Name L.
Aravind
[aka Aravind Lakshminarayanan
Iyer]
Address
Building
38A Room 5N505
National Library of Medicine,
National Institutes of Health,
Tel (301)
594 2445
E-mail aravind
at mail.nih.gov
Nationality Hindu
Indian
Employment history
- October
2002-Present
Principal Investigator, Computational Biology
Branch, NCBI, NLM, NIH
- December
1999- October 2002
Staff Scientist, Computational Biology
Branch, NCBI, NLM, NIH
- December
1998-November 1999
Research Assistant,
-September
1997-December 1998
Burroughs-Wellcome Research Fellow,
NCBI, NLM, NIH
-September
1996-September 1997
Regents Fellow,
-June 1995-June
1996
Research Assistant,
Education
|
Degree |
Year of passing |
Grade obtained |
|
Ph.D.
Biology |
December 1999 |
GPA: 4 |
|
M.Sc.
Biotechnology |
May 1996 |
1st class with distinction (Rank 1) |
|
B.Sc.
Microbiology (Principal), Physics, Chemistry & Zoology (Adjunct) |
3-year degree course Passed in June 1994 |
1st class with distinction (Rank 1) |
|
Higher
secondary certificate (Science stream) |
Passed in March 1991 Maharashtra |
Grade 1 with distinction
(top 1% in the state board) |
|
Secondary
school certificate |
Passed in March 1989 Maharashtra |
1st class with distinction
(top 2% in the state board) |
Skills
1) Computational Biology
-Thorough understanding of sequence similarity search and alignment
techniques.
-Extensive familiarity with 3D structure visualization, manipulation
and modeling methods.
2) Computers
-Operating systems: Unix, Windows and MacOS
-Languages: PERL, C++ and QBASIC
3) Morphology and developmental biology
-Good knowledge of chordate, cnidarian, arthropod anatomy and
development.
-Have experience in molecular techniques used to study development.
4) Experimental Molecular Biology
-Recombinant DNA technology: DNA/RNA extraction,
cloning and expression techniques.
5) Human Languages
-Fluent in English, working knowledge of Sanskrit,
Grantha/ManipravaLa (Southern Prakrit), Tamil, Hindi and German.
Awards and
scholarships
1) Citation from the Human Genome Consortium for
contributions to the analysis of the human genome sequence (2002).
2) Special Research Scholarship of the
Burroughs-Wellcome Fund (1997–1999) for the genome analysis of Plasmodium falciparum.
2) Regents Scholarship (1996-1997) for pursuing
Graduate studies at
3) University Medal (
4) Research Scholarship from Indian Institute of
Science, Centre for Theoretical Studies, for pursuing a project on analysis of
ancient protein domains (Summer, 1995).
5) Department of Biotechnology (Govt. of India) Award-
Grant for pursuing Masters in Biotechnology in any of the 6 first tier
biotechnology training centers of India. (1994-1996).
6) Jawarharlal Nehru Student Award for research
project of evolution of DNA binding domains (Summer 1993).
7) MES College Award for
best paper titled “Bacterial taxonomy”
8) Jidnysa award for best
Essay titled “Evolution of Mira-type variable stars” in all India Science Competition
(1992).
9) Jidnysa award for best
Essay titled “DNA to protein: what do we really know?” in all India Science
Competition (1992).
I obtained a
Masters Degree in Biotechnology from the
AREAS
OF RESEARCH, INTERESTS AND EDUCATION
Primary Areas
of Research
1) Evolutionary
classification of proteins.
2) Understanding large-scale evolutionary trends
in genome evolution.
3) Reconstruction of functional networks of
regulatory proteins and metabolic enzyme pathways from genome sequence.
4) Prediction of novel biochemical activities
and biological functions of proteins, and inference of organismal biology from
comparative sequence and genome analysis.
5) Understanding the fundamental interactions
between natural selection and structural/genomic constraints in shaping protein
domain diversity.
Other Areas
of Research
1) Evolution
of tetrapods with special emphasis on pre-mammalian- synapsid and archosaur
phylogeny.
2) Understanding
the diversity of colony structures in microbes.
3) Determination of diversity and behavioral
observations on cicadelloids, aphids, ephemeropterans, ichneumonoid
hymenopterans and their parasites.
Other
Academic Interests
1) Astronomy: Observation of variable stars (e.g.
rho Persei, lambda Tauri, mu Cephei,
2) Origin and evolution of
Indo-European texts (especially Indo-Iranian), mythology and languages.
3) Studies in Indian and Central Asian history:
Impact of Indo-European, Turkic and Mongolic expansions on Outer Eurasia.
Non-Academic Interests
1) Cricket
2) Traditional Archery (with
long bow and composite bow)
-Gleanings
from genome sequences of pathogenic microbes. The
-Ancient
and recent protein domains: what do they tell us?
-Sequences
to biology.
-Evolutionary
mobility of protein domains: deciphering regulatory architectures in proteins.
Integrated Genetics Inc.,
-The
‘Proteinscape’ of Life.
-Understanding
pathobiology: A genomic viewpoint. Laboratory of Infectious Diseases, NIH,
-Multiple
independent origins of DNA replication: The transition from RNA to DNA.
-Structural
and functional diversification of Eukaryotes.
-A journey
back in time: Reconstructing the earliest proteins. Indian
-Mining
for biochemistries: discovery of novel enzymes and small molecule binding
domains. Astra-Zeneca Foundation,
-The
provenance and the ontology of the cyclic nucleotide-signaling pathway.
Gordon Conference,
-Biochemical activities: How do they emerge
in proteins? Center for Biotechnology,
-The P-loop NTPases: A natural history.
