globe
  1. Core Text 1 item
    1. Understanding Bioinformatics - Marketa J Zvelebil, Jeremy O. Baum 2008

      Book Essential

  2. Post-Genomic Science: 18 items
    1. Useful Chapters to Consult as Background Knowledge From ‘Understanding Bioinformatics’ 10 items
      Please note that this book does not substitute readings provided during the lectures on specific subjects.
      1. Protein Structure - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 2.1, 2.2

      2. Dealing with Databases - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 3.1‐3.3

      3. Revealing Genome Features - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 9.1, 9.3, 9.6, 9.7

      4. Gene Detection and Genome Annotation - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 10.5, 10.6

      5. Predicting Secondary Structures - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 12.1, 12.2, 12.4

      6. Analyzing Structure-Function Relationships - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 14.1‐14.3

      7. Proteome and Gene Expression Analysis - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential

      8. Systems Biology - Marketa J. Zvelebil, Jeremy O. Baum 2008

        Chapter Essential 17.1, 17.2

    2. Structural Diversity of the Human Genome and Disease Susceptibility - Richard S. Smith, Maria Gutierrez-Arcelus 2008

      Article Essential

    3. Gene Expression Networks - John C Rockett, David J. Dix 2006

      Article Essential

    4. Microarray Bioinformatics - Andrew P. Stubbs, Stefan J. L. Van Yper, Peter J. van der Spek 2008

      Article Essential

    5. Microarrays: Use in Gene Identification - David R. Rank, David K. Hanzel 2006

      Article Essential

    6. Gene Expression Databases - Alvis Brazma, Ugis Sarkans 2007

      Article Essential

  3. Post-Genomic Science and in-silico Analysis: 0 items
  4. Introduction to Practical Bioinformatics: 9 items
    1. Bioinformatics - Wojciech Makałowski, Victoria Shabardina, Izabela Makałowska 2018

      Chapter Essential

    2. Issues in Searching Molecular Sequence Databases - Stephen F. Altschul, Mark S. Boguski, Warren Gish, John C. Wootton 1994

      Article Essential

    3. In Silico Gene Expression Analysis – an Overview - David Murray, Peter Doran, Padraic MacMathuna, Alan C Moss 2007

      Article Essential

  5. Recent Advances in Analysing Gene Function: 7 items
    1. DOUBLE CHECK THIS WEEKS LECTURE

    2. Epigenetic Inheritance in Arabidopsis: Selective Silence - Daniel Zilberman, Steven Henikoff 2005

      Article Essential

    3. Activation Tagging in Arabidopsis - Detlef Weigel, Ji Hoon Ahn, Et al 2000

      Article Essential

  6. Reading Week: 0 items
  7. RNA Interference: 8 items
    1. Silencing Human Cancer: Identification and Uses of MicroRNAs - Francisco E. Nicolas, Sara Lopez-Gomollon, Alfonso F. Lopez-Martinez, Tamas Dalmay 2011

      Article Recommended

    2. RNA Interference - Gregory J. Hannon 2002

      Article Further

    3. RNA Interference: A Promising Approach to Antiviral Therapy? - Jose M Silva, Scott M Hammond, Gregory J Hannon 2002

      Article Further

    4. Modulation of HIV-1 Replication by RNA Interference - Jean-Marc Jacque, Karine Triques, Mario Stevenson 2002

      Article Further

  8. See Handouts Previous Week as Well as This Week: 10 items
    1. Transcription Factors - David S Latchman 2007

      Article Further

  9. Transcriptional Signalling Networks: 0 items
  10. Gene Expression/Functional Analysis: 26 items
    inferring and Modelling Gene and Protein Networks
    1. Transcription Factors - David S Latchman 2007

