Gribskov:Interesting Papers

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The next journal club will be Tuesday, 10/27/2009 at 1:30 PM, G-336


Contents

Next Journal Club Paper

2009/11/24

Presenter: Aditi Gupta

Topic: Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines. Xu, X., Ji, Y. & Stormo, G. D. pdf

Last Journal Club Paper

  • Michael 10/13/2009

Netlogo and FramStick

Schedule 2009

Every other Tuesday at 1:30pm

Upcoming:

  • Aditi Gupta
  • James Hengenius

To be scheduled:

  • Greg Ziegler
  • Doug Yatcilla
  • Reazur Rahman
  • Kejie Li
  • Qiong Wu
  • Prasad Siddavatam
  • Michael Gribskov

Journals

These are a few of the leading journals you probably should be reading

Genetics Computational Biology Genomics / Proteomics


Proteins Evolution General Focus

Interesting Papers

If you use one of the articles below, please remove it from this section and add it as the current paper, above. After your presentation, move it to the Past Journal Club Papers section

Combining RNA interference and kinase inhibitors against cell signalling components involved in cancer
Title and Link Authors Submitted by
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert Aditi 28 July, 2009
Evolution and Functions of Long Noncoding RNAs Chris P. Ponting, Peter L. Oliver and Wolf Reik Aditi 7 May, 2009
Discovery of biological networks from diverse functional genomic data. Genome Biol. 2005;6(13). Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Prasad 9:26, 26 March 2008 (EDT)
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics. 2005 Nov 1;21(21):4026-32. Markowetz F, Bloch J, Spang R. Prasad 9:21, 26 March 2008 (EDT)
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 34, 166 - 176 (2003). Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Prasad 9:15, 26 March 2008 (EDT)
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics, pp. 1914-1927, 2004. Chen HC, Lee HC, Lin TY, Li WH, Chen BS. Prasad 9:02, 26 March 2008 (EDT)
Network Legos Building Blocks of Cellular Wiring Diagrams Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), volume 4453 of Lecture Notes in Computer Science, pp. 47-61, 2007. T. M. Murali and Corban G. Rivera. Prasad 5:52, 14 March 2008 (EDT)
Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins. 2000 Nov 15;41(3):415-27. Uversky VN, Gillespie JR, Fink AL. Gribskov 10:52, 3 August 2006 (EDT)
Toward automatic reconstruction of a highly resolved tree of life. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Gribskov 10:19, 3 August 2006 (EDT)
Proteome survey reveals modularity of the yeast cell machinery. Gavin A.C. et alia Gribskov 10:13, 3 August 2006 (EDT)
Codon usage domains over bacterial chromosomes. Bailly-Bechet M, Danchin A, Iqbal M, Marsili M, Vergassola M. Gribskov 10:06, 3 August 2006 (EDT)
Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nakamura Y,Itoh T,Matsuda H, Gojobori T. Gribskov 09:34, 3 August 2006 (EDT)
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Tettlin, H. et alia (Gribskov 09:28, 3 August 2006 (EDT))


Analysis and prediction of functional sub-types from protein sequence alignments. Hannenhalli SS, Russell RB. Gribskov 09:16, 3 August 2006 (EDT)


An online literature mining tool for protein phosphorylation unknown
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome unknown
Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family unknown
Considerations in the identification of functional RNA structural elements in genomic alignments Tomas Babak , Benjamin J Blencowe and Timothy R Hughes likejie 12:51, 9 Feb 2007 (EDT)
Deletion of Ultraconserved Elements Yields Viable Mice Nadav Ahituv1, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A. Pennacchio1, Edward M. Rubin rahmanr 11:20, 14 Nov 2007 (EDT)


Past Journal Club Papers

  • Michael 10/13/2009

Netlogo and FramStick


  • Prasad 10/06/2009

Shuangge Ma , and Michael R. Kosorok

Identification of differential gene pathways with principal component analysis

Bioinformatics Advance Access published on April 1, 2009, DOI 10.1093/bioinformatics/btp085. Bioinformatics 25: 882-889.

  • Qiong Wu 2009/09/15

Brewster C, Jupp S, Luciano J, Shotton D, Stevens RD, Zhang Z. Issues in learning an ontology from text. BMC Bioinformatics. 2009 May 6;10 Suppl 5:S1.


  • Kejie Li 2009/09/01

Topic: General introduction of GPU programming CUDA from Nvidia


  • Reazur Rahman 2009/06/02


  • Doug Yatcilla - April 14 2009

In addition to the paper below, the general topic of how to make your life easier using the department's computers will be discussed.
Bianca Schroeder and Garth A. Gibson. Disk failures in the real world: What does an mttf of 1,000,000 hours mean to you? In Proceedings of the 5th USENIX Conference on File and Storage Technologies (FAST), February 2007.


