.
Trends in biochemical sciences 2001;26(10):579-82.
2001: L Aravind
DOMON: an ancient extracellular domain in dopamine beta-monooxygenase and other proteins.
Trends in biochemical sciences 2001;26(9):524-6.
2001: V Anantharaman; Eugene V Koonin; L Aravind
Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold.
Human molecular genetics 2001;10(16):1627-30.
2001: L Aravind; Eugene V Koonin
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.
Genome research 2001;11(8):1365-74.
2001: Alejandro A Schäffer; L Aravind; Thomas L Madden; S Shavirin; John L Spouge; Yuri I Wolf; Eugene V Koonin; Stephen F Altschul
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
Nucleic acids research 2001;29(14):2994-3005.
2001: L Aravind
The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation.
Trends in biochemical sciences 2001;26(5):273-5.
2001: Lakshminarayan M Iyer; Eugene V Koonin; L Aravind
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.
Proteins 2001;43(2):134-44.
2001: Vivek Anantharaman; Eugene V Koonin; L Aravind
TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes.
FEMS microbiology letters 2001;197(2):215-21.
2001: Vivek Anantharaman; Eugene V Koonin; L Aravind
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.
Journal of molecular biology 2001;307(5):1271-92.
2001: L Aravind; Eugene V Koonin
THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases.
Trends in biochemical sciences 2001;26(4):215-7.
2001: Kira S Makarova; L Aravind; Yuri I Wolf; Roman L Tatusov; KW Minton; Eugene V Koonin; Michael J Daly
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.
Microbiology and molecular biology reviews : MMBR 2001;65(1):44-79.
2001: L Aravind; V M Dixit; Eugene V Koonin
Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons.
Science (New York, N.Y.) 2001;291(5507):1279-84.
2001: Eugene V Koonin; Yuri I Wolf; L Aravind
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.
Genome research 2001;11(2):240-52.
2001: Lakshminarayan M Iyer; L Aravind; P Bork; Kay Hofmann; AR Mushegian; I B Zhulin; Eugene V Koonin
Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Genome biology 2001;2(12):RESEARCH0051.
2001: Eugene V Koonin; Kira S Makarova; L Aravind
Horizontal gene transfer in prokaryotes: quantification and classification.
Annual review of microbiology 2001;55():709-42.
2001: L Aravind; Eugene V Koonin
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.
Genome biology 2001;2(3):RESEARCH0007.
2000: Eugene V Koonin; L Aravind
Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation.
Current biology : CB 2000;10(21):R774-6.
2000: L Aravind
Exploring histones and their relatives with the Histone Sequence Database.
Trends in genetics : TIG 2000;16(11):517-8.
2000: Vivek Anantharaman; L Aravind
Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors.
Trends in biochemical sciences 2000;25(11):535-7.
2000: L Aravind; H Watanabe; David Lipman; Eugene V Koonin
Lineage-specific loss and divergence of functionally linked genes in eukaryotes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(21):11319-24.
2000: Eugene V Koonin; Y I Wolf; A S Kondrashov; L Aravind
Bacterial homologs of the small subunit of eukaryotic DNA primase.
Journal of molecular microbiology and biotechnology 2000;2(4):509-12.
2000: L Aravind; Kira S Makarova; Eugene V Koonin
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
Nucleic acids research 2000;28(18):3417-32.
2000: L Aravind
The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases.
Trends in biochemical sciences 2000;25(9):421-3.
2000: L Aravind; Eugene V Koonin
Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system.
Genome research 2000;10(8):1172-84.
2000: L Aravind
Guilt by association: contextual information in genome analysis.
Genome research 2000;10(8):1074-7.
2000: A D Garcia; L Aravind; Eugene V Koonin; Bernard Moss
Bacterial-type DNA holliday junction resolvases in eukaryotic viruses.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(16):8926-31.
2000: L Aravind; Eugene V Koonin
SAP - a putative DNA-binding motif involved in chromosomal organization.
Trends in biochemical sciences 2000;25(3):112-4.
2000: G. SUBRAMANIAN; E V Koonin; L Aravind
Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum.
Infection and immunity 2000;68(3):1633-48.
2000: Michael Galperin; L Aravind; Eugene V Koonin
Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea.
FEMS microbiology letters 2000;183(2):259-64.
2000: Kira S Makarova; L Aravind; Eugene V Koonin
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae.
Trends in biochemical sciences 2000;25(2):50-2.
2000: Darren A Natale; Uma Shankavaram; Michael Galperin; Yuri I Wolf; L Aravind; Eugene V Koonin
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Genome biology 2000;1(5):RESEARCH0009.
2000: L Aravind; Eugene V Koonin
The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates.
Genome biology 2000;1(4):RESEARCH0007.
2000: Eugene V Koonin; Yuri I Wolf; L Aravind
Protein fold recognition using sequence profiles and its application in structural genomics.
Advances in protein chemistry 2000;54():245-75.
2000: Detlef D Leipe; L Aravind; Nick V Grishin; Eugene V Koonin
The bacterial replicative helicase DnaB evolved from a RecA duplication.
Genome research 2000;10(1):5-16.
2000: Steven A Sullivan; L Aravind; Izabela Makalowska; Andreas D Baxevanis; David Landsman
The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins.
Nucleic acids research 2000;28(1):320-2.
1999: Alejandro A Schäffer; Yuri I Wolf; C P Ponting; Eugene V Koonin; L Aravind; Stephen F Altschul
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
Bioinformatics (Oxford, England) 1999;15(12):1000-11.
