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OJB®

Online Journal of Bioinformatics ©

(Online J Bioinformatics©)

Established 1995

ISSN  1443-2250

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Managing Editors: Guerrini VH., DVM, MVSc, MCompSci, PhD (Bioinformatics, IE), Anna Wallentin Searle BA, MA (SE), Rachel Durnsford BA (AU). Scientific Board: Ben-Miled Z., BSc, MSc, PhD (Computer Engineering, USA), Bodèn M., BSc, MSc, PhD  (Machine learning and biological sequence analysis, AU),  Böhringer S., MD, BSc, MSc, PhD (Genetic analysis, DE), Bourne DWA., BPharm, PhD (Pharmacokinetics, USA),  Ceraj I DipEng, MSc (Software engineering, MIT, USA), Colomb RM BSc, PhD (Informatics, CA), Daggard G BSc, PhD (Genetics, AU), Dressel U  BSc, Hons, PhD (Genetics, DE), Dubitzky W., Dipl Ing, MSc, DPhil (Bioinformatics, DE), Filippich LJ., BSc, BVSc, PhD (Genetics, AU),   Gao S., BS, PhD (Bioinformatics, USA),  Harrison J., BSc, MSc, PhD (Data-mining, USA), Hughes I.   BVSc, PhD,  (Genetics AU), Maetschke SR MSc, PhD (Software development, machine learning, data mining, optimization, Image and signal processing, DE), Jiang Y., BSc, MSc, Msc, PhD, (Data analysis, oncology, USA), Lea R., BSc, PhD (Genetic analysis, AU), Lund EM., DVM, MPH, PhD (Informatics, USA), Olsson BE., BSc, MSc, PhD (Bioinformatics, SE), O'Kane KC., BS PhD (Bioinformatics, USA), Shen L., BSc, PhD (Advanced Machine Learning, USA), Song M., PhD (Text Mining, Bioinformatics, Information Retrieval and Information Visualization, USA), Teasdale RG., BSc, PhD (Computational Cell Biology, AU), Thongboonkerd V, MD, FRCPT (Proteomics, USA). Wang H.,  BEng, MSc, PhD (Gene expression analysis , Biomarker detection, ontology, Prediction, machine learning, artificial intelligence, UK), Wu D BS, PhD (Bioinformatics and drug design, USA), Yao J MSc,PhD (Plant genomics, USA ), Zou M., MSc, PhD (Cancer Biology and  Human Genetics, USA).

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2009 (2)

Comparative genomic study on context-dependence of CpG mutations:Acceleration effect of 5' T nucleotides and new evidence of strand assymetry in genes
Wang Y, Leung FC., 10 (2), 165-179,  2009

School of Biological Sciences and Genome Research Centre, University of Hong Kong, Pokfulam, Hong Kong
          Submitted Mar 11,  Reviewed May 27, Publish July 1 Review Report

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2009 (1)

DyeML: XML-based format for handling natural organic dyes
Aghoutane B, Benslimane R, Chenfour N, Elbannay O, Meknassi M 10 (1):156-164, 2009

Laboratoire de Transmission et Traitement de l’information (LTTI), Ecole Supérieure de Technologie and UFR Informatique Avancée, Faculté des sciences Dhar el mehraz, Fez, Morocco.
          Submitted Feb 24,  Reviewed May 22, Publish April 15 Review Report

Designing of drug for removal of methylation from Tcf21 gene in lung cancer
          Gupta SK, Singh A, Srivastava M 10 (1):149-155, 2009

Department of Bioinformatics, UIET, CSJM University and DOEACC center of Bioinformatics, India.
          Submitted Apr 27,  Reviewed May 16, Publish April 15 Review Report

Determination of antioxidant stability in heated mixture of oils by neural network
          Valantina R, Neelamegham P 10 (1):134-148, 2009

Department of Physics and Electrical Engineeering, SASTRA University, Tamilnadu, India.
          Submitted Apr 17,  Reviewed May 16, Publish May 30 Review Report

Towards establishing the molecular function of Pfam Domain DUF294 by sequence analysis and homology modeling
          Gononesekere NCW, Beaudry S, Tasovsky I 10 (1):125-133, 2009

Department of Chemistry and Biochemistry and Department of Biology, University of Northern Iowa, Cedar Falls, U.S.A.
          Submitted Apr 23,  Reviewed May 1, revised May 4, Publish May 30 Review Report

