Sequence Analysis and General Bioinformatics

• BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly
• Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly
• Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons
• Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons
• Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press
• Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall
• Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann
• Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press
• Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub
• Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings
• Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons
• Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press
• Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers
• Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley & Sons
• Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag
• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience
• Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press
• Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall
• Bioinformatics: A Primer, Charles Staben, 2001, Jones & Bartlett Pub
• Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics
• Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press
• Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co
• Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press
• Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science
• Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley & Sons
• Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press
• Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press
• Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society
• Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press
• Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press
• Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press
• Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press
• Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers
• Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc.
• Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd.
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press
• Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press
• Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co.
• Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press
• Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press
• High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub.
• Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press
• DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press
• Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter
• Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman & Hall
• Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press
• Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press
• Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press
• Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society
• Mathematical Methods for DNA Sequences, Michael S. Waterman (Editor), 1989, CRC Press

Programming Books for Bioinformatics

• Mastering Perl for Bioinformatics, James D. Tisdall, 2003, O'Reilly
• Genomic Perl: From Bioinformatics Basics to Working Code, Rex A. Dwyer, 2002, Cambridge University Press
• Beginning Perl for Bioinformatics, James Tisdall, 2001, O'Reilly
• Developing Bioinformatics Computer Skills, Cynthia Gibas, Per Jambeck, 2001, O'Reilly

General Genomics

• Functional Microbial Genomics (Volume 33), Brendan Wren, Nick Dorrell, 2003, Academic Press
• Discovering Genomics, Proteomics, and Bioinformatics, A. Malcolm Campbell, Laurie J. Heyer, 2002, Benjamin/Cummings
• Genomes, Terence A. Brown, 2002, John Wiley & Sons
• Essentials of Medical Genomics, Stuart M. Brown , 2002, John Wiley & Sons
• A Primer of Genome Science, Greg Gibson, Spencer V. Muse, 2002, Sinauer Associates
• Pathogen Genomics: Impact on Human Health, Karen Joy, Phd Shaw (Editors), 2002, Humana Press
• Genomics, John E. Antonopoulos, 2000, Xlibris Corporation
• Genomics and Proteomics: Functional and Computational Aspects, Sandor Suhai (Editor), 2000, Plenum Pub Corp
• Functional Genomics: A Practical Approach (The Practical Approach Series, 235), S. Hunt and F. Livesey (Editors), 2000, Oxford Univ Press
• Human Molecular Genetics, Andrew P. Read, Tom Strachan 1999, BIOS Scientific Publishers Ltd.
• Genomics: The Science and Technology Behind the Human Genome Project, Charles R. Cantor and Cassandra L. Smith, 1999, John Wiley & Sons
• Cells: A Laboratory Manual, 3 volumes, David L. Spector, Robert D. Goldman, Leslie A. Leinwand, 1998, Cold Spring Harbor Laboratory Press
• Genome Analysis: A Laboratory Manual, 4 volumes, Bruce Birren, et al. (Editors), 1997, Cold Spring Harbor Laboratory Press
• The Human Genome Project, N. G. Cooper (Editor), 1994, University Science Books

Comparative Genomics

• Handbook of Comparative Genomics: Principles and Methodology, Cecilia Saccone, Graziano Pesole, 2003, Wiley-Liss
• Sequence - Evolution - Function: Computational Approaches in Comparative Genomics, Eugene V. Koonin, Michael Y. Galperin, 2002, Kluwer Academic Publishers
• Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, David Sankoff and Joseph H. Nadeau, 2000, Kluwer Academic Pub
• Comparative Genomics, Melody Clark (Editor), 2000, Kluwer Academic Pub

