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alexl's library [80 articles]

Recent papers added to alexl's library.
  • Analysis of singleton ORFans in fully sequenced microbial genomes.
    Proteins, Vol. 53, No. 2. (1 November 2003), pp. 241-251.
    by N Siew, D Fischer
    posted to orfs by alexl on 2008-07-11 19:01:12 as **
  • Finding novel genes in bacterial communities isolated from the environment.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by L Krause, NN Diaz, D Bartels, RA Edwards, A Pühler, F Rohwer, F Meyer, J Stoye
    posted to metagenomes by alexl on 2008-06-17 22:25:39 as ** along with 1 person and 1 group azazello MBLAB
  • Heuristic approach to deriving models for gene finding.
    Nucleic Acids Res, Vol. 27, No. 19. (1 October 1999), pp. 3911-3920.
    by J Besemer, M Borodovsky
    posted to metagenomes by alexl on 2008-06-17 22:13:51 as ** along with 4 people and 2 groups GustavoLacerda azazello indigoviolet wenhan MBLAB EisenLab
  • Binning sequences using very sparse labels within a metagenome
    BMC Bioinformatics, Vol. 9 (28 April 2008), 215.
    by Chon-Kit K Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang
    posted to metagenomes by alexl on 2008-06-17 21:17:08 as ** along with 1 person and 1 group mjetten microbiology_nijmegen
  • Metagenomics: Read length matters
    Appl. Environ. Microbiol. (11 January 2008), AEM.02181-07.
    by Eric K Wommack, Jaysheel Bhavsar, Jacques Ravel
    posted to metagenomes by alexl on 2008-06-17 21:09:36 as ** along with 8 people and 2 groups bluto alexisfjdufresne jmeppley azazello kinestetika Thaverkamp skato_toyaku rvgomes Microbial-Ecology microbiology_nijmegen
  • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
    Nat Methods (29 April 2007)
    by Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C C Kyrpides
    posted to metagenomes by alexl on 2008-06-17 21:06:06 as ** along with 9 people and 5 groups jlgreen mjetten carlk Yanno oamg jmeppley bluto azazello GustavoLacerda iSEEM Green Lab microbiology_nijmegen Glimcher_Lab Bioinformatics
  • MEGAN analysis of metagenomic data.
    Genome Res, Vol. 17, No. 3. (March 2007), pp. 377-386.
    by DH Huson, AF Auch, J Qi, SC Schuster
    posted to metagenomes by alexl on 2008-06-17 21:01:46 as ** along with 4 people and 2 groups mjetten carpi azazello wenhan microbiology_nijmegen anammox
  • MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    Nucleic Acids Research, Vol. 34, No. 19. (November 2006), pp. 5623-5630.
    by Noguchi, Hideki, Park, Jungho, Takagi, Toshihisa
    posted to metagenomes by alexl on 2008-06-17 19:36:57 as ** along with 2 people mcox jmeppley
  • Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Shibu Yooseph, Weizhong Li, Granger Sutton
    posted to metagenomes by alexl on 2008-06-17 19:27:10 as ** along with 1 person neils
  • Gene prediction in metagenomic fragments: a large scale machine learning approach
    BMC Bioinformatics, Vol. 9 (28 April 2008), 217.
    by Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
    posted to metagenomes by alexl on 2008-06-17 19:26:18 as ** along with 2 people and 3 groups mjetten stajich microbiology_nijmegen anammox Berkeley Mycology
  • IMG/M: a data management and analysis system for metagenomes.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by VM Markowitz, NN Ivanova, E Szeto, K Palaniappan, K Chu, D Dalevi, IM Chen, Y Grechkin, I Dubchak, I Anderson, A Lykidis, K Mavromatis, P Hugenholtz, NC Kyrpides
    posted to metagenomes by alexl on 2008-06-17 19:25:25 as ** along with 3 people jyuh jmeppley Thaverkamp
  • Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques
    Distributed, High-Performance and Grid Computing in Computational Biology (2007), pp. 99-109.