Phylogenetic analysis, homology modeling, molecular dynamics and structure based designing of new inhibitors against cinnamyl alcohol dehydrogenase (CAD) cloned and sequenced from a 
leguminous tree subabul (Leucena leucocephala)

          Sekhar NP, Kumar RD, Sirisha VL, Prashant S Kavi Kishor PB 10 (1):103-124, 2009
Department of Genetics, Osmania University, Hyderabad, India.
          Submitted Apr 17,  Reviewed Apr 24, Accepted Apr 26, Publish May 30 Review Report

Prediction of 3- dimensional structure of GL12 of Homo Sapiens
          Sreekanth P, Narayan J 10 (1):98-102, 2009
Bioinformatics Centre, Amity Institute of Biotechnology, Amity University, India. .
          Submitted Aug 15,  Reviewed March 24, Accepted Mar 26, Publish April 30 Review Report

In silico identification of small interfering RNA (siRNA) in the putative genes of White Spot Syndrome virus

Singh V, Somvanshi P 10 (1):93-97, 2009
Bioinformatics Centre, Biotech Park, Lucknow, India.
          Submitted Aug 21,  Reviewed March 19, Accepted Mar 20, Publish April 21 Review Report

Genetic algorithm self-adaptive mutation rate for DNA folding (GASAMR)

Mezher MA, Khader AT 10 (1):82-92, 2009
School of Engineering and Design, School of Computer Science, UB8 3PH, West London, UK Brunel University, 11800, Universiti Sains Malaysia, Penang, Malaysia.
          Submitted Feb 1,  Reviewed March 11, Accepted Mar 14, Publish April 18 Review Report

A statistical method for verification of rareness in DNA sequences using sequence encoding

Meena K, Menaka K, Sundar TV, Subramanian KR 10 (1):74-81, 2009
         Departments of Computer Science,  I.T. & Applications and  M.C.A., Shrimati Indira Gandhi College and Postgraduate and Research Department of Physics, National College, India.
          Submitted Nov 1,  Reviewed March 9, Accepted Mar 11, Publish April 15 Review Report

Multiple contrast test for detecting monotonic dose-relationship and FDR-adjusted confidence intervals for selected parameters in a microarray setting

Lin D, Shkedy Z, Burzykowski T, Yekutieli D, De Bondt A, Göhlmann WHH, Talloen W, Bijnens L, 10 (1):67-73, 2009
Hasselt University, I-BioStat, Universitaire Campus, Diepenbeek, Belgium, Department of Statistics and Operation Research, School of Mathematical Sciences, Tel Aviv University, Ramat Aviv, Israel,  J&JPRD - Biometrics and 
         Clinical Informatics, Beerse, Belgium..
          Submitted Mar 1,  Reviewed March 9, Accepted Mar 11, Publish April 2 Review Report

Prediction 0f 3-dimensional structure of ORF3 protein of genotype 1 hepatitis E virus

Rathi B, Naik S, Sarangi AN, Aggarwal R, 10 (1):60-66, 2009
Biomedical Informatics Centre, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.
          Submitted Jan 6,  Reviewed March 6, Accepted Mar 11, Publish April 2 Review Report

A systematic approach to understanding E. coli responses to oxygen: from raw microarray data to pathways and published abstracts

Maleki-Dizaji S, Holcombe M, Rolfe MD, Fisher P  Green J, Poole RK, Graham AI, SYSMO-SUMO consortium, 10 (1):51-59, 2009

Department of Computer Science, The University of Sheffield, Sheffield S1 4DP, United Kingdom. Department of Molecular Biology and Biotechnology, The University of Sheffield , Sheffield S10 2TN, United Kingdom. Department of Computer Science, The 
              University of Manchester, Manchester M13 9PL, United Kingdom.
          Submitted Feb 13,  Reviewed Feb 15, Accepted Feb 16, Publish March 3 Review Report

In silico identification of tandem inter/intra-generic genetic elements (TIGE) using a random nucleotide generating Perl program: A potential approach for locating structure-function regions of  
recently sequenced genomes

Jha PK, Stashenko P, 10 (1):40-50, 2009

Division of Cytokine Biology, The Forsyth Institute, Harvard medical School Affiliate in Oral and Craniofacial Science, Boston, Massachussets, USA
Submitted Jan 23,  Reviewed Jan 29, Accepted Feb 1, Publish Feb 15 Review Report