      Article Recommended

    2. Pax 6: Mastering Eye Morphogenesis and Eye Evolution - Walter J Gehring, Kazuho Ikeo 1999

      Article Recommended

    3. Jasmonate-Regulated Arabidopsis Stress Signalling Network - Alessandra Devoto, John G. Turner 2005

      Article Recommended

    4. Integrating Genomes - D. R. Zerbino, B. Paten, D. Haussler 2012

      Article Recommended

    5. Computational Systems Biology - Hiroaki Kitano 2002

      Article Recommended

    6. A New Approach to Decoding Life: Systems Biology - Trey Ideker, Timothy Galitski, Leroy Hood 2001

      Article Recommended

    7. Milestones Network Dynamics and Cell Physiology - John J. Tyson, Kathy Chen, Bela Novak 2001

      Article Recommended

    8. The Nature of Systems Biology - Frank J. Bruggeman, Hans V. Westerhoff 2007

      Article Recommended

    9. Transcriptional Regulatory Code of a Eukaryotic Genome - Christopher T. Harbison, D. Benjamin Gordon, Richard A. Young 2004

      Article Recommended

    10. Systems Biology. Life's Complexity Pyramid - Zoltán N. Oltvai, Albert-László Barabási 2002

      Article Recommended

    11. Protein Networking: Insights Into Global Functional Organization of Proteomes - Enrico Pieroni, Sergio de la Fuente van Bentem 2008

      Article Recommended

  11. Inferring and Modelling Gene and Protein Networks: 9 items
    Protein Interaction Maps
    1. Protein Networking: Insights Into Global Functional Organization of Proteomes - Enrico Pieroni, Sergio de la Fuente van Bentem 2008

      Article Recommended

  12. High-throughput DNA-protein Interaction Technologies: 14 items
    chIP; chIP-CHIP; chIP-Seq
    1. ChIPping Away at Gene Regulation - Charles E Massie, Ian G Mills 2008

      Article Recommended

    2. Transcriptional Regulatory Code of a Eukaryotic Genome - Christopher T. Harbison, D. Benjamin Gordon, Richard A. Young 2004

      Article Recommended

    3. Genome-Wide Mapping of in Vivo Protein-DNA Interactions - David S. Johnson, Ali Mortazavi, Richard M. Myers, Barbara Wold 2007

      Article Recommended

    4. A New Approach to Decoding Life: Systems Biology - Trey Ideker, Timothy Galitski, Leroy Hood 2001

      Article Recommended

    5. Milestones Network Dynamics and Cell Physiology - John J. Tyson, Kathy Chen, Bela Novak 2001

      Article Recommended

    6. The Nature of Systems Biology - Frank J. Bruggeman, Hans V. Westerhoff 2007

      Article Recommended

  13. Proteomics in the Discovery of Signalling Pathways in Cancer Biology: 12 items
    1. Reviews: 3 items
      1. The Biological Impact of Mass-Spectrometry-Based Proteomics - Benjamin F. Cravatt, Gabriel M. Simon, John R. Yates III 2007

        Article Essential

    2. Research Papers: 4 items
      Signalling
      1. A Mammalian Organelle Map by Protein Correlation Profiling - Leonard J. Foster, Carmen L. de Hoog 2006

        Article Essential

      2. Large-Scale Proteomics Analysis of the Human Kinome - F. S. Oppermann, F. Gnad, Et al 2009

        Article Essential

    3. Research Papers: 3 items
      Cell Cycle
    4. Quantitative Proteomics - Ruedi Aebersold 2008

      Audio-visual document Essential MUST WATCH

  14. Introduction to Proteomics and Mass Spectrometry for Proteomics: 7 items
    1. Mass Spectrometry-Based Proteomics - Ruedi Aebersold, Matthias Mann 2003

      Article Essential general MS, instruments

    2. Mass Spectrometry and Protein Analysis - Bruno Domon, Ruedi Aebersold 2006

      Article Essential MS/MS exp, instruments

    3. Mass Spectrometry Technologies for Proteomics - B. Canas 2006

      Article Essential cover most aspects of proteomics

    4. Proteomics Analysis Step by Step Tutorial Educative File

      Document Essential Good tutorial to understand how proteins are identified by MS, first part easy to understand! End of tutorial, is very advanced, for keen proteomists!

