CURRICULUM VITAE

 

 
PERSONAL INFORMATION

 

Name                         L. Aravind

                                    [aka Aravind Lakshminarayanan Iyer]

 

Address                    National Center for Biotechnology Information,

                                    Building 38A Room 5N505

                                    National Library of Medicine,

                                    National Institutes of Health,

                                    Bethesda, MD 20894, USA

 

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, Texas A & M University

-September 1997-December 1998

       Burroughs-Wellcome Research Fellow, NCBI, NLM, NIH

-September 1996-September 1997

       Regents Fellow, Texas A & M University

-June 1995-June 1996

       Research Assistant, University of Pune

Education

Degree

Year of passing

Grade obtained

Ph.D. Biology

December 1999

Texas A & M University, USA

GPA: 4

M.Sc. Biotechnology

May 1996

Pune University, India.

1st class with distinction

(Rank 1)

B.Sc. Microbiology (Principal), Physics, Chemistry & Zoology (Adjunct)

3-year degree course

Passed in June 1994

Pune University, India.

1st class with distinction

(Rank 1)

Higher secondary certificate (Science stream)

Passed in March 1991

Maharashtra Board, India.

Grade 1 with distinction (top 1% in the state board)

Secondary school certificate

Passed in March 1989

Maharashtra Board, India.

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 Texas A&M University.

3)   University Medal (University of Poona) for best performing Master’s student in Biotechnology.

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).

 

BRIEF BIOGRAPHY AND SCIENTIFIC ACHIEVEMENTS TO DATE

I obtained a Masters Degree in Biotechnology from the University of Pune and subsequently moved to Texas A & M University, USA, for my doctoral studies in computational and evolutionary biology. I conducted most of my doctoral research at the National Center for Biotechnology Information/NIH, Maryland and graduated with a Doctorate in Biology from TAMU in December 1999. Currently, I work at the National Center for Biotechnology as a Principal Investigator, and with my group study a variety of problems related to protein-superfamily- and genome- evolution. My research group comprises of two post-doctoral fellows, two Staff Scientists and one graduate student.  My most important scientific achievements include: 1) Establishment of the deep events in the evolution of topoisomerases and primases, the DNA repair system and diverse DNA binding proteins. 2) Discovery of new domains involved in small molecule binding and elucidation of the evolutionary principles that determine their architectures. 3) The first quantitative estimates of the role of horizontal gene transfer in evolution. 4) Identification of the principal evolutionary events that determined the origin of multicellularity in eukaryotes. 5) Reconstruction of the earliest events that occurred close to the origin of the protein universe. 6) Establishment of the role of lineage specific gene expansions in the emergence of biological diversity. 7) Determination of the principal evolutionary events involved in the emergence of specialized Apicomplexan parasites from a generalized parasitic common ancestor. 8) Elucidating origins of the eukaryotic nonsense mediated RNA degradation system. 9) Elucidating origins of the ubiquitin conjugation system.

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, W Cygni, R Cygni) and deep sky objects.

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)
PROFESSIONAL ACTIVITIES AND BIBLIOGRAPHY

 

 

Selected Invited Talks

-The origin of animals: a genomic perspective. Cold Spring Harbor Laboratory, New York, 1998

-Gleanings from genome sequences of pathogenic microbes. The University of Texas Medical Branch, Galveston, Texas, 1998

-Ancient and recent protein domains: what do they tell us? University of Texas, South Western Medical Center, Texas, 1999

-Sequences to biology. Texas A & M University, Texas, 1999

-Evolutionary mobility of protein domains: deciphering regulatory architectures in proteins. Integrated Genetics Inc., Chicago, 2000

-The ‘Proteinscape’ of Life. Massachusetts General Hospital, Cancer Center, Massachusetts, 2000

-Understanding pathobiology: A genomic viewpoint. Laboratory of Infectious Diseases, NIH, Maryland, 2001

-Multiple independent origins of DNA replication: The transition from RNA to DNA. Cold Spring Harbor Laboratory, New York, 2001

-Structural and functional diversification of Eukaryotes. Harvard Medical School, Massachusetts, 2002

-A journey back in time: Reconstructing the earliest proteins. Indian Institute of Science, Bangalore, India, 2002

-Mining for biochemistries: discovery of novel enzymes and small molecule binding domains. Astra-Zeneca Foundation, Bangalore, India, 2002

-The provenance and the ontology of the cyclic nucleotide-signaling pathway. Gordon Conference, Mount Holyoke, 2002

-Biochemical activities: How do they emerge in proteins? Center for Biotechnology, University of Nebraska, Lincoln, 2003

-The P-loop NTPases: A natural history. Plenary Session, 3rd International Conference on AAA+ ATPases, Arlie, Virginia, 2003

-The evolutionary genomics of pathogen-host interactions. EU-USDA Meeting on emerging themes in host-pathogen interactions, Washington, D.C, 2003

-Evolution of signaling mechanisms. NCBS, Bangalore, India

-The comparative genomics of eukaryotic parasites. Society for Structural Genomics of parasitic protozoa Meeting, Seattle, Washington, April 2004

-Lateral transfers, lineage specific expansions and gene loss, and the natural history of the Apicomplexa. Gordon Conference, Regina Salve, RI, June 2004

-The origins of bio-catalysis. Gordon Conference, Meriden, NH, July 2004

-Natural history of Apicomplexa: a genomic perspective. Malaria Research Meeting, Baltimore, MD, December 2004

-Evolution of the engines of chromosomal dynamics. Gordon Conference, New London, NH, July 2005

-Reconstructing the major transitions in evolution. Philadelphia Forum for Bioinformatics, Philadelphia, PA, October 2005

-A Framework for functional analysis of proteins. University of Georgia, Athens, GA, April 2006

-Evolution of transcription factors and chromatin proteins in early branching eukaryotes. Gordon Conference, Regina Salve, RI, June 2006

-Exploring the evolution of epigenetic epigenetic control? Mount Sinai School of Medicine, Structural Biology Seminar Series, New York, NY, May 2007.

-Canonizing the rogues: provenance of key components of regulatory systems from selfish and mobile elements , Structural Biology Gordon Research Conference, Hinxton, UK, Aug 2007.

-Investigating the evolution of major signal transduction systems , MRC LMB Speaker series, Cambridge, UK, Aug 2007.

Other professional activities

-Editor and article author of the Wiley Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

 

-Currently on the editorial board of BMC Bioinformatics and Biology Direct

 

-Currently Editor and co-author of WILEY-VCH Verlag GmbH Textbook on “Protein Evolution”

 
-Referee for the following journals: Nature, Science, Molecular Cell, Cell, Proc Natl Acad Sci U S A, Bioinformatics, BioMedCentral, Genome Biology, Genome Research, Nucleic Acids Research, Journal of Molecular Biology, Journal of Structural Biology, Proteins, FEMS Microbiology Letters.

 

Other professional activities in NIH

Represent NCBI at the Graduate Partnership Program and currently mentor a graduate student from the Boston University via this program.
 
 
Journal Publications

 

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, Luscombe NM, Aravind L.

 

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, Madera M, Gough J, Aravind L, Sankaran K.

 

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, Makarova KS, Koonin EV, Aravind L.

 

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 cAMP phosphodiesterase binds nm23-H1 and promotes cancer metastasis.

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.

Ponomarev VA, Makarova KS, Aravind L, Koonin EV.

 

 

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.

HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold.

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.

Anantharaman V, Aravind L.

 

2002

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.