Derivation of a protein marker from  heat denatured protein aggregate

Lahiri T, Mishra H, Kumar U, Misra K, 10 (1):29-39, 2009

Division of Bioinformatics and Allied Sciences, Indian Institute of Information technology, Allahabad, India

Submitted Sep 27,   reviewed Jan 15, accepted Jan 15, publish Feb 15 Review Report

Identification of potential targets and lead molecules for designing inhibitory drugs against Chlamydophila pneumoniae

Reddy EH, Satpathy GR, 10 (1): 14-28, 2009

Department of Biotechnology and Medical Engineering, National Insitute of Technology, Rourkela-769008, India.

Submitted Nov 28,   reviewed Jan 5, accepted Jan 10, published Jan 30 Review Report

Homology modelling, molecular dynamics and docking studies of human GLUT5 protein involved in intestinal transport

Padmavathi GV, Nataraj Sekhar P, Saralakumari D 10 (1):1-13, 2009

Department of Biochemistry, Sri Krishnadevaraya University, Anantapur,  India, and Katholic University, (leuven, Belgium

Submitted Dec 3,   reviewed Dec 23,  Accepted Jan 4, published Jan 30  Review Report

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2008 (2)

In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets

Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D 9 (2):130-145, 2008

Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar (UttaraKhand), India

Submitted Jul29,   reviewed Sep 1,  accepted Nov 25, published Dec 30  Review Report

MOTIFA (Motif Analizer) examination of interregional and intraregional distribution of short DNA motifs

Sucaet Y, Magrath C 9 (2):121-129, 2008

          Biological and Environmental Science, Troy University, Troy, AL 36082, USA

         Submitted October 3,   reviewed October 17,  accepted October 23, published October 30  Review Report

Homology based 3D-structure modeling of glucose specific Sesbania stem lectin

Saxena S, Das HR, Das D, Biswas S 9 (2):113-120, 2008

Proteomics and Structural Biology Laboratory, Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road 110007, India

          Submitted August 2,   reviewed August 20,  accepted August 21, published August 28  Review Report

CateGOrizer: A web-based program to batch analyze gene ontology classification categories

Hu Zhi-Liang, Bao J, Reecy JM 9 (2):108-112, 2008

Department of Animal Science, Iowa State University, 2255 Kildee Hall and Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, Iowa 50011-3150, USA

          Submitted August 2,   Reviewed August 20,  Accepted August 21, published August 28  Review Report

In-silico study on interaction of active binding sites of proteins with calcium oxalate monohydrate

Bijarnia RK, Kaur T, Naik PK, Singla SK, Tandon C 9 (2):92-107, 2008

          Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan and Department of Biochemistry, Panjab University, India

          Submitted February 26,   Reviewed May 23,  Accepted August 10, publish August 25 Review Report

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2008 (1)

Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAP's

Tripathy KP, Roy S, Khan F Shasany AK, Sharma A, Khanuja SPS 9 (1):78-91, 2008

          Bioinformatics and In Silico Biology Division, Central Institute of Medicinal and Aromatic Plants (CSIR), Lucknow, India

          Submitted June 7,   Reviewed May 23, Accepted July 10, publish July 26 Review Report

Prediction of the putative function of mouse WDR13 protein

          Murthy BSN,  Pandit MW, Singh L. 9 (1):60-77, 2008

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007; India

          Submitted March 11   Reviewed May 13, Accepted June 16, publish June 26 Review Report

In silico experiments on a faulty ubiquitin-proteasome system in the pathogenesis of Parkinson's disease

Lecca P. 9 (1): 30-43, 2008
The Microsoft Research-University of Trento Centre for Computational and System Biology, Trento, Italy.
Submitted March 13   Reviewed March 27, Accepted April 8, publish April 30 Review Reports

A comparison of information on molecular interactions available in full-length publications versus abstracts
Mahadevan U, Bhate J, Raghunath A,  Kashyap S, Dey PC, Prakash N, Bhat B, Mol L, Wong, L 9 (1): 21-29, 2008
Molecular Connections Pvt. Ltd., Bangalore, India and Institute for Infocomm Research (I2R), Singapore.
Submitted November 18   Reviewed September 23, Accepted January 17 Review Reports

Elucidating the role of CREBBP co-activator in erythroid differentiation by literature mining and analysis