Plenary Session, 3rd International Conference on AAA+ ATPases,
-The evolutionary genomics of pathogen-host
interactions. EU-USDA Meeting on emerging themes in host-pathogen
interactions,
-Evolution of signaling mechanisms. NCBS,
-The comparative genomics of eukaryotic
parasites. Society for Structural Genomics of parasitic protozoa Meeting,
-Lateral transfers, lineage specific
expansions and gene loss, and the natural history of the Apicomplexa.
Gordon Conference,
-The origins of bio-catalysis. Gordon
Conference,
-Natural
history of Apicomplexa: a genomic perspective. Malaria Research Meeting,
-Evolution of the engines of chromosomal
dynamics. Gordon Conference,
-Reconstructing
the major transitions in evolution.
-A Framework
for functional analysis of proteins.
-Evolution of transcription factors and
chromatin proteins in early branching eukaryotes. Gordon Conference,
-Exploring the evolution of epigenetic epigenetic control?
-Canonizing the rogues: provenance of key components of regulatory systems from selfish and mobile elements
-Investigating the evolution of major signal transduction systems
Other professional activities
-Currently Editor and co-author of WILEY-VCH Verlag GmbH
Textbook on “Protein Evolution”
Other professional activities in NIH
2007
Bioessays. 2007 Jul;29(7):625-9.
The two faces of short-range evolutionary dynamics of regulatory
modes in bacterial transcriptional regulatory networks.
Balaji S, Aravind L.
BMC Bioinformatics. 2007 May 23;8(1):173
Discovering functional linkages and uncharacterized cellular
pathways using phylogenetic profile comparisons: a comprehensive assessment.
Jothi R, Przytycka TM, Aravind L.
Annu Rev Microbiol. 2007 Aug 16
Comparative Genomics of Protists: New Insights on Evolution of
Eukaryotic Signal Transduction and Gene Regulation.
Anantharaman V, Iyer LM, Aravind L.
Nat Immunol. 2007 Apr 29
Evolution and diversification of lamprey antigen receptors: evidence
for involvement of an AID-APOBEC family cytosine deaminase.
Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG, Pavlov YI, Aravind
L, Pancer Z.
Mol Microbiol. 2007 May;64(3):738-54.
An antisense RNA controls synthesis of an SOS-induced toxin evolved
from an antitoxin.
Kawano M, Aravind L, Storz G.
Infect Immun. 2007 Apr;75(4):2012-25.
Molecular factors and biochemical pathways induced by febrile
temperature in intraerythrocytic Plasmodium falciparum parasites.
Oakley MS, Kumar S, Anantharaman V, Zheng H, Mahajan B, Haynes JD,
Moch JK, Fairhurst R, McCutchan TF, Aravind L.
Biol Direct. 2007 Jan 24;2:4.
A novel superfamily containing the beta-grasp fold involved in
binding diverse soluble ligands.
Burroughs AM, Balaji S, Iyer LM, Aravind L.
2006
Nucleic Acids Res. 2006;34(22):6505-20. Epub 2006 Nov 27.
The natural history of the WRKY-GCM1 zinc fingers and the
relationship between transcription factors and transposons.
Babu MM, Iyer LM, Balaji S, Aravind L.
RNA Biol. 2006 Jan 23;3(1)
The NYN Domains: Novel Predicted RNAses with a PIN Domain-Like Fold.
Anantharaman V, Aravind L.
Cell Cycle. 2006 Oct;5(20):2354-63.
Estimating the prevalence and regulatory potential of the telomere
looping effect in yeast transcription regulation.
Babu MM, Balaji S, Iyer LM, Aravind L.
Hepatol Res. 2006 Dec;36(4):277-87.
Global transcriptional effects of PEG-IFN-alpha and ribavirin on
peripheral blood cells obtained from patients with chronic hepatitis C.
Balan V, Aravind L, Grill DE, Therneau TM, Sulkowski MS,
Nelson DR, Praestgaard J, Rosati M, Birse CE, Moore PA, Mani Subramanian G.
Biol Direct. 2006 Sep 5;1:25.
The signaling helix: a common functional theme in diverse signaling
proteins.
Anantharaman V, Balaji S, Aravind L.
J Mol Biol. 2006 Jul 7;
Evolutionary Genomics of the HAD Superfamily: Understanding the
Structural Adaptations and Catalytic Diversity in a Superfamily of
Phosphoesterases and Allied Enzymes.
Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L.
Genome Biol. 2006 Jul 19;7(7):R60
The prokaryotic antecedents of the Ubiquitin-signaling system and
the early evolution of ubiquitin-like beta-grasp domains.
Iyer LM, Burroughs MA, Aravind L.
J Mol Biol. 2006 Jun 30;360(1):213-27. Epub 2006 May 3.
Comprehensive Analysis of Combinatorial Regulation using the
Transcriptional Regulatory Network of Yeast.
Balaji S, Babu MM, Iyer LM,
J Mol Biol. 2006 Jun 30;360(1):204-12. Epub 2006 Apr 27.
Uncovering a Hidden Distributed Architecture Behind Scale-free
Transcriptional Regulatory Networks.
Balaji S, Iyer LM, Aravind L, Babu MM.
Curr Opin Struct Biol. 2006 Jun;16(3):409-19.
Comparative genomics and structural biology of the molecular innovations
of eukaryotes.
Aravind L, Iyer LM, Koonin EV.
Cell Cycle. 2006 Apr;5(7):775-82.
The HIRAN domain and recruitment of chromatin remodeling and repair
activities to damaged DNA.
Iyer LM, Babu MM, Aravind L.
J Bacteriol. 2006 Apr;188(8):2761-73.
A database of bacterial lipoproteins (DOLOP) with functional
assignments to predicted lipoproteins.
