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ASSEMBLY

Genome-wide detection of segmental duplications and potential
assembly errors in the human genome sequence
J Cheung, Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui,and Stephen W Scherer.
Genome Biology 2003, 4:R25.

Consed: A Graphical Tool for Sequence Finishing
David Gordon, Chris Abajian, and Phil Green
http://www.genome.org/cgi/content/abstract/8/3/195http://www.genome.org/cgi/content/abstract/8/3/195

Large-Scale Copy Number Polymorphism in the Human Genome
Jonathan Sebat,1 B. Lakshmi,1 Jennifer Troge,1 Joan Alexander,1 Janet Young,2 Pär Lundin,3 Susanne Månér,3 Hillary Massa,2 Megan Walker,2 Maoyen Chi,1 Nicholas Navin,1 Robert Lucito,1 John Healy,1 James Hicks,1 Kenny Ye,4 Andrew Reiner,1 T. Conrad Gilliam,5 Barbara Trask,2 Nick Patterson,6 Anders Zetterberg,3 Michael Wigler1* 
Science 23 July 2004:
Vol. 305. no. 5683, pp. 525 - 528
DOI: 10.1126/science.1098918
http://www.sciencemag.org/cgi/content/abstract/305/5683/525

Proof and evolutionary analysis of
ancient genome duplication in the yeast Saccharomyces cerevisiae
Manolis Kellis, Bruce W. Birren, & Eric S. Lander
Nature 2004
http://web.mit.edu/manoli/www/publications/Kellis_Nature_04.pdf

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
Kelly A. Frazer1,6, Laura Elnitski2,3, Deanna M. Church4, Inna Dubchak5 and Ross C. Hardison3 
http://www.genome.org/cgi/content/abstract/13/1/1

PCAP: A Whole-Genome Assembly Program
Xiaoqiu Huang1,4, Jianmin Wang1, Srinivas Aluru2, Shiaw-Pyng Yang3 and LaDeana Hillier
http://www.genome.org/cgi/content/abstract/13/9/2164

De Novo Repeat Classification and Fragment Assembly
Paul A. Pevzner1, Haixu Tang1 and Glenn Tesler
http://www.genome.org/cgi/content/abstract/14/9/1786

GENE FINDING

Christine G Elsik, Aaron J Mackey, Justin T Reese, Natalia V Milshina, David S Roos, George M Weinstock (2007), "Creating a honey bee consensus gene set", Genome Biology, 8:R13

Keith Knapp and Yi-Ping Phoebe Chen (2007), "An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy", Nucleic Acids Research, 35:317-324.

Lutz Krause, Alice C. McHardy, Tim W. Nattkemper, Alfred Pühler, Jens Stoye Folker Meyer (2007), "GISMO -- gene identification using a support vector machine for ORF classification", Nucleic Acids Research, 35(2):540-549.

Scott Mann, Jinyan Li, Yi-Ping Phoebe Chen (2007), "A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts", Nucleic Acids Research, 35(2):e12.

Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A M Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair R R Forrest, Wynand B Alkema, Sin Lam Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki (2006), "Genome-wide analysis of mammalian promoter architecture and evolution", Nature Genetics, 38:626-635. 
Li-Wei Chang, Rakesh Nagarajan, Jeffrey A. Magee, Jeffrey Milbrandt, and Gary D. Stormo (2006), "A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles", Genome Research, 16(3):405-413. 

Sara J. Cooper, Nathan D. Trinklein, Elizabeth D. Anton, Loan Nguyen, and Richard M. Myers (2006), "Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome", Genome Research, 16(1):1-10. 

Laura Elnitski, Victor X. Jin, Peggy J. Farnham, and Steven J.M. Jones (2006), "Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques", Genome Research, 16(12):1455-1464. 

Ekaterina O Ermakova, Ramil N Nurtdinov, Mikhail S Gelfand (2006), "Fast rate of evolution in alternatively spliced coding regions of mammalian genes", BMC Genomics, 7:84. 

JJ Gordon, MW Towsey, JM Hogan, SA Mathews, P Timms (2006), "Improved prediction of bacterial transcription start sites", Bioinformatics, 22(2):142-148. 

Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, and Jens Stoye (2006), "Finding novel genes in bacterial communities isolated from the environment", Bioinformatics, 22:e281-e289. 

Nan Li, Martin Tompa (2006), "Analysis of computational approaches for motif discovery", Algorithms for Molecular Biology, 1:8. 

Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder, and Mark Gerstein (2006), "Predicting essential genes in fungal genomes", Genome Research, 16(9):1126-1135. 

Sören Sonnenburg, Alexander Zien, and Gunnar Rätsch (2006), "ARTS: accurate recognition of transcription starts in human", Bioinformatics, 22:e472-e480. 

Maike Tech, Peter Meinicke (2006), "An unsupervised classification scheme for improving predictions of prokaryotic TIS", BMC Bioinformatics, 7:121. 

Marijke J van Baren, Michael R Brent (2006), "Iterative gene prediction and pseudogene removal improves genome annotation", Genome Research, 16(5):678-685.