Iyer J, Raghunath A, Bhate J, Wong L, 9 (1): 12-20, 2008
Molecular Connections Pvt. Ltd, Basavanagudi, Bangalore, India, and National Institute of Singapore, Singapore.
          Submitted December 27   Reviewed January 23, Accepted January 25   Review Reports

In silico analysis of P5CS gene evolution in plants

Kumari A1,  Patade VY, Suprasanna P, 9 (1): 1-11, 2008

Plant Cell Culture Technology Section,  Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 084. India.
          Submitted August 3   Reviewed August 23, December 16  Published January 12  Review Reports

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2007 (2)

Molecular evolution of archaeal CRISPR and Cas genes

Chatterjee R, Dutta A, Chaudhuri K, 8 (2): 189-204, 2007

Molecular & Human Genetics Division  Indian Institute of Chemical Biology, Jadavpur, Kolkata-700 032, India.

Submitted October 12   Reviewed November 15   Published November 29  Review Reports

Structure and function prediction of a hypothetical protein (Q307B9_SPIPL) of Spirulina platensis (Nordstedt) Geitler
Lakshmi PTV, Uma Maheswari S, Annamalai A, 8 (2): 179-188, 2007.
Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University,  Tamil Nadu, India, and School of Dietetics and Human Nutrition, McGill University, Macdonald Campus,  Montreal, Quebec, Canada.
          Submitted August 15   Reviewed August 28   Published September 23 Review Reports

Constructing phylogeny from whole genome alignment

Chan PY, Lam TW, Liu CM, Yiu SM 8 (2) : 165-178, 2007
Department of Computer Science, The University of Hong Kong, Hong Kong

Submitted July 14   Reviewed August 14, 22   Revised August 24  Published August 28  Review Reports

The 3D structure of the Japanese Encephalitis helicase, using homology based molecular modelling techniques

Vlachakis D, Brancale A  8 (2) : 154-164, 2007
Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, United Kingdom
          Submitted August 2   Reviewed August 5   Revised August 6  Published August 14  Review Reports

Shape-to-String Mapping: A Novel Approach To Clustering Time-Index Biomics Data

         Antoine W, Miernyk JA  8 (2) : 139-153, 2007
          Department of Biochemistry USDA, Agricultural Research Service, Plant Genetics Research Unit and Interdisciplinary Plant Group, University of Missouri, Columbia, USA
          Submitted June 20   Reviewed July 5-6   Revised July 14   Published July 16  Review Reports

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2007 (1)

In-silico TAT-PTD prediction for cell penetrating peptides.

Tandon C, Aggarwal A, Goel P, Sengupta D, Naik P,  8 (1) : 115-138, 2007

 Department of Biotechnology and Bioinformatics, Jaypee University of Information technology, Himachal, Pradesh, India

Binding Modes, binding Affinities and ADME Screening of HIV-1 NNRTI Inhibitor: Efavirnez and its analogues.

Sengupta D, Verma D, Naik PK 8 (1) : 99-114, 2007

Department of Bioinformatics and Biotechnology, Jaypee University of Information Technology, Waknaghat, Distt.-Solan, Himachal Pradesh, India.

A Unified Framework for Finding Differentially Expressed Genes in MPTP Mouse Model for Parkinson’s Disease

Shaik J, Yeasin M 8 (1) : 84-98, 2007

          CVPIA LAB, Department of Electrical and Computer Engineering, University of Memphis, Memphis, Tennessee, 38152, United States.

In silico Cis-regulatory Element Analysis of Seed Storage Protein Promoters Cloned from Different Cultivars of Wheat, Rice and Oat

Yadav D,  Singh VK, Singh NK 8 (1) : 75-83, 2007

   Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities G.B. pant University of Agriculture and Technology, Pantnagar (Uttarakhand) ²National Research Center on Plant 

          Biotechnology, Indian Agriculture Research Institute, New Delhi 110012

 In Silico Identification of Antioxidant gene G6PD in Caenorhabditis elegans

Jitendra N, Prachi S, Alpana V, Shakti S 8 (1) : 61-74, 2007

 Bioinformatics Centre, AIB, Amity University, Noida, UP, INDIA

An Indigenous Integration System for Biodiversity Databases

          Sarinder KKS¹, Lim LHS¹ , Dimyati K², Merican AF¹ 8 (1) : 56-60, 2007
Institute of Biological Sciences, Faculty of Science, University of Malaya, and Department of Electrical Engineering, Faculty of Engineering, University of Malaya.