Proteomics

• Proteins and Proteomics: A Laboratory Manual, Richard J. Simpson (Editor), Cold Spring Harbor Laboratory
• Proteomics in Practice: A Laboratory Manual of Proteome Analysis , Reiner Westermeier, Tom Naven, 2002, John Wiley & Sons
• Posttranslational Modifications of Proteins: Tools for Functional Proteomics (Methods in Molecular Biology, Vol 194) , Christoph Kannicht (Editor), 2002, Humana Press
• Peptide Arrays on Membrane Supports: Synthesis and Applications (Springer Lab Manual), Joachim Koch, Michael Mahler (Editors), 2002, Springer Verlag
• Proteomics , Timothy Palzkill, 2002, Kluwer Academic Publishers
• Introduction to Proteomics: Tools for the New Biology , Daniel C. Liebler (Editor), 2001, Humana Press
• Proteome Research: Mass Spectrometry (Principles and Practice) , P. James (Editor), 2001, Springer Verlag
• Interpreting Protein Mass Spectra: A Comprehensive Resource , A. Peter Snyder, 2000, American Chemical Society
• Protein Sequencing and Identification Using Tandem Mass Spectrometry , Michael Kinter, Nicholas E. Sherman, 2000, Wiley-Interscience
• From Genome to Proteome: Advances in the Practice and Application of Proteomics, Michael J. Dunn (Editor), 2000, Vch Verlagsgesellschaft Mbh
• Proteomics: From Protein Sequence to Function, S. Pennington (Editor), M. Dunn (Editor), 2000, Springer Verlag
• Proteome Research: Two-Dimensional Gel Electrophoresis and Detection Methods (Principles and Practice), T. Rabilloud (Editor), 2000, Springer Verlag
• Proteome and Protein Analysis, R. M. Kamp, D. Kyriakidis, th Choli-Papadopoulou (Editor), 1999, Springer Verlag
• Proteome Research: New Frontiers in Functional Genomics, M. R. Wilkins, et al. (Editors), 1997, Springer Verlag

Protein Structure

• Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
• Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line
• Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press
• Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press
• Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
• Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht, 1999, Freeman

Pharmacogenomics

• Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Mark A. Rothstein (Editor), 2003, Wiley-Liss
• Pharmacogenomics: The Search for Individualized Therapies, Julio Licinio, Ma-Li Wong (Editors), 2002, John Wiley & Sons
• Pharmacogenomics, Werner Kalow, Urs A. Meyer, Rachel Tyndale (Editors), 2001, Marcel Dekker
• Pharmacogenetics and Pharmcogenomics: Recent Conceptual and Technical Advances (Pharmacology, Volume 61, Number 3, 2000), Elliot S. Vesell (Editor), 2000, S. Karger Publishing
• Pharmacogenetics, Wendell Weber, 1997, Oxford University Press

DNA Microarrays

• Statistical Analysis of Gene Expression Microarray Data, T. P. Speed (Editor), 2003, CRC Press
• Microarray Gene Expression Data Analysis: A Beginner's Guide, Helen C. Causton, John Quackenbush, Alvis Brazma, 2003, Blackwell Publishers
• The Analysis of Gene Expression Data (Statistics for Biology and Health), G. Parmigiani, E. S. Garrett, R. A. Irizarry, S. Zeger , Graeme Clark (Editors), 2003, Springer Verlag
• A Practical Approach to Microarray Data Analysis, Daniel P. Berrar, Werner Dubitzky, Martin Granzow (Editors), 2002, Kluwer Academic Publishers
• DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Pierre Baldi, G. Wesley Hatfield, 2002, Cambridge University Press
• DNA Microarrays: A Molecular Cloning Manual, David Bowtell, Joseph Sambrook (Editors), 2002, Cold Spring Harbor Laboratory
• DNA Array Image Analysis: Nuts & Bolts, Gerda Kamberova, Shishir Shah, 2002, DNA Press
• Microarray Analysis, Mark Schena, 2002, John Wiley & Sons
• A Biologist's Guide to Analysis of DNA Microarray Data, Steen Knudsen, 2002, John Wiley & Sons
• Microarrays for an Integrative Genomics (Computational Molecular Biology), Isaac S. Kohane, Alvin Kho, Atul J. Butte, 2002, MIT Press
• Microarrays for the Neurosciences: An Essential Guide (Cellular and Molecular Neuroscience), Daniel H. Geschwind, Jeffrey P. Gregg (Editors), 2002, MIT Press
• DNA Microarrays: Gene Expression Applications, Bertrand Jordan (Editor), 2001, Springer Verlag
• DNA Arrays: Methods and Protocols (Methods in Molecular Biology, Volume 170), Jang B. Rampal (Editor), 2001, Humana Press
• DNA Arrays: Technologies and Experimental Strategies, Elena V. Grigorenko (Editor), 2001, CRC Press
• Microarray Biochip Technology, Mark Schena (Editor), 2000, Eaton Pub
• Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series), Michael McClelland (Editor), Arthur B. Pardee (Editor), 1999, Eaton Pub
• DNA Microarrays: A Practical Approach (Practical Approach Series 205), Mark Schena (Editor), 1999, Oxford Univ Press
• cDNA Preparation and Characterization (Methods in Enzymology Volume 303), S.M. Weissman (Editor), 1999, Academic Press