    by Nigel Mccoy, Shaun Mahony, Aaron Golden
    posted to metagenomes by alexl on 2008-06-17 19:24:07 as **
  • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Mario Stanke, Oliver Schoffmann, Burkhard Morgenstern, Stephan Waack
    posted to gene_finding by alexl on 2008-06-11 16:25:57 as ** along with 3 people and 1 group azazello wenhan GustavoLacerda MBLAB
  • AUGUSTUS: ab initio prediction of alternative transcripts.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by M Stanke, O Keller, I Gunduz, A Hayes, S Waack, B Morgenstern
    posted to gene_finding by alexl on 2008-06-11 16:23:46 as ** along with 1 person wenhan
  • Automatic generation of gene finders for eukaryotic species
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Kasper Munch, Anders Krogh
    posted to gene_finding by alexl on 2008-06-10 19:24:55 as ** along with 2 people and 1 group kaspermunch GustavoLacerda Bioinformatics
  • Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
    Bioinformatics (Oxford, England), Vol. 20, No. 7. (1 May 2004), pp. 1157-1169.
    by V Brendel, L Xing, W Zhu
    posted to est_dna by alexl on 2008-06-08 21:35:19 as **
  • SPA: a probabilistic algorithm for spliced alignment.
    PLoS genetics, Vol. 2, No. 4. (April 2006)
    by E van Nimwegen, N Paul, R Sheridan, M Zavolan
    posted to est_dna by alexl on 2008-06-08 21:00:19 as **
  • Gene prediction: compare and CONTRAST
    Genome Biology, Vol. 8, No. 12. (2007)
    by Paul Flicek
    posted to gene_finding by alexl on 2008-06-06 15:58:06 as ** along with 4 people Borelli wenhan dewaldron yoanjacquemin
  • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    Nat Rev Genet, Vol. 9, No. 1. (January 2008), pp. 62-73.
    by Michael R Brent
    posted to gene_finding by alexl on 2008-06-06 15:22:22 as ** along with 7 people GustavoLacerda jyuh dchughes jermth wenhan renatomilani drbal
  • Re-prediction of protein-coding genes in the genome of Amsacta moorei entomopoxvirus.
    Journal of virological methods, Vol. 146, No. 1-2. (December 2007), pp. 389-392.
    by FB Guo, XJ Yu
    posted to viral-gene by alexl on 2008-05-26 00:30:01 as **
  • Conrad: Gene prediction using conditional random fields
    Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1389-1398.
    by David Decaprio, Jade P Vinson, Matthew D Pearson, Philip Montgomery, Matthew Doherty, James E Galagan
    posted to gene_finding by alexl on 2008-05-26 00:22:27 as ** along with 2 people and 1 group indigoviolet wenhan EisenLab
  • Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
    Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1362-1377.
    by Nitin Gupta, Stephen Tanner, Navdeep Jaitly, Joshua N Adkins, Mary Lipton, Robert Edwards, Margaret Romine, Andrei Osterman, Vineet Bafna, Richard D Smith, Pavel A Pevzner
    posted to mcmc-gene by alexl on 2008-05-26 00:20:55 as ** along with 2 people nitiniitk nedwards
  • Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54.
    by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira
    posted to gene_finding by alexl on 2008-05-23 20:44:48 as ** along with 4 people and 2 groups dpollard wenhan zwang acarbo Bioinformatics EisenLab
  • An empirical analysis of training protocols for probabilistic gene finders.
    BMC bioinformatics, Vol. 5 (2004)
    by WH Majoros, SL Salzberg
    posted to gene_finding by alexl on 2008-05-23 17:54:12 as **
  • When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 30, No. 6. (June 2008), pp. 601-605.
    by SW Roy, M Irimia
    posted to splicing by alexl on 2008-05-23 00:38:56 as **
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2878-2879.
    by WH Majoros, M Pertea, SL Salzberg
    posted to gene_finding by alexl on 2008-05-22 23:53:48 as read along with 2 people and 1 group indigoviolet GustavoLacerda EisenLab
  • Efficient decoding algorithms for generalized hidden Markov model gene finders.