Unbalanced Factorial Design: Type I, II and III Sums of Squares
Boyacioglu H, Baskan O 8 (1) : 56-55, 2007

Ege University Faculty of Science, Department of Statistics, Bornova, Turkey

Comparative analysis of MMFF94x and AMBER99 force fields using aspartic-serine-metallo proteases and Sugar-Binding Proteins as different data sets.
          Singh H, Marla SS, Verma D 8 (1) : 45-55, 2007

Biotechnology and Bioinformatics Department, Jaypee University of Information Technology, Waknaghat, Solan (H.P.) India 173215

Database and interactome map of genes involved in oral cancer

Gadewal NS, Zingde SM 8 (1) : 41-44, 2007

Bioinformatics centre (BTIS Sub-DIC) and Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India

PIDA: A new algorithm for pattern identification
Putonti C, Pettitt BM, Reid JG, Fofanov Y 8 (1) : 30-40, 2007
Departments of Computer Science, Biology and Biochemistry, and Chemistry, University of Houston, Houston Texas, USA

Plasma proteome knowledgebase: exploring disease biomarker correlations
Iyer J, Srinivas VM, Khamari L, Sequeira JM, Das N, Periasamy UR, Bhate 8 (1) : 18-29, 2007
Molecular Connections Pvt. Ltd., Bangalore, India

A comparison of information on molecular interactions available in full-length publications versus abstracts
Mahadevan U, Bhate J, Raghunath A,  Kashyap S, Dey PC, Prakash N, Bhat B, Zachariah LL, Wong, L 8 (1) : 8-17, 2007
Molecular Connections Pvt. Ltd., Bangalore, India, and National Institute of Singapore, Republic of Singapore

In silico tools for evaluation of conservation homology among interleukins.
Krupanidhi S, Madhukar SS, Doughman SD  8 (1) : 1-7, 2007
Department of Biosciences, Sri Sathya Sai Institute of  Higher Learning, Prasanthinilayam, Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai-600 119 TN, India and  Department of

          Nutrition, University of North Carolina, Chapel Hill, NC 27599 USA.

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2006 (2)

Plant promoter prediction tool and isolation of a promoter from Porteresis coarctata
Mahalakshmi S, Krishna NC, Rao KV,  Reddy VD  7 (2) : 118 - 139, 2006
Centre for Plant Molecular Biology, Osmania University, Hyderabad, India and SR Software, Jubilee Hills, Hyderabad, India

A flexible spot recognition method for SNP microarray systems
Huang CY, Liu L 7 (2) : 101-117, 2006
          Center for Pharmacogenomics and Complex Disease Research, University of Medicine & Dentistry of New Jersey, Newark, NJ 07101, USA  and Department of Applied Mathematics, Chung Yuan Christian  University,
          Chung-Li, Taiwan 32023, ROC

A computer-intensive method to analyse microarray experiments with a very small number of replications in case of heteroscedasticity
Muhammad MA, Neuhäuser M 7 (2) : 90-100, 2006
          Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Hufelandstr. 55, D-45122 Essen and Department of Mathematics and Technique, RheinAhrCampus, Koblenz . University of Applied 

          Science, Südallee 2, D-53424 Remagen, Germany.

In silico Homology modeling and Structure assessment of Holo (Acyl Carrier Protein) synthetase from Treponema pallidum
Dowlathabad MR,  Venkata RD, Rallapalli R 7 (2) : 85 - 89, 2006
Department of Biotechnology, Bioinformatics Laboratory and Department of Microbiology, Sri Krishnadevaraya University, Anantapur-AP India

Structural Classification of Protein Using Surface Roughness Index
Singha S1, Lahiri T1, Dasgupta AK, Chakrabarti P 7 (2) : 74-84, 2006

 Department of Biotechnology, Institute of Engineering & Technology, U. P. Technical University, Sitapur Road, Lucknow, India

Genomic predictions for T Lymphocyte epitopes on Plasmodium falciparum (Malaria)
          Singh SP, Khan F Mishra BN 7 (2) : 69-73, 2006
 Department of Biotechnology, Institute of Engineering & Technology, U. P. Technical University, Sitapur Road, Lucknow-226021 (U.P.)  India

