To search for papers
To browse for papers from bioinformatics-related conferences
To browse for papers from bioinformatics-related journals
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 .
Multiple sequence alignment
- Edgar RC, Batzoglou S (2006) Multiple sequence alignment. Curr Opin
Struct Biol 16: 368–373.
- Edgar RC (2004) MUSCLE: A multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5: 113.
- Do CB, Mahabhashyam MS, Brudno M, Batzoglou S (2005) ProbCons:
Probabilistic consistency-based multiple sequence alignment. Genome Res
15: 330–340.
- Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: Improvement
in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511–518.
- Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for
fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217.
- Wallace IM, O’Sullivan O, Higgins DG, Notredame C (2006) M-Coffee:
Combining multiple sequence alignment methods with T-Coffee. Nucleic
Acids Res 34: 1692–1699.
- Pei J, Sadreyev R, Grishin NV (2003) PCMA: Fast and accurate multiple
sequence alignment based on profile consistency. Bioinformatics 19: 427–
428.
- Pei J, Grishin NV (2006) MUMMALS: Multiple sequence alignment
improved by using hidden Markov models with local structural
information. Nucleic Acids Res 34: 4364–4374.
- Raphael B, Zhi D, Tang H, Pevzner P: A novel method for multiple
alignment of sequences with repeated and shuffled elements.
Genome Res 2004, 14:2336-2346.
Motif finding
- Eden, Eran; Lipson, Doron; Yogev, Sivan; Yakhini, Zohar. 2007. Discovering motifs in ranked lists of DNA sequences.. PLoS Comput Biol 3 (3):e39.
- Ng, P; Keich, U. 2008. GIMSAN: a Gibbs motif finder with significance analysis. BIOINFORMATICS 24 (19):2256-2257
- Chen, XY; Hughes, TR; Morris, Q. 2007. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. BIOINFORMATICS 23 (13):I72-I79
- Frickey, T; Weiller, G. 2007. Mclip: motif detection based on cliques of gapped local profile-to-profile alignments. BIOINFORMATICS 23 (4):502-503
- Fratkin, E; Naughton, BT; Brutlag, DL; Batzoglou, S. 2006. MotifCut: regulatory motifs finding with maximum density subgraphs. BIOINFORMATICS 22 (14):E150-E157
- Hon, LS; Jain, AN. 2006. A deterministic motif finding algorithm with application to the human genome. BIOINFORMATICS 22 (9):1047-1054 .
- Leung, HCM; Chin, FYL. 2006. Finding motifs from all sequences with and without binding sites. BIOINFORMATICS 22 (18):2217-2223.
- Mendes, ND; Casimiro, AC; Santos, PM; Sa-Correia, I; Oliveira, AL; Freitas, AT. 2006. MUSA: a parameter free algorithm for the identification of biologically significant motifs. BIOINFORMATICS 22 (24):2996-3002.
- Thompson WA, Newberg LA, Conlan S, McCue LA, and Lawrence CE. (2007) The Gibbs Centroid Sampler. Nucleic Acids Res . PubMed: 17483517 . doi: 10.1093/nar/gkm265 .
- Newberg LA, Thompson WA, Conlan S, Smith TM, McCue LA, and Lawrence CE. (2007) A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction. Bioinformatics . PubMed: 17488758 . doi: 10.1093/bioinformatics/btm241 .
- Thompson W, Rouchka EC, and Lawrence CE. (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res . 31 (13):3580-3585. PubMed: 12824370 . doi: 10.1093/nar/gkg608 .
- Thompson W, Palumbo MJ, Wasserman WW, Liu JS, and Lawrence CE. (2004) Decoding human regulatory circuits. Genome Res . 14 (10A):1967-1974. PubMed: 15466295 . doi: 10.1101/gr.2589004 .
Finding motif modules
- Siddharthan R (2008) PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling. PLoS Comput Biol 4(8): e1000156. doi:10.1371/journal.pcbi.1000156.
- Noto and Craven, Learning Probabilistic Models of cis -Regulatory Modules that Represent Logical and Spatial Aspects , European Conference on Computational Biology (ECCB) 2006 . Also appeared in
Bioinformatics 2007 23(2):e156-e162; doi:10.1093/bioinformatics/btl319.