Babu MM, Priya ML, Selvan AT,
J Mol Biol. 2006 Feb 28;
Evolutionary Dynamics of Prokaryotic
Transcriptional Regulatory Networks.
Madan Babu M,
Teichmann SA, Aravind L.
Virus Res. 2006 Apr;117(1):156-84.
Evolutionary genomics of
nucleo-cytoplasmic large DNA viruses.
Iyer LM, Balaji S, Koonin EV, Aravind L.
J Cell Sci. 2006 Jan 15;119(Pt 2):370-9.
The Shwachman-Bodian-Diamond syndrome
gene encodes an RNA-binding protein that localizes to the pseudopod of Dictyostelium
amoebae during chemotaxis.
Wessels D, Srikantha T, Yi S, Kuhl S, Aravind L, Soll DR.
J Mol Biol. 2006 Feb 24;356(3):823-42.
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.
Anantharaman V, Aravind L.
Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):51-6.
Molecular cloning, expression, and
structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing
metalloenzyme.
Park JH, Aravind L, Wolff EC, Kaevel J, Kim YS, Park MH.
Trends Microbiol. 2006 Jan;14(1):11-4.
Adaptive evolution by optimizing
expression levels in different environments.
Babu MM, Aravind L.
Bioinformatics.
2006 Feb 1;22(3):257-63.
The ASCH superfamily: novel domains with
a fold related to the PUA domain and a potential role in RNA metabolism.
Iyer LM, Burroughs AM, Aravind L.
2005
Nucleic Acids Res. 2005 Jul 21;33(13):3994-4006.
Discovery of the principal specific
transcription factors of Apicomplexa and their implication for the evolution of
the AP2-integrase DNA binding domains.
Balaji S, Babu MM, Iyer LM, Aravind L.
Nucleic Acids Res. 2005 Jul 15;33(12):3875-96.
Origin and evolution of the
archaeo-eukaryotic primase superfamily and related palm-domain proteins:
structural insights and new members.
Iyer LM, Koonin
EV, Leipe DD, Aravind L.
Exp Parasitol. 2005 Aug;110(4):389-93.
Plasmodium falciparum: characterization
of a late asexual stage golgi protein containing both ankyrin and DHHC domains.
Seydel KB, Gaur D, Aravind L, Subramanian G, Miller LH.
Bioinformatics. 2005 Jun 15;21(12):2805-11.
MEDS and PocR are novel domains with a
predicted role in sensing simple
hydrocarbon derivatives in prokaryotic
signal transduction systems.
Anantharaman V, Aravind L.
FEMS Microbiol Rev. 2005 Apr;29(2):231-62.
The many faces of the helix-turn-helix
domain: transcription regulation and beyond.
Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer
LM.
Genome Biol. 2005;6(1):R4.
Identification of the prokaryotic
ligand-gated ion channels and their implications for the mechanisms and origins
of animal Cys-loop ion channels.
Tasneem A, Iyer
LM, Jakobsson E, Aravind L.
2004
Cell Cycle. 2004 Dec;3(12):1612-37.
Comparative genomics, evolution and
origins of the nuclear envelope and nuclear pore complex. Mans BJ, Anantharaman
V, Aravind L, Koonin EV.
Cell Cycle. 2004 Nov;3(11):1440-50.
Novel predicted peptidases with a
potential role in the ubiquitin signaling pathway.
Iyer LM, Koonin
EV, Aravind L.
Nucleic Acids Res. 2004 Oct 5;32(17):5260-79.
Comparative genomics of the FtsK-HerA
superfamily of pumping ATPases: implications for the origins of chromosome
segregation, cell division and viral capsid packaging.
Iyer LM,
J Mol Biol. 2004 Oct 8;343(1):1-28
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.
Leipe DD, Koonin
EV, Aravind L.
Genome Res. 2004 Sep;14(9):1686-95.
Comparative analysis of apicomplexa and
genomic diversity in eukaryotes.
Templeton TJ, Iyer LM, Anantharaman V,
Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L.
Proteins. 2004 Sep 1;56(4):795-807.
The SHS2 module is a common structural
theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and
MTH1598/TM1083 superfamilies.
Anantharaman V, Aravind L.
Nature. 2004 Jul 18
De-ubiquitination and ubiquitin ligase
domains of A20 downregulate NF-kappaB signalling.
Wertz IE, O'Rourke KM, Zhou H, Eby M, Aravind L, Seshagiri S, Wu P, Wiesmann
C, Baker R, Boone DL, Ma A, Koonin EV,
Dixit VM.
BMC Genomics. 2004 Jul 16;5(1):45.
Novel conserved domains in proteins with
predicted roles in eukaryotic cell-cycle regulation, decapping and RNA
stability.
Anantharaman V, Aravind L.
Trends Genet. 2004 Jul;20(7):292-9.
Evolution of cell-cell signaling in
animals: did late horizontal gene transfer from bacteria have a role?
Iyer LM, Aravind L, Coon SL, Klein DC, Koonin EV.
Mol Cell. 2004 Jun 18;14(6):841-7.
The C. elegans Polycomb Gene sop-2
Encodes an RNA Binding Protein.
Zhang H, Christoforou A, Aravind L, Emmons SW, Van Den Heuvel S,
Haber DA.
Gene. 2004 Jun 23;335:73-88.
Evolution of bacterial RNA polymerase:
implications for large-scale bacterial
phylogeny, domain accretion, and
horizontal gene transfer.
Iyer LM, Koonin
EV, Aravind L.
Curr Opin Struct Biol. 2004 Jun;14(3):283-91.
Structure and evolution of
transcriptional regulatory networks.
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA.
J Exp Med. 2004 Jun 7;199(11):1533-44.