    BMC Bioinformatics, Vol. 6 (2005)
    by WH Majoros, M Pertea, AL Delcher, SL Salzberg
    posted to gene_finding by alexl on 2008-05-22 22:36:02 as read along with 2 people nedwards mdimon
  • Gene finding in novel genomes.
    BMC Bioinformatics, Vol. 5 (14 May 2004)
    by I Korf
    posted to gene_finding by alexl on 2008-05-22 18:52:43 as read along with 5 people and 1 group LeightonP indigoviolet wenhan GustavoLacerda cmzmasek EisenLab
  • notes The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.
    by F Martin, A Aerts, D Ahren, A Brun, EGJ Danchin, F Duchaussoy, J Gibon, A Kohler, E Lindquist, V Pereda, A Salamov, HJ Shapiro, J Wuyts, D Blaudez, M Buee, P Brokstein, B Canback, D Cohen, PE Courty, PM Coutinho, C Delaruelle, JC Detter, A Deveau, S Difazio, S Duplessis, L Fraissinet-Tachet, E Lucic, P Frey-Klett, C Fourrey, I Feussner, G Gay, J Grimwood, PJ Hoegger, P Jain, S Kilaru, J Labbe, YC Lin, V Legue, F Le Tacon, R Marmeisse, D Melayah, B Montanini, M Muratet, U Nehls, H Niculita-Hirzel, Oudot-Le MP Secq, M Peter, H Quesneville, B Rajashekar, M Reich, N Rouhier, J Schmutz, T Yin, M Chalot, B Henrissat, U Kues, S Lucas, Y Van de Peer, GK Podila, A Polle, PJ Pukkila, PM Richardson, P Rouze, IR Sanders, JE Stajich, A Tunlid, G Tuskan, IV Grigoriev
    posted to fungi by alexl on 2008-04-18 17:39:05 as ** along with 6 people manzanita jamselem neils biomcgary cmzmasek urgi
  • Gene prediction with a hidden Markov model and a new intron submodel.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by M Stanke, S Waack
    posted to branch_point by alexl on 2008-03-08 03:15:45 as ** along with 3 people and 2 groups indigoviolet stajich wenhan EisenLab Berkeley Mycology
  • A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.
    Science, Vol. 307, No. 5706. (7 January 2005), pp. 82-86.
    by N Hall, M Karras, JD Raine, JM Carlton, TW Kooij, M Berriman, L Florens, CS Janssen, A Pain, GK Christophides, K James, K Rutherford, B Harris, D Harris, C Churcher, MA Quail, D Ormond, J Doggett, HE Trueman, J Mendoza, SL Bidwell, MA Rajandream, DJ Carucci, JR Yates, FC Kafatos, CJ Janse, B Barrell, CM Turner, AP Waters, RE Sinden
    posted to complete_genome by alexl on 2008-02-26 22:05:47 as ** along with 4 people maxell Sharpshoot becarmson mdimon
  • Curation of the Plasmodium falciparum genome
    Trends in Parasitology, Vol. 20, No. 12. (December 2004), pp. 548-552.
    by Andrew E Berry, Malcolm J Gardner, Gert-Jan Caspers, David S Roos, Matthew Berriman
    posted to complete_genome by alexl on 2008-01-03 23:32:36 as ** along with 1 person shung
  • Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi.
    Nature, Vol. 414, No. 6862. (22 November 2001), pp. 450-453.
    by MD Katinka, S Duprat, E Cornillot, G Méténier, F Thomarat, G Prensier, V Barbe, E Peyretaillade, P Brottier, P Wincker, F Delbac, H El Alaoui, P Peyret, W Saurin, M Gouy, J Weissenbach, CP Vivarès
    posted to complete_genome by alexl on 2007-12-12 01:42:28 as ** along with 1 person raiyar
  • Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins
    Fungal Genetics and Biology, Vol. 43, No. 5. (May 2006), pp. 343-356.