Conservation of the regulatory pho-box in acetoacetyl-CoA reductase promoters across bacterial PHB biosynthetic metabolic pathway
           Khan F, Singh SP, Mishra BN 7 (2) : 57-68, 2006

 Department of Biotechnology, Institute of Engineering & Technology, U. P. Technical University, Sitapur Road, Lucknow-226021 (U.P.) India

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2006(1)

Extending the Dynamic Range of Signal Intensities in DNA Microarrays
Choi D, O’Malley JP, Lasarev MR, Lapidus J, Lu X, Pattee P, Nagalla SR 7 (1) : 46-56, 2006
            Division of Biostatistics, Department of Public Health and Preventive Medicine, Center for Biomarker Discovery, Department of Pediatrics, Center for Research on Occupational and Environmental  Toxicology,
            Oregon Health & Science University, Oregon, USA

Comparative structure analysis of Chorismate synthase 

            Marla S , Yalamanchili HK,  Gelli P, Singh HK, Praveen G, Ghatta G, Srikanth S, Goutham K. 7 (1) : 35-45, 2006

Biotechnology and Bioinformatics Department, JayaPrakash University of Information technology, Solan, India.

Statistical Potential Determining Protein Interaction Sites

Williams G 7 (1) : 32-34, 2006
Wolfson Centre for Age Related Diseases, The Wolfson Wing, Hodgkin Building, Kings College London, United Kingdom

Classification of incipient Alzheimer patients using gene expression data: Dealing with potential misdiagnosis
            Robbins K, Joseph S, Zhang W, Rekaya R,  Bertrand JK 7 (1) : 22-31, 2006

Department of Animal and Dairy Science, and Statistics, University of Georgia, Athens, Georgia USA.

Clusterer: extendable java application for sequence grouping and cluster analyses

Klepac-Ceraj V, Ceraj I, Polz MF, 7 (1) 15-21, 2006
 Information Services and Technology, and Department of Civil and Environmental Engineering, Massachusets Institute of  Technology (MIT), Cambridge, Massachusets,  USA.

A correction for expression value dependencies in Affymetrix

Broemel F, Kruse E, Neuhäuser M, Dürig J, JÖckel KH, 7 (1) : 1-14, 2006

 Institute for Medical Informatics, Biometry and Epidemiology, and Department of Hematology, University Hospital, Essen and Department of Botany, Faculty of Biology,  Technical University,  Darmstadt, Germany.

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2005(2)

Boosting Speed of MS/MS Peptide Sequencing via Database Search by Spectral Profile Comparison
 Liu J, Carrillo B, Yanofsky C, Beaudrie C, Morales F, Kearney R  6 (2) 174-183, 2005

Department of Biomedical Engineering, McGill University, Montreal Quebec, Canada.

The Effect of Inverse Document Frequency Weights on DNA Sequence Retrieval
O'Kane KC 6 (2) 162-173, 2005

Department of Computer Science, The University of Northern Iowa, Cedar Falls, Iowa 50613-0507, USA.

Binding of fork head protein to DNA partly determined by base cooperation.
Mach V  6 (2) 149-161, 2005
             Institute of Entomology, Czech Academy of Sciences, České Budějovice, Czech Republic. Department of Computer Science and Mathematics, Ariel Academic College in Yudea and Samaria and ELTA Systems Ltd. Israel

In silico identification of cis-regulatory elements in Mesorhizobium loti

 Khan F, Agrawal S, Mishra BN 6 (2) : 129-141, 2005
 Department of Biotechnology, Institute of Engineering & Technology and Jawahar Lal Nehru Center of Advanced Research, Bangalore, India.
 

DNA microarray model for computation of absolute gene expression level

Xu, M 6 (2) : 121-128, 2005

Gene21st, 19 Belcourt Rd. Worcester, MA 01605, USA.

MIPE an XML format to facilitate the storage and exchange of PCR-related data

Aerts JA, Veenendaal T 6 (2) : 114-120, 2005.

Bioinformatics Group, Roslin Institute, United Kingdom, Animal Breeding and Genetics Group, Wageningen University, The Netherlands.

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2005 (1)

Automated Long Oligo Design on Consensus Regions of Similar Genomes
Schretter C, Milinkovitch MC 6 (1) 107 -113, 2005
Unit of Evolutionary Genetics (UEG), Institute of Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB).