A Multidomain Adhesion Protein Family
Expressed in Plasmodium falciparum Is Essential for
Transmission to the Mosquito.
Pradel G, Hayton K, Aravind L, Iyer LM, Abrahamsen MS, Bonawitz A, Mejia C,
Templeton TJ.
Proteins. 2004 Jun 1;55(4):977-91.
The emergence of catalytic and structural
diversity within the beta-clip fold.
Iyer LM, Aravind L.
Genome Biol. 2004;5(5):R30.
A novel family of P-loop NTPases with an
unusual phyletic distribution and
transmembrane segments inserted within
the NTPase domain.
Aravind L, Iyer LM, Leipe DD, Koonin EV.
Science. 2004 Apr 16;304(5669):441-5.
Complete genome sequence of the
apicomplexan, Cryptosporidium parvum.
Abrahamsen MS, Templeton TJ, Enomoto S,
Abrahante JE, Zhu G, Lancto CA,
Deng M, Liu C, Widmer G, Tzipori S, Buck
GA, Xu P, Bankier AT, Dear PH,
Konfortov BA, Spriggs HF, Iyer L,
Anantharaman V, Aravind L, Kapur V.
J Struct Biol. 2004 Apr-May;146(1-2):11-31.
Evolutionary history and higher order
classification of AAA+ ATPases.
Iyer LM, Leipe
DD, Koonin EV, Aravind L.
Cancer Cell. 2004 Feb;5(2):137-49.
Prune
D'Angelo A, Garzia L, Andre A, Carotenuto
P, Aglio V, Guardiola O, Arrigoni
G, Cossu A, Palmieri G, Aravind L, Zollo M.
Nucleic Acids Res. 2004 Feb 27;32(4):1439-47.
A bipolar DNA helicase gene, herA,
clusters with rad50, mre11 and nurA genes in
thermophilic archaea.
Constantinesco F, Forterre P, Koonin EV, Aravind L, Elie C.
2003
Cell. 2003 Dec 26;115(7):771-85.
Plasmodium biology: genomic gleanings.
Aravind L, Iyer LM, Wellems TE, Miller LH.
Genome Biol. 2003;4(12):R81. Epub 2003
Nov 26.
New connections in the prokaryotic
toxin-antitoxin network: relationship with
the eukaryotic nonsense-mediated RNA
decay system.
Anantharaman V, Aravind L.
Curr Opin Microbiol. 2003 Oct;6(5):490-7.
Evolutionary connections between
bacterial and eukaryotic signaling systems: a
genomic perspective.
Aravind L, Anantharaman V, Iyer LM.
J Mol Biol. 2003 Oct 31;333(4):781-815.
Evolution and classification of P-loop
kinases and related proteins.
Leipe DD, Koonin
EV, Aravind L.
Genome Biol. 2003;4(10):R64.
The two faces of Alba: the evolutionary
connection between proteins participating in chromatin structure and RNA
metabolism.
Aravind L, Iyer LM, Anantharaman V.
BMC Genomics. 2003 Aug 12
Application of comparative genomics in the identification and
analysis of novel families of membrane-associated receptors in bacteria.
Anantharaman V, Aravind L.
Mol Microbiol. 2003 Aug;49(4):977-89.
Multiple transporters associated with malaria parasite responses to
chloroquine and quinine.
Mu J, Ferdig MT, Feng X, Joy DA, Duan J, Furuya T, Subramanian G, Aravind
L, Cooper RA, Wootton JC, Xiong M, Su XZ.
J Mol Microbiol Biotechnol. 2003;5(4):225-9.
Gene duplication with displacement and rearrangement: origin of the
bacterial replication protein PriB from the single-stranded DNA-binding protein
Ssb.
Cell Cycle. 2003 Jul-Aug;2(4):369-76.
Provenance of SET-Domain Histone Methyltransferases Through
Duplication of a Simple Structural Unit.
Aravind L, Iyer LM.
FEMS Microbiol Lett. 2003 May 16; 222(1):17-23.
Aravind L, Anantharaman V.
EMBO J. 2003 Apr 15;22(8):1725-31.
Diversification and spectral tuning in marine proteorhodopsins.
Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich
EN, Spudich JL, Beja O.
Cell Cycle. 2003 Mar-Apr; 2(2):123-6.
Scores of RINGS
but no PHDs in ubiquitin signaling.
Aravind L, Iyer LM, Koonin EV.
Genome Biol. 2003; 4(2):R11.
Evolutionary history, structural features
and biochemical diversity of the NlpC/P60 superfamily of enzymes.
Curr Opin Struct Biol. 2002 Jun; 12(3):392-9.
Trends in protein evolution inferred from
sequence and structure analysis.
Aravind L, Mazumder R, Vasudevan S, Koonin EV.
Genome Res. 2002 Jul; 12(7):1048-59.
The role of lineage-specific gene family
expansion in the evolution of eukaryotes.
Lespinet O, Wolf YI, Koonin EV, Aravind
L.
Genome Biol. 2002;3(5):research0023.
The
GOLD domain, a novel protein module involved in Golgi function and secretion.
Anantharaman V, Aravind L.
Proteins. 2002 Jul 1; 48(1):1-14.
Monophyly of class I aminoacyl tRNA
synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains:
implications for protein evolution in the RNA.
Aravind L, Anantharaman V, Koonin EV.
Cell Death Differ. 2002 Apr
;9(4):394-404.
Origin and evolution of eukaryotic
apoptosis: the bacterial connection.
Koonin
EV, Aravind L.
Proc Natl Acad Sci
U S A. 2002 Apr 2;99(7):4644-9.
The complete genome of hyperthermophile Methanopyrus
kandleri AV19 and monophyly of archaeal methanogens.