    by Amber V Wymelenberg, Patrick Minges, Grzegorz Sabat, Diego Martinez, Andrea Aerts, Asaf Salamov, Igor Grigoriev, Harris Shapiro, Nik Putnam, Paula Belinky, Carlos Dosoretz, Jill Gaskell, Phil Kersten, Dan Cullen
    posted to fungi by alexl on 2007-10-16 14:22:40 as read along with 1 person GustavoLacerda
  • Hidden Markov models for speech recognition
    by XD Huang, Y Ariki, MA Jack
    posted to math_hmm by alexl on 2007-10-15 18:26:01 as **
  • Wobble Splicing Reveals the Role of the Branch Point Sequence-to-NAGNAG Region in 3' Tandem Splice Site Selection
    Mol. Cell. Biol., Vol. 27, No. 16. (15 August 2007), pp. 5835-5848.
    by Kuo-Wang Tsai, Woan-Yuh Tarn, Wen-Chang Lin
    posted to branch_point by alexl on 2007-10-12 23:25:18 as **
  • Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
    Nat Biotech, Vol. 22, No. 6. (June 2004), pp. 695-700.
    by Diego Martinez, Luis F Larrondo, Nik Putnam, Maarten D Gelpke, Katherine Huang, Jarrod Chapman, Kevin G Helfenbein, Preethi Ramaiya, Chris J Detter, Frank Larimer, Pedro M Coutinho, Bernard Henrissat, Randy Berka, Dan Cullen, Daniel Rokhsar
    posted to fungi by alexl on 2007-10-10 19:20:38 as read
  • The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans
    Science, Vol. 307, No. 5713. (25 February 2005), pp. 1321-1324.
    by Brendan J Loftus, Eula Fung, Paola Roncaglia, Don Rowley, Paolo Amedeo, Dan Bruno, Jessica Vamathevan, Molly Miranda, Iain J Anderson, James A Fraser, Jonathan E Allen, Ian E Bosdet, Michael R Brent, Readman Chiu, Tamara L Doering, Maureen J Donlin, Cletus A D'Souza, Deborah S Fox, Viktoriya Grinberg, Jianmin Fu, Marilyn Fukushima, Brian J Haas, James C Huang, Guilhem Janbon, Steven J Jones, Hean L Koo, Martin I Krzywinski, June K Kwon-Chung, Klaus B Lengeler, Rama Maiti, Marco A Marra, Robert E Marra, Carrie A Mathewson, Thomas G Mitchell, Mihaela Pertea, Florenta R Riggs, Steven L Salzberg, Jacqueline E Schein, Alla Shvartsbeyn, Heesun Shin, Martin Shumway, Charles A Specht, Bernard B Suh, Aaron Tenney, Terry R Utterback, Brian L Wickes, Jennifer R Wortman, Natasja H Wye, James W Kronstad, Jennifer K Lodge, Joseph Heitman, Ronald W Davis, Claire M Fraser, Richard W Hyman
    posted to fungi by alexl on 2007-10-10 19:04:47 as ** along with 5 people and 3 groups labedan Cortel jwortman stajich dalloliogm Web2 splicing yeast
  • The genome sequence of the rice blast fungus Magnaporthe grisea
    Nature, Vol. 434, No. 7036., pp. 980-986.
    by Ralph A Dean, Nicholas J Talbot, Daniel J Ebbole, Mark L Farman, Thomas K Mitchell, Marc J Orbach, Michael Thon, Resham Kulkarni, Jin-Rong Xu, Huaqin Pan, Nick D Read, Yong-Hwan Lee, Ignazio Carbone, Doug Brown, Yeon Y Oh, Nicole Donofrio, Jun S Jeong, Darren M Soanes, Slavica Djonovic, Elena Kolomiets, Cathryn Rehmeyer, Weixi Li, Michael Harding, Soonok Kim, Marc-Henri Lebrun, Heidi Bohnert, Sean Coughlan, Jonathan Butler, Sarah Calvo, Li-Jun Ma, Robert Nicol, Seth Purcell, Chad Nusbaum, James E Galagan, Bruce W Birren
    posted to fungi by alexl on 2007-10-10 18:51:12 as ** along with 2 people and 1 group jwortman stajich Berkeley Mycology
  • The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.