Systems Biology, Genetic and Biochemical Network

• Handbook of Graphs and Networks : From the Genome to the Internet, Stefan Bornholdt, Heinz Georg Schuster (Editors), 2003, Vch Verlagsgesellschaft Mbh
• Computational Cell Biology, Christopher Fall, Eric Marland, John Wagner, John Tyson (Editors), 2002, Springer Verlag
• Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology), Julio Collado-Vides, Ralf Hofestadt (Editors), 2002, MIT Press
• Foundations of Systems Biology, Hiroaki Kitano (Editor), 2001, MIT Press
• Genomic Regulatory Systems: Development and Evolution, Eric H. Davidson , 2001, Academic Press
• Genes & Signals, Mark Ptashne, Alexander Gann, 2001, Cold Spring Harbor Laboratory
• Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), James M. Bower and Hamid Bolouri (Editors), 2001, MIT Press
• Protein-Protein Interactions: A Molecular Cloning Manual, Erica Golemis (Editor), 2001, Cold Spring Harbor Laboratory
• Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Eberhard O. Voit, 2000, Cambridge University Press
• Mathematical Physiology, James P. Keener, James Sneyd, 1998, Springer Verlag

DNA Sequencing

• DNA Sequencing: From Experimental Methods to Bioinformatics (Introduction to Biotechniques Series), Luke Alphey, 1997, Springer Verlag
• Automated DNA sequencing and analysis, Adams M.D., Fields C., Venter J.C. (Editors), 1994, Academic Press

Apart from above mentioned books, you can also find some useful books links at following mentioned URLs:

http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713

http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545

http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068

http://books.google.no/books?id=pxSM7R1sdeQC&dq=Pierre+baldi+%2B+bioinformatics&printsec=frontcover&source=bn&hl=en&ei=IoGRS6uCIJT-NYLA8Z0N&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q&f=false

http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826

If you think your favourite books are not listed then please write it down in comment section for the benefits of other users. Feel free to add many more books in comment section. 

At the Repository for Tomato Genomics Resources, we are working on Tomato Functional Genomics, using TILLING, Insertional Mutagenesis, proteomics, metabolomics approaches to study fruit ripening in tomato. The current aims of the group include using reverse and forward genetics strategies to isolate tomato mutants delayed in ripening, having high lycopene and folate content in tomato fruits and analysis of light and hormonal signal transduction pathways. For recent publications of the group see (Plant Physiol 161: 2085–2101, Plant Physiol 156: 1424-1438; Molecular Plant 3: 854-869; Plant Methods 6: 3; Plant Methods 5:18; Plant Signaling and Behavior 5:11.).

Currently we have one position available in the projects awarded to Prof. R.P. Sharma funded by Dept of Biotechnology. The qualification for this Position is as follows:

Research Assistant: Applicants should have experience in networking using R language and should be able to develop networks using the transcriptome, proteome and metabolite data sets. M.Tech. in Bioinformatics is required. The selected candidate would be paid Rs. 13,000/-pm- consolidated.

Candidates interested in above positions should send a one page statement clearly explaining how their skills are relevant to the position. The candidates should also enclose detailed CV and the name/email id for three referees. The candidates can send their application by email at rameshwar.sharma@uohyd.ac.in and y.sreelakshmi@uohyd.ac.in on or before December 10th, 2013. The position is purely temporary in nature. Shortlisted candidates would be called for interview. No TA/DA would be provided for attending the interview. We also have openings for CSIR-NET JRF candidates for pursuing PhD in above research areas.