Slesarev AI, Mezhevaya KV, Makarova
KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L,
Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV,
Kozyavkin SA.
Nucleic Acids Res. 2002 Apr
1;30(7):1427-64.
Comparative
genomics and evolution of proteins involved in RNA metabolism.
Anantharaman
V, Koonin EV, Aravind L.
J Mol Biol. 2002 Mar 15;317(1):41-72.
Classification
and evolution of P-loop GTPases and related ATPases.
Leipe
DD, Wolf YI, Koonin EV, Aravind L.
BMC Genomics. 2002 Mar 21;3(1):8.
Classification
and evolutionary history of the single-strand annealing proteins, RecT,
Redbeta, ERF and RAD52.
Iyer LM, Koonin EV, Aravind L.
Genome Biol. 2002;3(3):RESEARCH0012.
Extensive
domain shuffling in transcription regulators of DNA viruses and implications
for the origin of fungal APSES transcription factors.
Iyer LM, Koonin EV, Aravind L.
FEMS Microbiol Lett. 2002 Jan
22;207(1):55-61.
MOSC
domains: ancient, predicted sulfur-carrier domains, present in diverse
metal-sulfur cluster biosynthesis proteins including Molybdenum cofactor
sulfurases.
Anantharaman
V, Aravind L.
J Mol Microbiol Biotechnol. 2002 Jan;4(1):71-5
SPOUT: a class of methyltransferases that
includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of
predicted prokaryotic RNA methylases.
Anantharaman
V, Koonin EV, Aravind L.
Proteins. 2002 Mar
1;46(4):355-67.
Classification of the caspase-hemoglobinase fold: Detection of new
families and implications for the origin of the eukaryotic separins.
Aravind L, Koonin EV.
Appl Environ Microbiol. 2002 Jan;68(1):335-345.
Comparative Genomic Analysis of Archaeal
Genotypic Variants in a Single Population and in Two Different Oceanic
Provinces.
Beja
O, Koonin EV, Aravind L, Taylor LT, Seitz H, Stein JL, Bensen DC,
Feldman
RA, Swanson RV, DeLong EF.
2001
Genome Biol.
2001;2(12):RESEARCH0051.
Quod erat demonstrandum? The mystery of
experimental validation of apparently erroneous computational analyses of
protein sequences.
Iyer LM, Aravind L, Bork P,
Hofmann K, Mushegian AR, Zhulin IB, Koonin EV.
Nucleic Acids Res.
2002 Jan 15;30(2):482-96.
A DNA repair system specific for thermophilic Archaea and bacteria
predicted by genomic context analysis.
J Virol. 2001 Dec;75(23):11720-34.
Common origin of four
diverse families of large eukaryotic DNA viruses.
Iyer LM, Aravind L, Koonin EV.
Trends Biochem Sci. 2001 Oct;26(10):579-82.
The CHASE domain: a
predicted ligand-binding module in plant cytokinin receptors and other
eukaryotic and bacterial receptors.
Anantharaman V, Aravind L.
Methods Enzymol. 2001;341:3-28.
A natural classification
of ribonucleases.
Aravind L, Koonin EV.
Trends Biochem Sci. 2001 Sep;26(9):524-6.
DOMON: an ancient
extracellular domain in dopamine beta-monooxygenase and other proteins.
Aravind L.
Annu Rev Microbiol. 2001;55:709-42.
Horizontal gene transfer in prokaryotes: quantification and
classification.
Koonin EV,
Hum Mol Genet. 2001 Aug 1;10(16):1627-30.
Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are,
respectively, active and inactivated enzymes sharing a common transglutaminase
fold.
Anantharaman V, Koonin
EV, Aravind L.
Genome Res. 2001 Aug;11(8):1365-74.
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.
Aravind L, Koonin EV.
Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005.
Improving the accuracy
of PSI-BLAST protein database searches with composition-based statistics and
other refinements.
Schaffer AA, Aravind L, Madden TL, Shavirin S,
Spouge JL, Wolf YI, Koonin EV,
Altschul SF.
Curr Opin Genet Dev. 2001 Jun 1;11(3):247-257.
Computational analysis of human disease-associated genes and their
protein products.
Sreekumar KR, Aravind L, Koonin EV.
Trends Biochem Sci. 2001 May;26(5):273-5.
The WWE domain: a common
interaction module in protein ubiquitination and ADP ribosylation.
Aravind L.
Nucleic Acids Res. 2001 May 1;29(9):1884-1891.
Cloning the human and
mouse MMS19 genes and functional complementation of a yeast mms19 deletion
mutant.
Queimado L, Rao M,
Schultz RA, Koonin EV, Aravind L,
Nardo T, Stefanini M,
Friedberg EC.
Genetics. 2001 May;158(1):95-107.
Saccharomyces cerevisiae
SMT4 Encodes an Evolutionarily Conserved Protease With a Role in Chromosome
Condensation Regulation.
Strunnikov AV, Aravind L, Koonin EV.
FEMS Microbiol Lett. 2001 Apr 13;197(2):215-21.
TRAM, a predicted
RNA-binding domain, common to tRNA uracil methylation and adenine thiolation
enzymes.
Anantharaman V, Koonin
EV, Aravind L.
Trends Biochem Sci. 2001 Apr;26(4):215-7.
THUMP - a predicted
RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA
methylases.
Aravind L, Koonin EV.
J Mol Biol. 2001 Apr 13;307(5):1271-92.
Regulatory potential,
phyletic distribution and evolution of ancient, intracellular
small-molecule-binding domains.
Anantharaman V, Koonin
EV, Aravind L.
Genome Biol. 2001;2(3):RESEARCH0007.