    5. Proteomics Beyond Large-Scale Protein Expression Analysis - Paul J Boersema, Abdullah Kahraman, Paola Picotti 2015

      Article Essential

  15. Proteomics Workflow for Mass Spectrometry: 29 items
    1. Mass Spectrometry-Based Proteomics - Ruedi Aebersold, Matthias Mann 2003

      Article Essential general MS, instruments

    2. Mass Spectrometry Technologies for Proteomics - B. Canas 2006

      Article Essential MS proteomics workflows,+quant +PTMs

    3. Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology - Jürgen Cox, Matthias Mann 2011

      Article Essential review on MS proteomics, PTMs, interaction, quantitative….

    4. Mass Spectrometry and Protein Analysis - Bruno Domon, Ruedi Aebersold 2006

      Article Recommended MS/MS exp, instruments

    5. Achieving In-Depth Proteomics Profiling by Mass Spectrometry - Natalie G. Ahn, John B. Shabb, William M. Old, Katheryn A. Resing 2007

      Article Recommended MS/MS for proteomics

    6. The Biological Impact of Mass-Spectrometry-Based Proteomics - Benjamin F. Cravatt, Gabriel M. Simon, John R. Yates III 2007

      Article Recommended

    7. Mass Spectrometry for Proteomics - Xuemei Han, Aaron Aslanian, John R Yates 2008

      Article Recommended

    8. Mass Spectrometry-Based Proteomics - Ruedi Aebersold, Matthias Mann 2003

      Article Essential general MS, instruments

    9. Mass Spectrometry and Protein Analysis - Bruno Domon, Ruedi Aebersold 2006

      Article Essential MS/MS exp, instruments

    10. Mass Spectrometry Technologies for Proteomics - B. Canas 2006

      Article Essential Cover most aspects of proteomics

    11. The Biological Impact of Mass-Spectrometry-Based Proteomics - Benjamin F. Cravatt, Gabriel M. Simon, John R. Yates III 2007

      Article Further

    12. Quantitative Mass Spectrometry in Proteomics: A Critical Review - Marcus Bantscheff, Markus Schirle, Et al 2007

      Article Recommended

    13. Quantitative Plant Proteomics - Laurence V. Bindschedler, Rainer Cramer 2011

      Article Recommended Review of quantitative methods alternative to SILAC. Include examples from plant proteomics studies, Must read, as relevant quantitative methods, for human biology.

    14. Quantitative Mass Spectrometry-Based Proteomics: An Overview - Miroslav Nikolov, Carla Schmidt, Henning Urlaub 2012

      Chapter Recommended Good definitions

    15. Advances in High-Resolution Accurate Mass Spectrometry Application to Targeted Proteomics - Antoine Lesur, Bruno Domon 2015

      Article Recommended SRM or MRM , Targeted quantitative proteomics, new advancements, for those who wants to know more.

    16. Multidimensional Proteomics for Cell Biology - Mark Larance, Angus I. Lamond 2015

      Article Recommended Quant proteomics, de novo synthesis and protein interactions. An advanced , but very useful read, upto date, well documented, for those who want to get in more details.

  16. Proteomics Workflow for Mass Spectrometry II: 15 items
    1. Mass Spectrometry Technologies for Proteomics - B. Canas 2006

      Article Essential MS proteomics workflows,+quant +PTMs

    2. Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology - Jürgen Cox, Matthias Mann 2011

      Article Essential review on MS proteomics, PTMs, interaction, quantitative….