- Li H., Zhu Q., He X., Sinha S. and Halfon M. (2003) Large-scale analysis of transcriptional cis -regulatory modules reveals both common features and distinct subclasses . Nucleic Acids Res . 31 (13):3580-3585. PubMed: 12824370 . doi: 10.1093/nar/gkg608 .
- Gupta M. and Liu J. De novo cis-regulatory module elicitation for eukaryotic genomes.
PNAS May 17, 2005 vol. 102 no. 20 7079-7084.
- V. X. Jin, A. Rabinovich, S. L. Squazzo, R. Green, and P. J. Farnham.
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1.
Genome Res., December 1, 2006; 16(12): 1585 - 1595.
- G. Kreiman.
Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes.
Nucleic Acids Res., May 20, 2004; 32(9): 2889 - 2900.
- Aerts S, Van Loo P., Thijs G, Moreau Y. and De Moor B.. Computational detection of cis -regulatory modules.
Bioinformatics Vol. 19 Suppl. 2 2003.
pages ii5-ii14
Whole genome alignment
- 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.
Phylogenetic footprinting
- Blanchette M, Tompa M., Discovery of regulatory elements by a computational method for phylogenetic footprinting, Genome Res. 2002 May;12(5):739-48.
- E. Berezikov, V. Guryev, R. H.A. Plasterk, and E. Cuppen, CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting,
Genome Res., January 1, 2004; 14(1): 170 - 178.
- Y. Liu, X. S. Liu, L. Wei, R. B. Altman, and S. Batzoglou, Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics,
Genome Res., March 1, 2004; 14(3): 451 - 458.
- A. Sosinsky, B. Honig, R. S. Mann, and A. Califano,
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting,
PNAS, April 10, 2007; 104(15): 6305 - 6310.
Genome-wide motif finding
- 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.
RNA secondary structure prediction
- Chuong B. Do , Chuan-Sheng Foo and Serafim Batzoglou, A max-margin model for efficient simultaneous alignment and folding of RNA sequences, Bioinformatics 2008, 24(13):i68-i76
- Xu X, Ji Y, Stormo GD, RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment, BIOINFORMATICS 2007, 23(15):1883-1891
- Do CB, Woods DA, Batzoglou S, CONTRAfold: RNA secondary structure prediction without physics-based models, BIOINFORMATICS 2006,: 22(14):E90-E98
- Witwer C, Hofacker IL, Stadler PF, Prediction of consensus RNA secondary structures including pseudoknots, IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS, 2004, 1 Issue: 2 Pages: 66-77
RNA structure alignment and motif search
- Havgaard JH, Torarinsson E, Gorodkin J. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol. 2007 Oct 12;3(10):1896-908
- Torarinsson E, Havgaard JH, Gorodkin J, Multiple structural alignment and clustering of RNA sequences, BIOINFORMATICS 2007, 23(8):926-932
- Siebert S, Backofen R, A dynamic programming approach for finding common patterns in RNAs , JOURNAL OF COMPUTATIONAL BIOLOGY 2007, 14(1): 33-44
- Hamada M, Tsuda K, Kudo T, et al. Mining frequent stem patterns from unaligned RNA sequences, BIOINFORMATICS 2006, 22(20): 2480-2487
- Tabei Y, Tsuda K, Kin T, et al. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments, BIOINFORMATICS 2006, 22(14): 1723-1729
- Dalli D, Wilm A, Mainz I, et al. STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time, BIOINFORMATICS 2006, 22(13): 1593-1599
- Hochsmann M, Voss B, Giegerich R, Pure multiple RNA secondary structure alignments: A progressive profile approach, IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS Volume: 1 Issue: 1 Pages: 53-62 Published: JAN-MAR 2004
- Reeder J, Reeder J, Giegerich R, Locomotif: from graphical motif description to RNA motif search, BIOINFORMATICS 2007, 23(13): I392-I400
- Yao Z, Weinberg Z, Ruzzo WL. CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics. 2006 Feb 15;22(4):445-52.
- Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R., RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Res. 2001 Nov 15;29(22):4724-35
- Michal S, Ivry T, Cohen O, Sipper M, Barash D., Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System., IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):596-610.
