Schedule of Easy Chair meetings, Summer, 2013

DATE	LEADER	TOPIC	NOTES
Aug 6	Dr. Ruth Green, and Curtis Klumas	RNA Processing: what might we learn from RNA-Seq data?	Paper 1, Paper 2
June 25	Curtis Klumas	Comparison of De Novo and Reference-based RNA-seq Assemblers and Aligners.	A project done for problems solving in GBCB
June 4	Mahdi Nabiyouni	Dindel: accurate indel calls from short-read data.	Notes
May 21	Delasa Aghamirzaie	Modeling and Identifying Regulatory Modules in (Glycine max) Soybean Time Series Gene Expression Data using Bayesian Networks.	Notes

Interesting papers ^{Updated 06/2013} [Top]

• Rogers MF, Thomas J, Reddy AS, Ben-Hur A.
  SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data
  Genome Biol. 2012 Jan 31;13(1):R4
  

• Soneson C, Delorenzi M.
  A comparison of methods for differential expression analysis of RNA-seq data.
  BMC Bioinformatics. 2013 Mar 9;14:91
  

• Sokolov A, Funk C, Graim K, Verspoor K, Ben-Hur A.
  Combining heterogeneous data sources for accurate functional annotation of proteins
  BMC Bioinformatics. 2013;14 Suppl 3:S10.
  

• Yang X, Zhang H, Li L.
  Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis
  Plant J. 2012 May;70(3):421-31.
  

• Gabriele Sales, Enrica Calura, Paolo Martini and Chiara Romualdi et al.
  Graphite Web: web tool for gene set analysis exploiting pathway topology
  Nucleic Acids Research, 2013, 1 - 9.
  

• Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, et al.
  Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
  Plant Cell. 2012 Sep;24(9):3530-57.
  

• Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S.
  PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species.
  Plant Cell. 2011 Mar;23(3):895-910.
  

• Braun P, Carvunis AR, Charloteaux B, Dreze M, Ecker JR, et.el
  Evidence for network evolution in an Arabidopsis interactome map.
  Science. 2011 Jul 29;333(6042):601-7.
  

• Kim-Anh Le Cao1, Ignacio Gonzalez, and Sebastien Dejean
  integrOmics: an R package to unravel relationships between two omics datasets
  Bioinformatics, Volume 25, Issue 21Pp. 2855-2856.
  

• Marek Mutwil, Bjorn Usadel, Moritz Schutte, Ann Loraine, Oliver Ebenhoh, and Staffan Persson
  Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm
  Plant Physiology January 2010 vol. 152 no. 1 29-43.
  

• Naren Sundaravaradan, K. S. M. Tozammel Hossain, Vandana Sreedharan, Douglas J. Slotta, John Paul C. Vergara, Lenwood S. Heath, Naren Ramakrishnan
  Extracting temporarl signatures for comprehending systems biology models
  KDD 2010: 453-462
  

• Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ. et al.
  Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
  Plant Cell. 2012 Sep;24(9):3530-57.