To look for possible topics

List of bioinformatics topics in Wikipedia

To search for papers

PubMed at U.S. National Library of Medicine

To browse for papers from bioinformatics-related journals

• Bioinformatics
• BMC Bioinformatics
• Nucleic Acids Research
• IEEE/ACM Transactions on Computational Biology and Bioinformatics
• Genome Biology
• Genome Research

(For Bioinformatics and Genome Research, UTSA does not have online access to articles published within one year. Sometimes you may be able to get a copy from the author's website).

Possible Topics and some papers for you to start with

Some papers I listed here are reviews. If you decide to do that topic, read the review and select a few representative methods to go a little deeper .

• Delcher AL, Phillippy A, Carlton J, Salzberg SL., Fast algorithms for large-scale genome alignment and comparison., Nucleic Acids Res. 2002 Jun 1;30(11):2478-83
• Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L., Parametric alignment of Drosophila genomes., PLoS Comput Biol. 2006 Jun 23;2(6):e73.
• Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S., Glocal alignment: finding rearrangements during alignment. Bioinformatics. 2003;19 Suppl 1:i54-62.
• Bray N, Dubchak I, Pachter L., AVID: A global alignment program. Genome Res. 2003 Jan;13(1):97-102
• Brudno M, Do CB, Cooper GM, Kim MF, Davydov E; NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S., LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA, Genome Res. 2003 Apr;13(4):721-31
• Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004 Jul;14(7):1394-403
• Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B. DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics. 2005 Mar 22;6:66
• Kahveci T, Ljosa V, Singh AK., Speeding up whole-genome alignment by indexing frequency vectors. Bioinformatics. 2004 Sep 1;20(13):2122-34.
• Kent WJ. BLAT--the BLAST-like alignment tool., Genome Res. 2002 Apr;12(4):656-64.
• Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W., Human-mouse alignments with BLASTZ., Genome Res. 2003 Jan;13(1):103-7.

• Down TA, Bergman CM, Su J, Hubbard TJ., Large-scale discovery of promoter motifs in Drosophila melanogaster., PLoS Comput Biol. 2007 Jan 19;3(1):e7.
• Sabatti C, Rohlin L, Lange K, Liao JC., Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites., Bioinformatics. 2005 Apr 1;21(7):922-31.
• Bussemaker HJ, Li H, Siggia ED., Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis., Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10096-100.
• Elemento O, Tavazoie S (2005) Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 6: R18.

• Microarray Factsheet from NCBI website
• Probe design
  • Gasieniec L, Li CY, Sant P, Wong PW. Randomized probe selection algorithm for microarray design. J Theor Biol. 2007 Oct 7;248(3):512-21.
  • Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001 Dec;2(4):329-40. [PubMed]
  • L. Kaderali and A. Schliep, Selecting signature oligonucleotides to identify organisms using DNA arrays, Bioinformatics 18 (2002), pp. 1340–1349.
• Tiling array
  • A. Schliep and R. Krause, Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach, Algorithms in Bioinformatics, Pages 383-394, Springer Berlin / Heidelberg, 2007
  • Graf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P., Optimized design and assessment of whole genome tiling arrays. Bioinformatics. 2007 Jul 1;23(13):i195-204.
  • Sharp AJ, Itsara A, Cheng Z, Alkan C, Schwartz S, Eichler EE. Optimal design of oligonucleotide microarrays for measurement of DNA copy-number.Hum Mol Genet. 2007 Nov 15;16(22):2770-9. 2007
  • Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. Design optimization methods for genomic DNA tiling arrays.Genome Res. 2006 Feb;16(2):271-81.
  • Huber W, Toedling J, Steinmetz LM. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics. 2006 Aug 15;22(16):1963-70.
• Exon array
  • Xing Y, Kapur K, Wong WH., Probe selection and expression index computation of Affymetrix Exon Arrays., PLoS ONE. 2006 Dec 20;1:e88.
  • Lee C, Wang Q., Bioinformatics analysis of alternative splicing., Brief Bioinform. 2005 Mar;6(1):23-33.
• CGH array
  • Munch K, Gardner PP, Arctander P, Krogh A. A hidden Markov model approach for determining expression from genomic tiling micro arrays.BMC Bioinformatics. 2006 May 3;7:239.
  • Picard F, Robin S, Lebarbier E, Daudin JJ. A segmentation/clustering model for the analysis of array CGH data., Biometrics. 2007 Sep;63(3):758-66.
  • Stjernqvist S, Ryden T, Skold M, Staaf J.Continuous-index hidden Markov modelling of array CGH copy number data., Bioinformatics. 2007 Apr 15;23(8):1006-14.
  • Shi Y, Klustein M, Simon I, Mitchell T, Bar-Joseph Z., Continuous hidden process model for time series expression experiments., Bioinformatics. 2007 Jul 1;23(13):i459-67.
  • Rueda OM, Diaz-Uriarte R., Flexible and accurate detection of genomic copy-number changes from aCGH., PLoS Comput Biol. 2007 Jun 22;3(6):e122. Epub 2007 May 16.
  • Gaeta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM., iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences., Bioinformatics. 2007 Jul 1;23(13):1580-7.
  • Hu J, Gao JB, Cao Y, Bottinger E, Zhang W., Exploiting noise in array CGH data to improve detection of DNA copy number change., Nucleic Acids Res. 2007;35(5):e35.
  • Marioni JC, Thorne NP, Tavare S., BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data, Bioinformatics. 2006 May 1;22(9):1144-6.

• Eddy SR., Computational genomics of noncoding RNA genes., Cell. 2002 Apr 19;109(2):137-40.
• Berezikov E, Cuppen E, Plasterk RH., Approaches to microRNA discovery. Nat Genet. 2006 Jun;38 Suppl:S2-7
• Bentwich I., Prediction and validation of microRNAs and their targets, FEBS Lett. 2005 Oct 31;579(26):5904-10.
• Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes.PLoS Comput Biol. 2007 Jul 6;3(7):e126
• Horesh Y, Amir A, Michaeli S, Unger R., A rapid method for detection of putative RNAi target genes in genomic data., Bioinformatics. 2003 Oct;19 Suppl 2:ii73-80

• Nguyen C, Gardiner KJ, Cios KJ., A hidden Markov model for predicting protein interfaces., J Bioinform Comput Biol. 2007 Jun;5(3):739-53.
• Cui X, Vinar T, Brejova B, Shasha D, Li M., Homology search for genes., Bioinformatics. 2007 Jul 1;23(13):i97-103.
• Bagos PG, Liakopoulos TD, Hamodrakas SJ., Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins., BMC Bioinformatics. 2006 Apr 5;7:189.
• Aydin Z, Altunbasak Y, Borodovsky M., Protein secondary structure prediction for a single-sequence using hidden semi-Markov models., BMC Bioinformatics. 2006 Mar 30;7:178.