Combining Kernel Dimension-Reduction with Regularized Classifiers for Tissue Categorization
Shen L, Tan EC 6 (1) : 91-106, 2005
School of Computer Engineering, Nanyang Technological University, Singapore, 639798.

In silico identification and modelling of a putative iron-regulated TonB-dependant outer membrane receptor protein from the genome of Leptospira interrogans serovar Lai
Sritharan M, Ramadevi S, Pasupala N, Asuthkar S, Tajne S 6 (1) : 74-90, 2005

Department of Animal Sciences, University of Hyderabad, Hyderabad, India; Informatics Division, GVK Biosciences Pvt Ltd, Hyderabad, India

Eulerian Superpath Approach to Correct Sequencing Error in Shotgun Assembly

Shi W, Zhou W, Zheng W 6 (1) : 65-73, 2005

School of Information Technology, Deakin University, Australia, Institute of High Performance Computing, Department of Computer Science and Technology Tsinghua University, China.

From prediction of subcellular localization to functional classification: Discrimination of DNA- packing and other nuclear proteins
Höglund A, Dönnes P, Adolph HW, Kohlbacher O 6 (1) : 51-64, 2005
 Department(s) of Simulation of Biological Systems, WSI/ZBIT, Eberhard Karls University Tübingen, Sand 14, D-72076 Tübingen and Biochemistry and Center for Bioinformatics, Saarland University, D-66041,

Saabrücken, Germany

Substitution of polymorphic amino acids in proteins:Predicting functional alterations using amino acid properties.
Baksi K, Bhattacharyya NP.  6 (1) : 42-50, 2005

Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700 064, India.

Morphometric and Distance Computational Software for evolutionary studies.
Carvajal-Rodríguez A, Rodríguez MG  6 (1) : 34-41, 2005.
Departamento de Bioquímica, Genética e Inmunología, Facultad de Ciencias, Universidad de Vigo, 36310 VIGO, Spain

Support vector machines and bioinformatics

Sethi RJ 6 (1) : 22-33, 2005.

Computer Science and Engineering Department and Marlan & Rosemary Bourns College of Engineering, University of California-Riverside, USA

A novel method to predict protein subcellular localizations
Huang J, Shi F, 6 (1) : 8-21, 2005.
Schools of Computer Science, Science, Mathematics and Statistics, Huazhong Agricultural University, Wuhan, Hubei province, P.R. China.

MolVRML: build VRML models of 3D molecular structures
Zou Y,  6 (1) :1-7, 2005.
School of Computer Science and Information Technology, RMIT University, VIC 3001 Australia

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2004

Prediction of transcriptional regulation by Dlx and Msx homeodomain proteins
Swarnalatha M, Jutur PP, Amouda V, Mathur PP, Reddy AR 5 : 132-145, 2004

Bioinformatics Centre, Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India

In silico gene identification and homology modeling of Chorismate synthase in Clostridium difficile

Sunita T, Ramadevi S 5 :129-131, 2004.

Informatics Division, GVK Biosciences Pvt Ltd, Hyderabad, India

MCM-Based clustering for time-course gene expression data

Wu FX, Zhang WJ, Kusalik AJ 5 :102-128, 2004

Division of Biomedical Engineering, Department of Computer Science, University of Saskatchewan, Saskatoon, Canada

Parallel DNA fragment assembly algorithm based on Eulerian superpath

Zheng W, Shi W, Zhou W  5 : 91-101, 2004

Institute of High Performance Computing Department of Computer Science and Technology Tsinghua University, China and School of Information Technology, Deakin University, Australia.

Bayesian mixture modelling of species divergence
Adam A, Mengersen K, Baker P 5 : 69-90, 2004.

INSEE, CREST, Paris, France, Queensland University of Technology and CMIS, CSIRO, Australia

Reliability of RNA secondary structure prediction with XNAfold

Zou Y 5 : 59-68, 2004.

School of Agriculture and Food Systems, University of Melbourne and School of Computer Science and Information Technology, RMIT University VIC 3001 Australia.

Wave analysis of microarray expression as predictor of gene expression in tumors.

Gupta A, Agrawal S 5 : 49-58, 2004.

Indian Institute of Information Technology Allahabad, Deoghat Jhalwa Campus, RajRooppur Road, India

Phylogenetic clustering and secondary structural analysis of Plant Terpenoid Synthases

Singh IV, Agrawal S, Khan F,  Mishra BN 5 : 32-48, 2004.