    Science, Vol. 317, No. 5843. (7 September 2007), pp. 1400-1402.
    by CA Cuomo, U Güldener, JR Xu, F Trail, BG Turgeon, A Di Pietro, JD Walton, LJ Ma, SE Baker, M Rep, G Adam, J Antoniw, T Baldwin, S Calvo, YL Chang, D Decaprio, LR Gale, S Gnerre, RS Goswami, K Hammond-Kosack, LJ Harris, K Hilburn, JC Kennell, S Kroken, JK Magnuson, G Mannhaupt, E Mauceli, HW Mewes, R Mitterbauer, G Muehlbauer, M Münsterkötter, D Nelson, K O'donnell, T Ouellet, W Qi, H Quesneville, MI Roncero, KY Seong, IV Tetko, M Urban, C Waalwijk, TJ Ward, J Yao, BW Birren, HC Kistler
    posted to fungi by alexl on 2007-10-10 18:37:41 as ** along with 1 person jamselem
  • Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    Nature, Vol. 438, No. 7071., pp. 1105-1115.
    by James E Galagan, Sarah E Calvo, Christina Cuomo, Li-Jun Ma, Jennifer R Wortman, Serafim Batzoglou, Su-In Lee, Meray Baştürkmen, Christina C Spevak, John Clutterbuck, Vladimir Kapitonov, Jerzy Jurka, Claudio Scazzocchio, Mark Farman, Jonathan Butler, Seth Purcell, Steve Harris, Gerhard H Braus, Oliver Draht, Silke Busch, Christophe D'Enfert, Christiane Bouchier, Gustavo H Goldman, Deborah Bell-Pedersen, Sam Griffiths-Jones, John H Doonan, Jaehyuk Yu, Kay Vienken, Arnab Pain, Michael Freitag, Eric U Selker, David B Archer, Miguel, Berl R Oakley, Michelle Momany, Toshihiro Tanaka, Toshitaka Kumagai, Kiyoshi Asai, Masayuki Machida, William C Nierman, David W Denning, Mark Caddick, Michael Hynes, Mathieu Paoletti, Reinhard Fischer, Bruce Miller, Paul Dyer, Matthew S Sachs, Stephen A Osmani, Bruce W Birren
    posted to fungi by alexl on 2007-10-10 18:30:46 as ** along with 1 person radek
  • The genome sequence of the filamentous fungus Neurospora crassa.
    Nature, Vol. 422, No. 6934. (24 April 2003), pp. 859-868.
    by JE Galagan, SE Calvo, KA Borkovich, EU Selker, ND Read, D Jaffe, W FitzHugh, LJ Ma, S Smirnov, S Purcell, B Rehman, T Elkins, R Engels, S Wang, CB Nielsen, J Butler, M Endrizzi, D Qui, P Ianakiev, D Bell-Pedersen, MA Nelson, M Werner-Washburne, CP Selitrennikoff, JA Kinsey, EL Braun, A Zelter, U Schulte, GO Kothe, G Jedd, W Mewes, C Staben, E Marcotte, D Greenberg, A Roy, K Foley, J Naylor, N Stange-Thomann, R Barrett, S Gnerre, M Kamal, M Kamvysselis, E Mauceli, C Bielke, S Rudd, D Frishman, S Krystofova, C Rasmussen, RL Metzenberg, DD Perkins, S Kroken, C Cogoni, G Macino, D Catcheside, W Li, RJ Pratt, SA Osmani, CP DeSouza, L Glass, MJ Orbach, JA Berglund, R Voelker, O Yarden, M Plamann, S Seiler, J Dunlap, A Radford, R Aramayo, DO Natvig, LA Alex, G Mannhaupt, DJ Ebbole, M Freitag, I Paulsen, MS Sachs, ES Lander, C Nusbaum, B Birren
    posted to fungi by alexl on 2007-10-10 18:22:58 as ** along with 5 people and 1 group sdinka jwortman stajich GustavoLacerda bootsy Berkeley Mycology
  • Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
    Nature, Vol. 438, No. 7071., pp. 1151-1156.