1999: L Aravind; G. SUBRAMANIAN
Origin of multicellular eukaryotes - insights from proteome comparisons.
Current opinion in genetics & development 1999;9(6):688-94.
1999: L Aravind; Eugene V Koonin
DNA-binding proteins and evolution of transcription regulation in the archaea.
Nucleic acids research 1999;27(23):4658-70.
1999: Michael Galperin; D A Natale; L Aravind; Eugene V Koonin
A specialized version of the HD hydrolase domain implicated in signal transduction.
Journal of molecular microbiology and biotechnology 1999;1(2):303-5.
1999: Eugene V Koonin; L Aravind; Kay Hofmann; J Tschopp; V M Dixit
Apoptosis. Searching for FLASH domains.
Nature 1999;401(6754):662; discussion 662-3.
1999: L Aravind; Eugene V Koonin
G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins.
Trends in biochemical sciences 1999;24(9):342-4.
1999: Detlef D Leipe; L Aravind; Eugene V Koonin
Did DNA replication evolve twice independently?
Nucleic acids research 1999;27(17):3389-401.
1999: Kira S Makarova; L Aravind; Eugene V Koonin
A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.
Protein science : a publication of the Protein Society 1999;8(8):1714-9.
1999: Yuri I Wolf; L Aravind; Nick V Grishin; Eugene V Koonin
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.
Genome research 1999;9(8):689-710.
1999: L Aravind; C P Ponting
The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins.
FEMS microbiology letters 1999;176(1):111-6.
1999: Kira S Makarova; L Aravind; Michael Galperin; Nick V Grishin; Roman L Tatusov; Yuri I Wolf; Eugene V Koonin
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Genome research 1999;9(7):608-28.
1999: C P Ponting; L Aravind; J Schultz; P Bork; Eugene V Koonin
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Journal of molecular biology 1999;289(4):729-45.
1999: Yuri I Wolf; L Aravind; Eugene V Koonin
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange.
Trends in genetics : TIG 1999;15(5):173-5.
1999: C P Ponting; P Bork; J Schultz; L Aravind
No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho.
Trends in biochemical sciences 1999;24(5):177-8.
1999: L Aravind; Eugene V Koonin
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches.
Journal of molecular biology 1999;287(5):1023-40.
1999: CP Ponting; L Aravind
START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins.
Trends in biochemical sciences 1999;24(4):130-2.
1999: L Aravind; Eugene V Koonin
DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
Nucleic acids research 1999;27(7):1609-18.
1999: L Aravind; Andrew F. Neuwald; C P Ponting
Sec14p-like domains in NF1 and Dbl-like proteins indicate lipid regulation of Ras and Rho signaling.
Current biology : CB 1999;9(6):R195-7.
1999: L Aravind; Eugene V Koonin
Novel predicted RNA-binding domains associated with the translation machinery.
Journal of molecular evolution 1999;48(3):291-302.
1999: L Aravind; DR Walker; Eugene V Koonin
Conserved domains in DNA repair proteins and evolution of repair systems.
Nucleic acids research 1999;27(5):1223-42.
1999: L Aravind; V M Dixit; Eugene V Koonin
The domains of death: evolution of the apoptosis machinery.
Trends in biochemical sciences 1999;24(2):47-53.
1999: L Aravind; Eugene V Koonin
Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain.
Journal of molecular biology 1999;285(4):1353-61.
1999: L Aravind
An evolutionary classification of the metallo-beta-lactamase fold proteins.
In silico biology 1999;1(2):69-91.
1998: L Aravind; Eugene V Koonin
The HD domain defines a new superfamily of metal-dependent phosphohydrolases.
Trends in biochemical sciences 1998;23(12):469-72.
1998: L Aravind; Roman L Tatusov; Yuri I Wolf; D R Walker; E V Koonin
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles.
Trends in genetics : TIG 1998;14(11):442-4.
1998: C J Leonard; L Aravind; Eugene V Koonin
Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily.
Genome research 1998;8(10):1038-47.
1998: L Aravind; David Landsman
AT-hook motifs identified in a wide variety of DNA-binding proteins.
Nucleic acids research 1998;26(19):4413-21.
1998: L Aravind; Detlef D Leipe; Eugene V Koonin
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Nucleic acids research 1998;26(18):4205-13.
1998: L Aravind; Eugene V Koonin
Phosphoesterase domains associated with DNA polymerases of diverse origins.
Nucleic acids research 1998;26(16):3746-52.
1998: L Aravind; Eugene V Koonin
The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair.
Trends in biochemical sciences 1998;23(8):284-6.
1998: L Aravind; C P Ponting
Homologues of 26S proteasome subunits are regulators of transcription and translation.
Protein science : a publication of the Protein Society 1998;7(5):1250-4.
1998: Eugene V Koonin; L Aravind
Genomics: re-evaluation of translation machinery evolution.
Current biology : CB 1998;8(8):R266-9.
1998: L Aravind; Michael Galperin; Eugene V Koonin
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold.
Trends in biochemical sciences 1998;23(4):127-9.
1998: L Aravind; Eugene V Koonin
A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease.
Trends in biochemical sciences 1998;23(1):17-9.
1997: L Aravind; C P Ponting
The GAF domain: an evolutionary link between diverse phototransducing proteins.
Trends in biochemical sciences 1997;22(12):458-9.
1997: C P Ponting; L Aravind
PAS: a multifunctional domain family comes to light.
Current biology : CB 1997;7(11):R674-7.