wenhan's library 337 articles Export

	Genes in prokaryotic genomes and their computational prediction [My Copy] In Computational Methods for Understanding Bacterial and Archaeal Genoms In Series on Advances in Bioinformatics and Computational Biology, Vol. 7 by R. K. Azad edited by Y. Xu, J. P. Gogarten posted to 200806_prop by wenhan on 2008-06-27 20:26:40 as
	Prokaryotic gene identification in silico [My Copy] In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics by M. Borodovsky, R. Azad edited by M. J. Dunn, L. B. Jorde, P. F. R. Little, S. Subramaniam posted to 200806_prop by wenhan on 2008-06-25 22:54:54 as
	Comparative analysis of mouse and human DNA and applications to exon prediction [My Copy] In RECOMB 2000 (2000) by Batzoglou, Pachter, Mesirov, Berger, Lander posted to 200806_prop by wenhan on 2008-06-25 22:41:42 as
	Applications of generalized pair hidden Markov models to alignment and gene finding problems. [My Copy] J Comput Biol, Vol. 9, No. 2. (2002), pp. 389-399. by L. Pachter, M. Alexandersson, S. Cawley posted to 200806_prop by wenhan on 2008-06-25 22:24:41 as along with 2 people and 1 group GustavoLacerda azazello MBLAB
	Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 78, No. 3. (March 1981), pp. 1596-1600. by J. C. Shepherd posted to 200806_prop by wenhan on 2008-06-25 22:23:04 as
	Mining Genes in DNA Using GeneScout [My Copy] by Michael M. Yin, Jason T. L. Wang posted to 200806_prop by wenhan on 2008-06-25 22:20:11 as along with 1 person GustavoLacerda
	Identification of new human cadherin genes using a combination of protein motif search and gene finding methods. [My Copy] Journal of molecular biology, Vol. 337, No. 2. (19 March 2004), pp. 307-317. by J. C. Höng, N. V. Ivanov, P. Hodor, et al.M. Xia, N. Wei, R. Blevins, D. Gerhold, M. Borodovsky, Y. Liu posted to 200806_prop by wenhan on 2008-06-25 21:59:45 as
	Effects of choice of DNA sequence model structure on gene identification accuracy. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 7. (1 May 2004), pp. 993-1005. by R. K. Azad, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:59:12 as
	Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. [My Copy] Briefings in bioinformatics, Vol. 5, No. 2. (June 2004), pp. 118-130. by R. K. Azad, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:58:50 as along with 1 person jmartin49
	Three new isoforms of Caenorhabditis elegans UNC-89 containing MLCK-like protein kinase domains. [My Copy] Journal of molecular biology, Vol. 342, No. 1. (3 September 2004), pp. 91-108. by T. M. Small, K. M. Gernert, D. B. Flaherty, K. B. Mercer, M. Borodovsky, G. M. Benian posted to 200806_prop by wenhan on 2008-06-25 21:58:28 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Identification of proteins associated with murine cytomegalovirus virions. [My Copy] Journal of virology, Vol. 78, No. 20. (October 2004), pp. 11187-11197. by L. M. Kattenhorn, R. Mills, M. Wagner, et al.A. Lomsadze, V. Makeev, M. Borodovsky, H. L. Ploegh, B. M. Kessler posted to 200806_prop by wenhan on 2008-06-25 21:58:08 as
	Statistical significance in biological sequence analysis. [My Copy] Brief Bioinform, Vol. 7, No. 1. (March 2006), pp. 2-24. by A. Y. Mitrophanov, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:55:19 as along with 4 people druvus treangen Ayest xili03
	Protein secondary structure prediction with semi Markov HMMs. [My Copy] Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Vol. 4 (2004), pp. 2964-2967. by Z. Aydin, Y. Altunbasak, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:54:28 as
	Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets. [My Copy] International journal of bioinformatics research and applications, Vol. 2, No. 2. (2006), pp. 193-217. by S. B. Kim, K. L. Tsui, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:54:07 as
	Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. [My Copy] International journal of bioinformatics research and applications, Vol. 2, No. 3. (2006), pp. 305-324. by S. Ekisheva, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:53:48 as
	Convergence rate estimation for the TKF91 model of biological sequence length evolution. [My Copy] Mathematical biosciences, Vol. 209, No. 2. (October 2007), pp. 470-485. by A. Y. Mitrophanov, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:52:01 as
	Exonization of the LTR transposable elements in human genome [My Copy] BMC Genomics, Vol. 8 (28 August 2007), 291. by Jittima Piriyapongsa, Nalini Polavarapu, Mark Borodovsky, John Mcdonald posted to 200806_prop by wenhan on 2008-06-25 21:51:41 as along with 3 people and 1 group cisevol yoanjacquemin FMoncini BergmanLab
	Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. [My Copy] Journal of theoretical biology, Vol. 246, No. 1. (7 May 2007), pp. 113-128. by A. Y. Mitrophanov, G. Churchward, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:51:21 as
	Evaluating the protein coding potential of exonized transposable element sequences [My Copy] Biology Direct, Vol. 2 (26 November 2007), 31. by Jittima Piriyapongsa, Mark T. Rutledge, Sanil Patel, Mark Borodovsky, King I. Jordan posted to 200806_prop by wenhan on 2008-06-25 21:50:43 as along with 2 people and 1 group GustavoLacerda cisevol BergmanLab
	Computational prediction of eukaryotic protein-coding genes. [My Copy] Nature reviews. Genetics, Vol. 3, No. 9. (September 2002), pp. 698-709. by Michael Q. Zhang posted to 200806_prop by wenhan on 2008-06-25 21:50:25 as along with 5 people and 3 groups rshe jmartin49 indigoviolet dchughes GustavoLacerda EisenLab G4ID Genetics-of-Gambling
	Identification of protein coding regions in the human genome by quadratic discriminant analysis. [My Copy] Proc Natl Acad Sci U S A, Vol. 94, No. 2. (21 January 1997), pp. 565-568. by M. Q. Zhang posted to 200806_prop by wenhan on 2008-06-25 21:49:47 as along with 1 person and 1 group indigoviolet EisenLab
	Recognizing exons in genomic sequence using GRAIL II. [My Copy] Genetic engineering, Vol. 16 (1994), pp. 241-253. by Y. Xu, R. Mural, M. Shah, E. Uberbacher posted to 200806_prop by wenhan on 2008-06-25 21:47:30 as
	SGP-1: prediction and validation of homologous genes based on sequence alignments. [My Copy] Genome Res, Vol. 11, No. 9. (September 2001), pp. 1574-1583. by T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds, R. Guigó posted to 200806_prop by wenhan on 2008-06-25 21:47:05 as along with 2 people and 1 group orzenil indigoviolet EisenLab
	Spidey: a tool for mRNA-to-genomic alignments. [My Copy] Genome research, Vol. 11, No. 11. (November 2001), pp. 1952-1957. by S. J. Wheelan, D. M. Church, J. M. Ostell posted to 200806_prop by wenhan on 2008-06-25 21:46:33 as along with 1 person azazello
	Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. [My Copy] Bioinformatics (Oxford, England), Vol. 15, No. 10. (October 1999), pp. 776-784. by A. Wagner posted to 200806_prop by wenhan on 2008-06-25 21:46:10 as
	Computational discovery of internal micro-exons. [My Copy] Genome research, Vol. 13, No. 6A. (June 2003), pp. 1216-1221. by N. Volfovsky, B. J. Haas, S. L. Salzberg posted to 200806_prop by wenhan on 2008-06-25 21:45:51 as along with 3 people and 1 group thegoose2 azazello tharris C. elegans / WormBase
	Optimal spliced alignment of homologous cDNA to a genomic DNA template. [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 3. (March 2000), pp. 203-211. by J. Usuka, W. Zhu, V. Brendel posted to 200806_prop by wenhan on 2008-06-25 21:45:24 as along with 2 people rshe GustavoLacerda
	Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. [My Copy] Journal of molecular biology, Vol. 297, No. 5. (14 April 2000), pp. 1075-1085. by J. Usuka, V. Brendel posted to 200806_prop by wenhan on 2008-06-25 21:44:16 as along with 1 person rshe
	Estimation and reliability of molecular sequence alignments. [My Copy] Biometrics, Vol. 51, No. 1. (March 1995), pp. 100-113. by J. L. Thorne, G. A. Churchill posted to 200806_prop by wenhan on 2008-06-25 21:43:15 as
	A probabilistic model for detecting coding regions in DNA sequences. [My Copy] IMA journal of mathematics applied in medicine and biology, Vol. 11, No. 3. (1994), pp. 149-160. by A. Thomas, M. H. Skolnick posted to 200806_prop by wenhan on 2008-06-25 21:42:52 as
	Gene-finding approaches for eukaryotes. [My Copy] Genome research, Vol. 10, No. 4. (April 2000), pp. 394-397. by G. D. Stormo posted to 200806_prop by wenhan on 2008-06-25 21:42:14 as
	Combined use of sequence similarity and codon bias for coding region identification. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 1, No. 1. (1994), pp. 39-50. by D. J. States, W. Gish posted to 200806_prop by wenhan on 2008-06-25 21:41:55 as along with 2 people VGreiff azazello
	Computer methods to locate signals in nucleic acid sequences. [My Copy] Nucleic acids research, Vol. 12, No. 1 Pt 2. (11 January 1984), pp. 505-519. by R. Staden posted to 200806_prop by wenhan on 2008-06-25 21:40:11 as
	Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3589-3592. by A. Sosinsky, C. P. Bonin, R. S. Mann, B. Honig posted to 200806_prop by wenhan on 2008-06-25 21:39:51 as along with 2 people oelemento isimpson
	Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. [My Copy] Nucleic acids research, Vol. 22, No. 24. (11 December 1994), pp. 5156-5163. by V. V. Solovyev, A. A. Salamov, C. B. Lawrence posted to 200806_prop by wenhan on 2008-06-25 21:39:31 as
	Identification of protein coding regions in genomic DNA. [My Copy] Journal of molecular biology, Vol. 248, No. 1. (21 April 1995), pp. 1-18. by E. E. Snyder, G. D. Stormo posted to 200806_prop by wenhan on 2008-06-25 21:39:01 as
	Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum. [My Copy] Journal of molecular biology, Vol. 309, No. 2. (1 June 2001), pp. 347-360. by M. M. Slupska, A. G. King, S. Fitz-Gibbon, J. Besemer, M. Borodovsky, J. H. Miller posted to 200806_prop by wenhan on 2008-06-25 21:35:50 as
	Discovery of novel transcription factor binding sites by statistical overrepresentation. [My Copy] Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560. by S. Sinha, M. Tompa posted to 200806_prop by wenhan on 2008-06-25 21:35:20 as along with 11 people wowalz GustavoLacerda kaarsinogen dquest xiaobeizhao smiddha GeeSharpMinor xi03 xili03 ep161302 pradiptaray
	Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. [My Copy] Bioinformatics (Oxford, England), Vol. 15, No. 11. (November 1999), pp. 874-886. by A. M. Shmatkov, A. A. Melikyan, F. L. Chernousko, M. Borodovsky posted to 200806_prop by wenhan on 2008-06-25 21:34:41 as
	PipMaker---A Web Server for Aligning Two Genomic DNA Sequences [My Copy] Genome Res., Vol. 10, No. 4. (1 April 2000), pp. 577-586. by Scott Schwartz, Zheng Zhang, Kelly A. Frazer, et al.Arian Smit, Cathy Riemer, John Bouck, Richard Gibbs, Ross Hardison, Webb Miller posted to 200806_prop by wenhan on 2008-06-25 21:31:46 as along with 4 people Neeperando aprasad michC adijr
	MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3518-3524. by Scott Schwartz, Laura Elnitski, Mei Li, et al.Matt Weirauch, Cathy Riemer, Arian Smit, NISC Comparative Sequencing Program, Eric D. Green, Ross C. Hardison, Webb Miller posted to 200806_prop by wenhan on 2008-06-25 21:30:56 as along with 4 people danatcaret stharward druvus aprasad
	Bayesian segmentation of protein secondary structure. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 7, No. 1-2. (r 2000), pp. 233-248. by S. C. Schmidler, J. S. Liu, D. L. Brutlag posted to 200806_prop by wenhan on 2008-06-25 21:30:35 as
	GeneSeqer@PlantGDB: Gene structure prediction in plant genomes. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3597-3600. by S. D. Schlueter, Q. Dong, V. Brendel posted to 200806_prop by wenhan on 2008-06-25 21:30:06 as
	A decision tree system for finding genes in DNA. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 5, No. 4. (1998), pp. 667-680. by S. Salzberg, A. L. Delcher, K. H. Fasman, J. Henderson posted to 200806_prop by wenhan on 2008-06-25 21:28:37 as
	Microbial gene identification using interpolated Markov models [My Copy] Nucl. Acids Res., Vol. 26, No. 2. (15 January 1998), pp. 544-548. by S. L. Salzberg, A. L. Delcher, S. Kasif, O. White posted to 200806_prop by wenhan on 2008-06-25 21:28:02 as along with 7 people and 1 group tfuji Ayest ziquje gg bnchakraborty bluto jguinney MBLAB
	Ab initio gene finding in Drosophila genomic DNA. [My Copy] Genome research, Vol. 10, No. 4. (April 2000), pp. 516-522. by A. A. Salamov, V. V. Solovyev posted to 200806_prop by wenhan on 2008-06-25 21:27:33 as
	EcoGene: a genome sequence database for Escherichia coli K-12. [My Copy] Nucleic acids research, Vol. 28, No. 1. (1 January 2000), pp. 60-64. by K. E. Rudd posted to 200806_prop by wenhan on 2008-06-25 21:27:04 as
	Gene structure prediction using information on homologous protein sequence. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 12, No. 3. (June 1996), pp. 161-170. by I. B. Rogozin, L. Milanesi, N. A. Kolchanov posted to 200806_prop by wenhan on 2008-06-25 21:23:36 as
	Evaluation of Gene-Finding Programs on Mammalian Sequences [My Copy] Genome Res., Vol. 11, No. 5. (1 May 2001), pp. 817-832. by Sanja Rogic, Alan K. Mackworth, Francis B. Ouellette posted to 200806_prop by wenhan on 2008-06-25 21:22:56 as along with 3 people and 1 group jmartin49 indigoviolet ep161302 EisenLab
	Large scale bacterial gene discovery by similarity search. [My Copy] Nature genetics, Vol. 7, No. 2. (June 1994), pp. 205-214. by K. Robison, W. Gilbert, G. M. Church posted to 200806_prop by wenhan on 2008-06-25 21:22:23 as