    by William C Nierman, Arnab Pain, Michael J Anderson, Jennifer R Wortman, Stanley H Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B Archer, Clara Bermejo, Joan Bennett, Paul Bowyer, Dan Chen, Matthew Collins, Richard Coulsen, Robert Davies, Paul S Dyer, Mark Farman, Nadia Fedorova, Natalie Fedorova, Tamara V Feldblyum, Reinhard Fischer, Nigel Fosker, Audrey Fraser, Jose L García, Maria J García, Arlette Goble, Gustavo H Goldman, Katsuya Gomi, Sam Griffith-Jones, Ryan Gwilliam, Brian Haas, Hubertus Haas, David Harris, H Horiuchi, Jiaqi Huang, Sean Humphray, Javier Jiménez, Nancy Keller, Hoda Khouri, Katsuhiko Kitamoto, Tetsuo Kobayashi, Sven Konzack, Resham Kulkarni, Toshitaka Kumagai, Anne Lafton, Jean-Paul Latgé, Weixi Li, Angela Lord, Charles Lu, William H Majoros, Gregory S May, Bruce L Miller, Yasmin Mohamoud, Maria Molina, Michel Monod, Isabelle Mouyna, Stephanie Mulligan, Lee Murphy, Susan O'Neil, Ian Paulsen, Miguel A Peñalva, Mihaela Pertea, Claire Price, Bethan L Pritchard, Michael A Quail, Ester Rabbinowitsch, Neil Rawlins, Marie-Adele Rajandream, Utz Reichard, Hubert Renauld, Geoffrey D Robson, Santiago R de Córdoba, Jose M Rodríguez-Peña, Catherine M Ronning, Simon Rutter, Steven L Salzberg, Miguel Sanchez, Juan C Sánchez-Ferrero, David Saunders, Kathy Seeger, Rob Squares, Steven Squares, Michio Takeuchi, Fredj Tekaia, Geoffrey Turner, Carlos, Janice Weidman, Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell, David W Denning
    posted to fungi by alexl on 2007-10-05 17:11:47 as **
  • Alternative splicing: a bioinformatics perspective.
    Mol Biosyst, Vol. 3, No. 7. (July 2007), pp. 473-477.
    by EN Ferreira, PA Galante, DM Carraro, SJ de Souza
    posted to splicing by alexl on 2007-09-04 22:58:08 as ** along with 2 people balicea seitentaisei
  • Introns and splicing elements of five diverse fungi.
    Eukaryot Cell, Vol. 3, No. 5. (October 2004), pp. 1088-1100.
    by DM Kupfer, SD Drabenstot, KL Buchanan, H Lai, H Zhu, DW Dyer, BA Roe, JW Murphy
    posted to branch_point by alexl on 2007-07-06 18:38:52 as ** along with 5 people and 2 groups penka jwestbrook GustavoLacerda angieju seitentaisei Nie King_Lab
  • A computational analysis of sequence features involved in recognition of short introns.
    Proc Natl Acad Sci U S A, Vol. 98, No. 20. (25 September 2001), pp. 11193-11198.
    by LP Lim, CB Burge
    posted to branch_point by alexl on 2007-07-06 18:36:17 as ** along with 3 people byy magnolia seitentaisei
  • SpliceMachine: predicting splice sites from high-dimensional local context representations
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1332-1338.
    by Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouze, Yves Van de Peer
    posted to branch_point by alexl on 2007-07-06 18:33:13 as ** along with 1 person wenhan
  • A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
    Nucl. Acids Res., Vol. 25, No. 15. (1 August 1997), pp. 3159-3163.
    by N Tolstrup, P Rouze, S Brunak
    posted to branch_point by alexl on 2007-07-06 18:29:13 as read along with 1 person seitentaisei
  • PseudoPipe: an automated pseudogene identification pipeline.
    Bioinformatics, Vol. 22, No. 12. (15 June 2006), pp. 1437-1439.
    by Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein
    posted to pseudogenes_eukaryotes by alexl on 2007-05-17 17:18:12 as read along with 3 people operon Jporci xingxu
  • Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein
    posted to pseudogenes_bacterial by alexl on 2007-05-04 20:10:13 as ** along with 1 person xingxu
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