- Liu J, Ma B, Zhang K., An algorithm for searching RNA motifs in genomic sequences., Biomol Eng. 2007 Sep;24(3):343-50.
- Nawrocki EP, Eddy SR., Query-dependent banding (QDB) for faster RNA similarity searches., PLoS Comput Biol. 2007 Mar 30;3(3):e56.
- Dowell RD, Eddy SR., Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints., BMC Bioinformatics. 2006 Sep 4;7:400.
- Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%, Bioinformatics. 2005 May 1;21(9):1815-24.
- Liu J, Ma B, Zhang K., An algorithm for searching RNA motifs in genomic sequences., Biomol Eng. 2007 Sep;24(3):343-50.
- Harmanci AO, Sharma G, Mathews DH., Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign., BMC Bioinformatics. 2007 Apr 19;8:1
Meta genomics
- M. Wu and J.A. Eisen, A simple, fast, and accurate method of phylogenomic inference. Genome Biology 2008, 9 : R151.
- Chen, K; Pachter L (2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLoS Comp Biol 1 : 24. doi : 10.1371/journal.pcbi.0010024
- Angly, F.E et al. The Marine Viromes of Four Oceanic Regions, PLoS Biol. 4:e368, 2008
- Ilias , Liu and Tavazoie, Predictive Behavior Within Microbial Genetic Networks , Science. 320:1313-7, 2008
- Piganeau G, Desdevises Y, Derelle E, et al. , Picoeukaryotic sequences in the Sargasso Sea metagenome, GENOME BIOLOGY 9(1):R5, 2008
- Pachter L, Interpreting the unculturable majority, NATURE METHODS, 4(6): 479-480, 2007
- Venter, JC; Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y, Smith HO (2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science 304 : 66–74. doi : 10.1126/science.1093857 . PMID 15001713
- Tyson, GW; Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004). " Insights into community structure and metabolism by reconstruction of microbial genomes from the environment ". Nature 428 : 37–43. doi : 10.1038/nature02340
- Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences , NUCLEIC ACIDS RESEARCH 34 (19):5623-5630, 2006
- Johnson PLF, Slatkin M. Inference of population genetic parameters in metagenomics: A clean look at messy data . GENOME RESEARCH, 16(10): 1320-1327, 2006
- Edwards, RA; Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F (2006). "Using pyrosequencing to shed light on deep mine microbial ecology". BMC Genomics 7 : 57. doi : 10.1186/1471-2164-7-57
- H. N. Poinar, C. Schwarz, Ji Qi, B. Shapiro, R. D. E. MacPhee, B. Buigues, A. Tikhonov, D. H. Huson, L. P. Tomsho, A. Auch, M. Rampp, W. Miller, S. C. Schuster, Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Science 311:392-394, 2006
- Meyer, F; Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008). "The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes". BMC Bioinformatics 9 : 0. doi : doi:10.1186/1471-2105-9-386
- Allen, EE; Banfield, JF (2005). "Community genomics in microbial ecology and evolution". Nature Reviews Microbiology 3 : 489–498. doi : 10.1038/nrmicro1157
Prediciton of Small non-coding RNA genes / targets
- 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
Application of Hidden Markov models
- 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.
Computational challenges associated with microarray technologies
- Probe design
- 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
Protein interaction networks / complex prediction
- Gunnar W. Klau , Andreas Rosenwald , Thomas Dandekar , Tobias Müller : Identifying functional modules in protein-protein interaction networks: an integrated exact approach. ISMB 2008
- Michihiro Araki , Alex Gutteridge , Wataru Honda , Minoru Kanehisa : Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. ISMB 2008
Electronic Edition (link) BibTeX
- Noga Alon , Phuong Dao , Iman Hajirasouliha , Fereydoun Hormozdiari , Süleyman Cenk Sahinalp : Biomolecular network motif counting and discovery by color coding. ISMB 2008
- Janusz Dutkowski , Jerzy Tiuryn : Identification of functional modules from conserved ancestral protein-protein interactions. RECOMB 2008
Topology of biological networks
- Wolf DM , Arkin AP . Motifs, modules and games in bacteria. Curr Opin Microbiol. 2003 Apr;6(2):125-34.
Biomedical text mining
Haplotype inferencing / SNP analysis