The DNA-repair protein
AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and
iron-dependent dioxygenases.
Aravind L, Koonin EV.
Proteins. 2001 May 1;43(2):134-44.
Adaptations of the helix-grip
fold for ligand binding and catalysis in the START domain superfamily.
Iyer LM, Koonin EV, Aravind L.
Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79.
Genome of the extremely
radiation-resistant bacterium Deinococcus radiodurans viewed from the
perspective of comparative genomics.
Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton
KW, Koonin EV, Daly MJ.
Science. 2001 Feb 16;291(5507):1279-84.
Apoptotic molecular
machinery: vastly increased complexity in vertebrates revealed by genome
comparisons.
Aravind L, Dixit VM, Koonin EV.
Nature. 2001
Feb 15;409(6822):860-921.
Initial sequencing and
analysis of the human genome.
[only protein/RNA
analysis group shown in alphabetical order]
Agarwala R, Aravind L, Bailey JA, Bateman A,
Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church
D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Haussler D,
Hermjakob, Kent J, Kitts P, Koonin EV,
Korf I, Kulp D, Lancet D, Lowe TM,
Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Smit AF, Stupka
E, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A,
Wolf YI, Wolfe KH
Genome Res. 2001 Feb;11(2):240-52.
Prediction of the
archaeal exosome and its connections with the proteasome and the translation
and transcription machineries by a comparative-genomic approach.
Koonin EV, Wolf YI, Aravind L.
2000
Genome Biol. 2000;1(5):RESEARCH0009.
Towards understanding
the first genome sequence of a crenarchaeon by genome annotation using clusters
of orthologous groups of proteins (COGs).
Natale DA,
Genetica. 2000;108(1):25-34.
Specific expansion of
protein families in the radioresistant bacterium Deinococcus radiodurans.
Genome Biol. 2000;1(4):RESEARCH0007.
The alpha/beta fold
uracil DNA glycosylases: a common origin with diverse fates.
Aravind L, Koonin EV.
Trends Biochem Sci. 2000 Nov;25(11):535-7.
Cache - a signaling
domain common to animal Ca(2+)-channel subunits and a class of prokaryotic
chemotaxis receptors.
Anantharaman V, Aravind L.
Trends Genet. 2000 Nov;16(11):517-8.
Exploring histones and
their relatives with the Histone Sequence Database.
Aravind L.
Curr Biol. 2000 Nov 2;10(21):R774-6
Dynein light chains of
the Roadblock/LC7 group belong to an ancient protein superfamily implicated in
NTPase regulation.
Koonin EV, Aravind L.
Mol Cell. 2000 Oct;6(4):961-7.
Identification of
paracaspases and metacaspases: two ancient families of caspase-like proteins,
one of which plays a key role in MALT lymphoma.
Uren GA, O'Rourke K, Aravind L, Pisabarro TM, Seshagiri S,
Koonin VE, Dixit
MV.
J Mol Microbiol Biotechnol. 2000 Oct;2(4):509-12.
Bacterial homologs of
the small subunit of eukaryotic DNA primase.
Koonin EV, Wolf YI,
Environ Microbiol. 2000 Oct;2(5):516-29.
Construction and
analysis of bacterial artificial chromosome libraries from a marine microbial
assemblage.
Beja O, Suzuki MT,
Koonin EV, Aravind L, Hadd A, Nguyen
LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, DeLong EF.
Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11319-24.
Lineage-specific loss
and divergence of functionally linked genes in eukaryotes.
Aravind L, Watanabe H, Lipman DJ, Koonin EV.
Science.
2000 Sep 15;289(5486):1902-6.
Bacterial rhodopsin: evidence
for a new type of phototrophy in the sea.
Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd
A, Nguyen LP, Jovanovich SB,
Gates CM, Feldman RA, Spudich
JL, Spudich EN, DeLong EF.
Nucleic Acids Res. 2000 Sep 15; 28(18):3417-32.
Holliday junction
resolvases and related nucleases: identification of new families, phyletic
distribution and evolutionary trajectories.
Aravind L,
Trends Biochem Sci. 2000 Sep;25(9):421-3.
The BED finger, a novel
DNA-binding domain in chromatin-boundary-element-binding
proteins and
transposases.
Aravind L.
Genome Res. 2000 Aug;10(8):1172-84.
Eukaryote-specific
domains in translation initiation factors: implications for translation
regulation and evolution of the translation system.
Aravind L, Koonin EV.
Genome Res. 2000 Aug;10(8):1074-7.
Guilt by association:
contextual information in genome analysis.
Aravind L.
J Mol Microbiol Biotechnol. 1999 Nov;1(2):303-5.
A specialized
version of the HD hydrolase domain implicated in signal transduction.
Galperin MY, Natale DA, Aravind L, Koonin EV.
J Mol Microbiol Biotechnol. 2000 Apr;2(2):191-4.
The ATP-cone: an evolutionarily
mobile, ATP-binding regulatory domain.
Cell.
2000 Jun 9;101(6):573-6
The impact of
comparative genomics on our understanding of evolution.
Koonin EV, Aravind L,
Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8926-31.
Bacterial-type DNA holliday
junction resolvases in eukaryotic viruses.
Garcia AD, Aravind L, Koonin EV, Moss B.
Adv Protein Chem. 2000;54:245-75
Protein fold recognition
using sequence profiles and its application in
structural genomics.
Koonin EV, Wolf YI, Aravind L.
Trends Biochem Sci. 2000 May;25(5):223-4.
The NACHT family - a new
group of predicted NTPases implicated in apoptosis and
MHC transcription
activation.
Koonin EV, Aravind L.
J Biol Chem. 2000 Apr 7;275(14):10331-41.