Department of Biotechnology, Institute of Engineering & Technology, Uttar Pradesh and Bioinformatics Division Indian Institute of Information Technology, Allahabad, India

GASP: a new genetic algorithm (based on) surviving probability.

Carvajal-Rodríguez A 5 : 23-31, 2004.

Departamento de Bioquímica, Genética e Inmunología, Facultad de Ciencias Universidad de Vigo, 36200 VIGO, Spain

Prediction of protein homo-oligomers by incorporating quasi-sequence-order effect

Zhang SW, Pan Q, Zhang HC, Wu YH, Shi JU 5 : 13-22, 2004.

Department of Automatic Control, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China

Molecular phylogenetics and functional evolution of major RNA recognition domains of recently cloned and characterized autoimmune RNA-binding particle

Suleymanoglu E 5: 1-12, 2004.

Institute of Biochemistry, University of Vienna, Medical Faculty, Vienna Biocenter, Dr. Bohr-Gasse 9/3, A-1030, Vienna, Austria

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2003

Identification of GltC transcription factor binding DNA motifs and its novel co-regulated genes in nitrogen fixing bacteria

Khan F,  Agrawal S,  Mishra BN 4:106-114, 2003

Biotechnology Program, Institute of Engineering & Technology,Sitapur road, Lucknow-22, India.

Matching carbohydrate-binding domains in Arabidopsis thaliana genome: development of a lectin database
              Moreno FB, Facó F, Ceccatto VM, Sampaio AH, Costa ABS, Freitas JLT, Nogueira LL, Lima ME,  Lima-Filho JL, Cavada BS, 4:96-105, 2003

Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE Campus do Pici, Universidade Estadual do Ceará (UECE) , Departamento de Engenharia de Pesca, Universidade

Federal do Ceará, Fortaleza-CE, Universidade Federal do Pernambuco (UFPE), Universidade Federal do Pernambuco(UFPE), Brazil.

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2002

In Silico Markovian Bioinformatics for predicting ¹Ha-NMR chemical shifts in mouse Epidermis Growth  Factor(mEGF).
Díaz HG, De Armas RR, Uriarte E. 3:83-95, 2002. 

Chemical Bio-actives Center, Department of Chemistry, Central University of "Las Villas" 54830, Cuba. Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela 15706, Spain

Simple Object Access Protocol (SOAP) for Bioinformatic Software Interoperability

Xia Y, Stinner RE, Wang X. 3:74-82, August 2002.

NSF Center for IPM North Carolina State University, Raleigh, NC 27695-7553, 2 Department of Plant Pathology North Carolina State University Raleigh, NC 27695, USA.

BAO, A Biological and Chemical Ontology For Information Integration

Ben-Miled Z, Webster YW, Nianhua L, Bukres O, Nayar AK, Martin J, Oppelt R. 3:60-73, June 2002

Electrical Engineering Department, Purdue School of Eng. &: Tech. Computer &: Information Science, Purdue School of Science, Lilly Corporate Center, Eli Lilly and Company, USA.

A software package for drawing ideograms automatically.

BÖhringer S, GÖdde R, BÖhringer D, Schulte T, Epplen JT 3 : 51-59, May 2002.
              Department of molecular human genetics,  Ruhr University Bochum, Department of ophthalmology, University clinics, Düsseldorf, Germany

The corporate information factory as a Bioinformatics framework

Casey, RM 3:42-50, April 2002.

Agilent Technologies, Inc. Information Technology, Agilent Technologies, Inc. Headquarters 395 Page Mill Rd. Palo Alto, CA 94306, USA

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2001

An unsupervised neural network approach for discovery of gene expression patterns in B-cell lymphoma .

Azuaje F, 2:26-41, 2001.

Department of Computer Science, Trinity College, Ireland

Development of a web-based informatics educational exercize in genomics.

Flower R 2:22-25, 2001

A/Professor, Department of Haematology and Transfusion Medicine, University of Sydney and Principal Scientist, PaLMS Transfusion Services, Northern Sydney Health

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1996-2000

Bioinformatics and Extended Markup Language (XML).
Guerrini VH, Jackson D 1:12-21, 2000.

Distributed Systems Technology Centre (DSTC) Pty. Ltd and school of Veterinary Science,  University of Queensland, St Lucia, Queensland 4172, Australia.

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