Interested candidates with CSIR-NET JRF can send their CV to the above email
addresses.

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Address of the bookmark: http://www.ogt.com/assets/0000/3190/NGS_Survey_2013_Infographic_Web.pdf

Highlights of our research include:

Optimization of microarray design, probe signal interpretation
Advanced models and tools for expression profiling
State-of-the-art applications and integrated analyses

Lab page @ http://bioinf.boku.ac.at/

Source:  Igor Ulitsky & Ron Shamir

Address of the bookmark: http://acgt.cs.tau.ac.il/guides/LiteratureGuide.htm

Postdoctoral position is available for three years to work on development of Bioinformatics resources for the analysis and visualization of ribosome profiling data. Ribosome profiling (ribo-seq) is a technology that allows mapping positions of the ribosomes on the whole transcriptome level with a nucleotide precision. The technology allows obtaining high resolution digital snapshots of gene expression in cells. The position is available starting on the 1st of October, 2013.

Candidate is expected to have Ph.D. in Bioinformatics or Computational Biology. Candidates with the degree in non-Biological disciplines such as Computer Science, Statistics, Applied Mathematics, Physics or Electrical Engineering will also be considered.

The position is available at LAPTI (http://lapti.ucc.ie) that is located in the Western Gate Building (http://www.stwarchitects.com/project-information.php?c=1&p=09993) at University College Cork. Western Gate Building Research Complex hosts several UCC departments and provides ideal environment for interdisciplinary research. Cork (sometimes referenced as “Venice of Ireland”) is the second most populous city in the Republic. It has friendly cosmopolitan atmosphere and vibrant culture. A number of American industrial giants such as Apple , EMC and Pfizer have chosen Cork as a home for their European headquarters.

The details of the application process are given at http://lapti.ucc.ie/jobs.html. To ensure prompt processing of your application use the subject line: ‘Postdoc computational’. All applications received prior to August the 1st are guaranteed equal consideration. However, applications at the later dates will also be considered until the position is filled.

For more info visit http://lapti.ucc.ie

Candidate Requirements:
A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered.

To Apply
To apply, please send your updated CV and cover letter to Dr. Rohit Gupta (rohit@strandls.com).

Source: http://www.strandls.com/application-scientist

Walk-in-Interview

Walk-in-interview will be held on February 11, 2014 at 10:00 A.M. at IASRI, New Delhi for a project “Whole Genome Sequencing and Development of Allied Genomics Resources in Two Commercially Important Fish-Labeo rohita and Clarias batrachus” funded by Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi for the following posts. The appointment will be on contractual basis upto September, 2016 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.

Senior Research Fellow Two

Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Biotechnology or equivalent with 1st Division

 Knowledge of Statistical Analysis /Bioinformatics tools/computer programming for computational genomics.

Emoluments for Research Associate: Consolidated Rs: 16000/- per month + 30% HRA (1st Two years) and Rs: 18000/- per month + 30% HRA (3rd Year)

Age Limit: Age should be not more than 35 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates as on date of interview).
Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph. Original certificates/ Degrees are needed to be produced at the time of interview. No T.A. /D.A. will be paid for appearing in the interview.

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Candidates having the below mentioned qualifications may appear for Walk in Interview at ICPO on 5th Feb 2014 between 10.00 AM and 12.00 PM under the NIF project entitled "Prediction of drug tragets of chemical constituents present within non-codified medicinal plants" under Dr Subhash M.Agarwal, Scientist C

Position : JRF
No of Post : One
Pay : Rs 12000/- + 30% HRA

Desired Profile : M.Sc in Bioinformatics with good academic record. Candidate with experience in database development and scripting would be preferred
Age Limit : Below 28 years
Period : 2 months

Interested candidates may send their applications with bio-data by email (smagarwal@gmail.com) or post addressed to Dr Subhash M Agarwal, Scientist C, Bioinformatics Division, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector 39, Noida-201301 so as to reach latest by 04.02.14

Deadline : 04.02.14

http://icmr.nic.in/icmrnews/icpo_jrf.pdf

* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
* Feature/Model Learning: developing algorithms and software

Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

http://research.janelia.org/peng/