Chitinases of the avian
malaria parasite Plasmodium gallinaceum,
a class of enzymes necessary for parasite invasion of the mosquito midgut.
Vinetz JM, Valenzuela
JG, Specht CA, Aravind L, Langer RC,
Ribeiro JM, Kaslow DC.
Curr Biol. 2000 Feb 24;10(4):R132-R134.
The U box is a modified RING
finger - a common domain in ubiquitination.
Aravind L, Koonin EV.
Trends Biochem
Sci. 2000
Mar;25(3):112-4.
SAP - a putative
DNA-binding motif involved in chromosomal organization.
Aravind L, Koonin EV.
Infect Immun. 2000 Mar;68(3):1633-48.
Comparative genome
analysis of the pathogenic spirochetes Borrelia
burgdorferi and Treponema pallidum.
Subramanian G, Koonin EV, Aravind
L.
FEMS Microbiol Lett. 2000 Feb 15;183(2):259-64.
Aldolases of the DhnA
family: a possible solution to the problem of pentose and hexose biosynthesis
in archaea.
Galperin MY, Aravind L, Koonin EV.
Trends Biochem Sci. 2000 Feb;25(2):50-2.
A novel superfamily of
predicted cysteine proteases from eukaryotes, viruses and chlamydia pneumoniae.
Curr Biol. 2000 Jan 27;10(2):R53-5.
The STAS domain - a link
between anion transporters and antisigma-factor antagonists.
Aravind L, Koonin EV.
Genome Res. 2000 Jan;10(1):5-16.
The bacterial
replicative helicase DnaB evolved from a RecA duplication.
Leipe DD, Aravind L, Grishin NV, Koonin EV.
Nucleic Acids Res. 2000 Jan 1;28(1):320-2.
The histone database: a
comprehensive WWW resource for histones and histone fold-containing proteins.
Sullivan SA, Aravind L, Makalowska I, Baxevanis AD,
Landsman D.
1999
Bioinformatics. 1999 Dec;15(12):1000-11.
IMPALA: matching a
protein sequence against a collection of PSI-BLAST-constructed position-specific
score matrices.
Schaffer AA, Wolf YI,
Ponting CP, Koonin EV, Aravind L,
Altschul SF.
Curr Opin Genet Dev. 1999 Dec;9(6):688-94.
Origin of multicellular
eukaryotes - insights from proteome comparisons.
Aravind L, Subramanian G.
Curr Biol. 1999 Nov 18;9(22):R836-7.
The fukutin protein
family - predicted enzymes modifying cell-surface molecules.
Aravind L, Koonin EV.
Science.
1999 Nov 19;286(5444):1571-7.
Genome sequence of the
radioresistant bacterium Deinococcus
radiodurans R1.
White O, Eisen JA,
Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC,
Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M,
Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C,
Nucleic Acids Res. 1999 Dec 1;27(23):4658-70.
DNA-binding proteins and
evolution of transcription regulation in the archaea.
Aravind L, Koonin EV.
Nature.
1999 Oct 14;401(6754):662-663.
Apoptosis. Searching for FLASH
domains.
Koonin EV, Aravind L, Hofmann K, Tschopp J, Dixit
VM.
Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11922-7.
Human and mouse homologs
of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB
superfamily.
Gerlach VL, Aravind L, Gotway G, Schultz RA, Koonin
EV, Friedberg EC.
Trends Biochem Sci. 1999 Sep;24(9):342-4.
G-patch: a new conserved
domain in eukaryotic RNA-processing proteins and type D retroviral
polyproteins.
Aravind L, Koonin EV.
Protein Sci. 1999 Aug;8(8):1714-9.
A superfamily of
archaeal, bacterial, and eukaryotic proteins homologous to animal
transglutaminases.
Genome Res. 1999 Aug;9(8):689-710.
Evolution of aminoacyl-tRNA
synthetases--analysis of unique domain architectures and phylogenetic trees
reveals a complex history of horizontal gene transfer events.
Wolf YI, Aravind L, Grishin NV, Koonin EV.
Nucleic Acids Res. 1999 Sep 1;27(17):3389-401.
Did DNA replication evolve
twice independently?
Leipe DD, Aravind L, Koonin EV.
FEMS Microbiol Lett. 1999 Jul 1;176(1):111-6.
The cytoplasmic helical
linker domain of receptor histidine kinase and methyl-accepting proteins is
common to many prokaryotic signalling proteins.
Aravind L, Ponting CP.
Genome Res. 1999 Jul;9(7):608-28.
Comparative genomics of
the Archaea (Euryarchaeota): evolution of conserved protein families, the
stable core, and the variable shell.
J Mol Biol. 1999 Jun 18;289(4):729-45.
Ponting CP, Aravind L, Schultz J, Bork P, Koonin
EV.
Eukaryotic signalling
domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene
transfer.
Trends Genet 1999 May;15(5):173-175
Rickettsiae and
Chlamydiae: evidence of horizontal gene transfer and gene exchange.
Wolf YI, Aravind L, Koonin EV
Trends Biochem Sci 1999 May;24(5):177-178
No Sec7-homology domain
in guanine-nucleotide-exchange factors that act on Ras and
Ponting CP, Bork P,
Schultz J, Aravind L
Trends Biochem Sci 1999 Apr;24(4):130-132
START: a lipid-binding
domain in StAR, HD-ZIP and signalling proteins.
Ponting CP, Aravind L
J Mol Biol 1999 Apr 16;287(5):1023-40
Gleaning non-trivial
structural, functional and evolutionary information about proteins by iterative
database searches.
Aravind L, Koonin EV
Nucleic Acids Res 1999 Mar 1;27(5):1223-1242.