  • Greg Ziegler 2009/04/07


  • 10 Feb - Qiong Wu

Genetic network inference as a series of discrimination tasks.
Kimura, S., Nakayama, S. and Hatakeyama, M. Bioinformatics. 2009 Feb 5. [Epub ahead of print]
doi:10.1093/bioinformatics/btp072

  • 27 Jan - Aditi

Clustering protein sequence and structure space with infinite Gaussian mixture models Dubey A, Hwang S, Rangel C, Rasmussen CE, Ghahramani Z, Wild DL

Pac Symp Biocomput. 2004:399-410 [1]

  • 12 Dec - Gribskov

Artificial ants deposit pheromone to search for regulatory DNA elements Yunlong Liu and Hiroki Yokota, BMC Genomics 2006, 7:221 doi:10.1186/1471-2164-7-221

  • 14 Nov, 2008 - Kejie Li

The Ascent of the Abundant: How Mutational Networks Constrain Evolution.Cowperthwaite MC, Economo EP, Harcombe WR, Miller EL, Meyers LA 2008 PLoS Computational Biology
pdf_link_here


  • 31 Oct, 2008 Prasad

Igor F, et al. (2008) Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci. 105:4323- 4328.



  • 3 oct, 2008

Stumpf M, et al. (2008) Estimating the size of the human interactome. Proc Natl Acad Sci. 105:6959-6964.

Some commentary on the paper:

  • 19 June, 2008

Title: Colored Petri net modeling and simulation of signal transduction pathways. NBCI abstract with Elsevier link.

  • 10th June,2008

Title: Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNS predicts alternative translation initiation sites LINK

  • 20th May, 2008

Title: The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication Link

Supplementary material HERE

  • 17th April, 2008 (Aditi)

Title: An Information Theoretic Exploratory Method for Learning Patterns of Conditional Gene Coexpression from Microarray Data PDF_link

  • 3rd April, 2008 (Kejie Li)

Topic: eQED: an efficient method for interpreting eQTL associations using protein networks PDF_link

Supplementary material HERE

  • 20 March, 2008 (Prasad Siddavatam)

Topic: Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12

  • 28 March, 2007 (Reazur Rahman)

Topic: Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design Paper

  • 21 February, 2007

Paper 1, [2]

Paper 2, [3]

  • 7 February, 2007

FANMOD: a tool for fast network motif detection, Sebastian Wernicke and Florian Rasche.

MAVisto: a tool for the exploration of network otifs, Falk Schreiber and Henning Schwöbbermeyer.

  • 24 January, 2007

Chasing a cellular fountain of youth, Ken Howard Wilan, Christopher Thomas Scott & Stephan Herrera

  • 10 January,2007

Novel unsupervised feature filtering of biological data. Varshavsky R, Gottlieb A, Linial M, Horn D.


  • 6 December 2006 - Emre Demirors

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements, Marie Dewannieux, Francis Harper, Aurélien Richaud, Claire Letzelter, David Ribet, Gérard Pierron, and Thierry Heidmann

  • 8 November 2006 - Damion Junk

Toward Automatic Reconstruction of a Highly Resolved Tree of Life, Francesca D. Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J. Creevey, Berend Snel, Peer Bork

  • Nov 2006 - Hao Jiang

Classifying Kinase Inhibitor-Likeness by Using Machine-Learning Methods. Hans Briem, Dr. *, Judith Günther, Dr.

  • 27 September 2006 - Gribskov

Dehydron: A Structurally Encoded Signal for Protein Interaction., Ariel Fernandez and Ridgway Scott

  • 13 September 2006 - Prasad

Phylogeny-independent detection of functional residues., Pazos F, Rausell A, Valencia A.

  • 12 July 2006 - Kejie Li
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots. link
  • 28 June 2006 - Greg Ziegler
    • Conformation Mining: an algorithm for finding biologically relevant conformations link
  • 12 Jan 2006 - Kejie Li:
    • Molecular modeling of phosphorylation sites in proteins using a database of local structure segments, [5]
  • 14 Dec 2005 - Emre Demirors:
    • Identification of clustered microRNAs using an ab initio prediction method., [6]
  • 30 Nov 2005 - Damion Junk:
    • Do universal codon-usage patterns minimize the effects of mutation and translation error?, Marquez, Smit, Knight [7]
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