TY - JOUR AU - Zhu, J. AU - Zhang, M. PY - 1999 DA - 1999// TI - SCPD: A Promoter Database of the Yeast Saccharomyces Cerevisiae JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.7.607 DO - 10.1093/bioinformatics/15.7.607 ID - Zhu1999 ER - TY - CHAP AU - Policriti, A. AU - Vitacolonna, N. AU - Morgante, M. AU - Zuccolo, A. PY - 2004 DA - 2004// TI - Structured Motifs Search BT - Symposium on Research in Computational Molecular Biology ID - Policriti2004 ER - TY - JOUR AU - Michailidis, P. AU - Margaritis, K. PY - 2002 DA - 2002// TI - On-line Approximate String Searching Algorithms: Survey and Experimental Results JO - International Journal of Computer Mathematics VL - 79 UR - https://doi.org/10.1080/00207160212111 DO - 10.1080/00207160212111 ID - Michailidis2002 ER - TY - JOUR AU - Sinha, S. AU - Tompa, M. PY - 2002 DA - 2002// TI - Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation JO - Nucleic Acids Research VL - 30 UR - https://doi.org/10.1093/nar/gkf669 DO - 10.1093/nar/gkf669 ID - Sinha2002 ER - TY - JOUR AU - Sinha, S. AU - Tompa, M. PY - 2003 DA - 2003// TI - YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg618 DO - 10.1093/nar/gkg618 ID - Sinha2003 ER - TY - CHAP AU - Pavesi, G. AU - Mauri, G. AU - Pesole, G. PY - 2004 DA - 2004// TI - A Consensus Based Algorithm for Finding Transcription Factor Binding Sites BT - Workshop on Genomes: Information Structure and Complexity ID - Pavesi2004 ER - TY - JOUR AU - Pavesi, G. AU - Mauri, G. AU - Pesole, G. PY - 2001 DA - 2001// TI - An algorithm for finding signals of unknown length in DNA sequences JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.suppl_1.S207 DO - 10.1093/bioinformatics/17.suppl_1.S207 ID - Pavesi2001 ER - TY - CHAP AU - Bailey, T. L. AU - Elkan, C. PY - 1995 DA - 1995// TI - The value of prior knowledge in discovering motifs with MEME BT - 3rd Int'l Conference on Intelligent Systems for Molecular Biology ID - Bailey1995 ER - TY - CHAP AU - Sagot, M. F. PY - 1998 DA - 1998// TI - Spelling Approximate Repeated or Common Motifs Using a Suffix Tree BT - 3rd Latin American Symposium on Theoretical Informatics UR - https://doi.org/10.1007/BFb0054337 DO - 10.1007/BFb0054337 ID - Sagot1998 ER - TY - JOUR AU - Friberg, M. AU - von Rohr, P. AU - Gonnet, G. PY - 2005 DA - 2005// TI - Scoring functions for transcription factor binding site prediction JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-84 DO - 10.1186/1471-2105-6-84 ID - Friberg2005 ER - TY - JOUR AU - van Helden, J. AU - Rios, A. AU - Collado-Vides, J. PY - 2000 DA - 2000// TI - Discovering regulatory elements in non-coding sequences by analysis of spaced dyads JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.8.1808 DO - 10.1093/nar/28.8.1808 ID - van Helden2000 ER - TY - JOUR AU - Eskin, E. AU - Pevzner, P. PY - 2002 DA - 2002// TI - Finding composite regulatory patterns in DNA sequences JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S354 DO - 10.1093/bioinformatics/18.suppl_1.S354 ID - Eskin2002 ER - TY - CHAP AU - Eskin, E. AU - Keich, U. AU - Gelfand, M. AU - Pevzner, P. PY - 2003 DA - 2003// TI - Genome-wide analysis of bacterial promoter regions BT - Pac Symp Biocomput ID - Eskin2003 ER - TY - JOUR AU - Marsan, L. AU - Sagot, M. PY - 2000 DA - 2000// TI - Extracting Structured Motifs Using a suffix Tree – Algorithms and Application to Promoter Consensus Identification JO - Journal of Computational Biology VL - 7 UR - https://doi.org/10.1089/106652700750050826 DO - 10.1089/106652700750050826 ID - Marsan2000 ER - TY - CHAP AU - Carvalho, A. AU - Freitas, A. AU - Oliveira, A. AU - Sagot, M. PY - 2004 DA - 2004// TI - Efficient Extraction of Structured Motifs Using Box-links BT - String Processing and Information Retrieval Conference UR - https://doi.org/10.1007/978-3-540-30213-1_37 DO - 10.1007/978-3-540-30213-1_37 ID - Carvalho2004 ER - TY - CHAP AU - Carvalho, A. AU - Freitas, A. AU - Oliveira, A. AU - Sagot, M. PY - 2005 DA - 2005// TI - A highly scalable algorithm for the extraction of cis-regulatory regions BT - Asia-Pacific Bioinformatics Conference UR - https://doi.org/10.1142/9781860947322_0027 DO - 10.1142/9781860947322_0027 ID - Carvalho2005 ER - TY - CHAP AU - Pisanti, N. AU - Carvalho, A. M. AU - Marsan, L. AU - Sagot, M. F. PY - 2006 DA - 2006// TI - RISOTTO: Fast extraction of motifs with mismatches BT - 7th Latin American Theoretical Informatics Symposium ID - Pisanti2006 ER - TY - CHAP AU - Carvalho, A. M. AU - Freitas, A. T. AU - Oliveira, A. L. AU - Sagot, M. F. PY - 2004 DA - 2004// TI - A parallel algorithm for the extraction of structured motifs BT - 19th ACM Symposium on Applied Computing ID - Carvalho2004 ER - TY - CHAP AU - Brazma, A. AU - Jonassen, I. AU - Vilo, J. AU - Ukkonen, E. PY - 1998 DA - 1998// TI - Pattern Discovery in Biosequences BT - International Colloquium on Grammatical Inference UR - https://doi.org/10.1007/BFb0054081 DO - 10.1007/BFb0054081 ID - Brazma1998 ER - TY - JOUR AU - Apostolico, A. AU - Parida, L. PY - 2004 DA - 2004// TI - Incremental Paradigms of Motif Discovery JO - Journal of Computational Biology VL - 11 UR - https://doi.org/10.1089/106652704773416867 DO - 10.1089/106652704773416867 ID - Apostolico2004 ER - TY - JOUR AU - Apostolico, A. AU - Comin, M. AU - Parida, L. PY - 2005 DA - 2005// TI - Conservative extraction of over-represented extensible motifs JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1051 DO - 10.1093/bioinformatics/bti1051 ID - Apostolico2005 ER - TY - CHAP AU - Zhang, M. AU - Kao, B. AU - Cheung, D. W. L. AU - Yip, K. PY - 2005 DA - 2005// TI - Mining Periodic Patterns with Gap Requirement from Sequences BT - ACM Int'l Conference on Management of Data ID - Zhang2005 ER - TY - JOUR AU - Benson, G. PY - 1999 DA - 1999// TI - Tandem repeats finder: a program to analyze DNA sequences JO - Nucleic Acids Research VL - 27 UR - https://doi.org/10.1093/nar/27.2.573 DO - 10.1093/nar/27.2.573 ID - Benson1999 ER - TY - JOUR AU - Thakurta, D. AU - Stormo, G. PY - 2001 DA - 2001// TI - Identifying target sites for cooperatively binding factors JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.7.608 DO - 10.1093/bioinformatics/17.7.608 ID - Thakurta2001 ER - TY - JOUR AU - Zaki, M. J. PY - 2001 DA - 2001// TI - SPADE: An Efficient Algorithm for Mining Frequent Sequences JO - Machine Learning Journal VL - 42 UR - https://doi.org/10.1023/A:1007652502315 DO - 10.1023/A:1007652502315 ID - Zaki2001 ER -