Conserved
domains in DNA repair proteins and evolution of repair systems
Aravind
L,
Curr Biol 1999 Mar 25;9(6):R195-7
Sec14p-like domains in
NF1 and dbl-like proteins indicate lipid regulation of ras and rho signaling.
Aravind L, Neuwald AF, Ponting CP
J Mol Evol 1999 Mar;48(3):291-302
Novel predicted
RNA-binding domains associated with the translation machinery.
Trends Biochem Sci 1999 Feb;24(2):47-53
The domains of death:
evolution of the apoptosis machinery.
Aravind L, Dixit VM, Koonin EV
Nucleic Acids Res 1999 Apr 1;27(7):1609-1618
DNA polymerase beta-like
nucleotidyltransferase superfamily: identification of three new families,
classification and evolutionary history.
Aravind L, Koonin EV
J Mol Biol 1999 Jan 29;285(4):1353-1361
Fold Prediction and
Evolutionary Analysis of the POZ Domain: Structural and Evolutionary
Relationship with the Potassium Channel
Tetramerization Domain.
Aravind
L, Koonin EV
Genome Res 1999 Jan;9(1):27-43
AAA+: A Class of
Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly
of Protein Complexes.
Neuwald AF, Aravind L, Spouge JL, Koonin EV
1998
Trends Biochem Sci 1998 Dec;23(12):469-72
The HD domain defines a
new superfamily of metal-dependent phosphohydrolases.
Aravind
L, Koonin EV
Science
1998 Dec 11;282(5396):2022-8
Comparison of the
complete protein sets of worm and yeast: orthology and divergence.
Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin
EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM,
Botstein D
Trends Genet 1998 Nov;14(11):442-4
Evidence for massive
gene exchange between archaeal and bacterial hyperthermophiles.
Aravind
L, Tatusov RL, Wolf YI,
Science
1998 Nov 6;282(5391):1126-32
Chromosome 2 sequence of
the human malaria parasite Plasmodium falciparum.
Gardner MJ, Tettelin H,
Carucci DJ, Cummings LM, Aravind L,
Koonin EV, Shallom S, Mason T, Yu K, Fujii C,Pederson J, Shen K, Jing J, Aston
C, Lai Z, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R,
White O, Smith HO, Fraser CM, Hoffman SL, et al
Genome Res 1998 Oct;8(10):1038-47
Novel families of
putative protein kinases in bacteria and archaea: evolution of the
"eukaryotic" protein kinase superfamily.
Leonard CJ, Aravind L, Koonin EV
Science
1998 Oct 23;282(5389):754-9
Genome sequence of an
obligate intracellular pathogen of humans: Chlamydia trachomatis.
Stephens RS, Kalman S,
Lammel C, Fan J, Marathe R, Aravind
L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW
Trends Biochem Sci 1998 Aug;23(8):284-6
The HORMA domain: a
common structural denominator in mitotic checkpoints, chromosome synapsis and
DNA repair.
Aravind
L, Koonin EV
Nucleic Acids Res 1998 Oct 1;26(19):4413-21
AT-hook motifs
identified in a wide variety of DNA-binding proteins.
Aravind
L, Landsman D
Nucleic Acids Res 1998 Sep 15;26(18):4205-13.
Toprim--a conserved catalytic
domain in type IA and II topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Aravind
L, Leipe DD, Koonin EV
Nucleic Acids Res 1998 Aug 15;26(16):3746-52
Phosphoesterase domains
associated with DNA polymerases of diverse origins.
Aravind
L, Koonin EV
Curr Biol 1998 Jul 2;8(14):R477-8
A colipase fold in the
carboxy-terminal domain of the Wnt antagonists—the Dickkopfs.
Aravind
L, Koonin EV
In Silico Biology, 1, 0008.
An evolutionary
classification of the metallo-ß-lactamase fold proteins.
Aravind
L
Science 1998
May 22; 280: 1167a
Second Family of Histone
Deacetylases
Aravind
L, Koonin EV
Protein Sci 1998 May;7(5):1250-4
Homologues of 26S
proteasome subunits are regulators of transcription and translation.
Aravind
L, Ponting CP
Curr Biol 1998 Apr 9;8(8):R266-9
Genomics: re-evaluation
of translation machinery evolution.
Koonin EV, Aravind L
Trends Biochem Sci 1998 Apr;23(4):127-9
The catalytic domain of
the P-type ATPase has the haloacid dehalogenase fold.
Aravind
L, Galperin MY, Koonin EV
Trends Biochem Sci 1998 Jan;23(1):17-9
A novel family of
predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ
exonuclease.
Aravind
L, Koonin EV
Curr Biol 1998 Feb 12;8(4):R111-3
Eukaryotic transcription
regulators derive from ancient enzymatic domains.
Aravind
L, Koonin EV
1997
Curr Biol 1997 Nov 1;7(11):R674-7
PAS: a multifunctional
domain family comes to light.
Ponting CP, Aravind L
Trends Biochem Sci 1997 Dec;22(12):458-9
The GAF domain: an
evolutionary link between diverse phototransducing proteins.
Aravind L,
Ponting CP
Book
chapters
The Evolutionary history of
proteins involved in Pre-replication complex assembly.
DNA replication and Human disease.
A comparative-Genomic view of the
Microbial Stress Response
Bacterial stress Responses, Edited by Gisela
Storz and Regine Hengge-Aronis
American Society for Microbiology
1752 N Street NW Washington, DC 20036-2804
In Silico approaches to functional
analysis of proteins
Encyclopedia of Genetics, Genomics, Proteomics
and Bioinformatics
John Wiley and Sons,
Gene Expression Studies in
Arabidopsis thaliana - a network perspective
Global Science Books
Ikenobe 3011-2,