    3. Quantitative Plant Proteomics - Laurence V. Bindschedler, Rainer Cramer 2011

      Article Essential

    4. Quantitative Mass Spectrometry-Based Proteomics: An Overview - Miroslav Nikolov, Carla Schmidt, Henning Urlaub 2012

      Chapter Essential quantitative proteomics, good descriptions/ definitions

    5. Mass Spectrometry for Proteomics - Xuemei Han, Aaron Aslanian, John R Yates 2008

      Article Recommended

    6. Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications - Boris Macek, Matthias Mann, Jesper V. Olsen 2009

      Article Essential EGFR activiation by lysophosphatidic acid LPA

    7. Technologies and Challenges in Large-Scale Phosphoproteomics - Kasper Engholm-Keller, Martin R. Larsen 2013

      Article Essential

    8. Advances in Quantitative Phosphoproteomics - Carol L. Nilsson 2012

      Article Recommended Phosphoproteomics workflow and examples

  17. Quantitative Proteomics and Phosphoproteomics (ctd): 10 items
    1. Two-Hybrid Technologies in Proteomics Research - Bernhard Suter, Saranya Kittanakom, Igor Stagljar 2008

      Article Recommended

    2. Studying Protein Complexes by the Yeast Two-Hybrid System - Seesandra V. Rajagopala, Patricia Sikorski, J. Harry Caufield, Andrey Tovchigrechko 2012

      Article Recommended

    3. Interactive Proteomics Research Technologies: Recent Applications and Advances - Julia Petschnigg, Jamie Snider, Igor Stagljar 2011

      Article Recommended

    4. CWC22 Connects Pre-mRNA Splicing and Exon Junction Complex Assembly - Anna-Lena Steckelberg, Volker Boehm, Agnieszka M. Gromadzka, Niels H. Gehring 2012

      Article Recommended

  18. Protein-protein Interaction and Recapitulation: 6 items
    1. Studying Protein Complexes by the Yeast Two-Hybrid System - Seesandra V. Rajagopala, Patricia Sikorski, J. Harry Caufield, Andrey Tovchigrechko 2012

      Article Recommended

    2. Interactive Proteomics Research Technologies: Recent Applications and Advances - Julia Petschnigg, Jamie Snider, Igor Stagljar 2011

      Article Recommended

    3. CWC22 Connects Pre-mRNA Splicing and Exon Junction Complex Assembly - Anna-Lena Steckelberg, Volker Boehm, Agnieszka M. Gromadzka, Niels H. Gehring 2012

      Article Recommended

    4. Two-Hybrid Technologies in Proteomics Research - Bernhard Suter, Saranya Kittanakom, Igor Stagljar 2008

      Article Recommended

  19. Proteomics and Cell Cycle: 16 items
    1. Generating and Navigating Proteome Maps Using Mass Spectrometry - Christian H. Ahrens, Erich Brunner, Et al 2010

      Article Recommended

    2. Is Proteomics the New Genomics? - Jürgen Cox, Matthias Mann 2007

      Article Recommended

    3. Reviews:

    4. The Biological Impact of Mass-Spectrometry-Based Proteomics - Benjamin F. Cravatt, Gabriel M. Simon, John R. Yates III 2007

      Article Recommended

    5. Research Papers:

    6. A Mammalian Organelle Map by Protein Correlation Profiling - Leonard J. Foster, Carmen L. de Hoog 2006

      Article Recommended

    7. Applications of Targeted Proteomics in Systems Biology and Translational Medicine - H. Alexander Ebhardt, Alex Root, Chris Sander, Ruedi Aebersold 2015

      Article Recommended

  20. Proteomics in Discovery of Cell Cycle Events: 7 items
    1. Mass Spectrometry-Based Proteomics - Ruedi Aebersold, Matthias Mann 2003

      Article Recommended

    2. Is Proteomics the New Genomics? - Jürgen Cox, Matthias Mann 2007

      Article Recommended

    3. The Biological Impact of Mass-Spectrometry-Based Proteomics - Benjamin F. Cravatt, Gabriel M. Simon, John R. Yates III 2007

      Article Recommended

    4. The ABC's (And XYZ's) of Peptide Sequencing - Hanno Steen, Matthias Mann 2004

      Article Recommended

All rights reserved ©