I have put together this list of articles primarily for students wish to join the group. If you are applying for a position, I suggest you read a few of these articles, and base a good project proposal on them. If your proposal is good I will do my utmost to find a position for you.
- I won't respond to unsolicited applications that don't reference any of these articles.
Pathogen Genomics and Metagenomics (2016 position)
- Lindgreen S, Adair KL, Gardner PP (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports.
- Peabody MA, Van Rossum T, Lo R, Brinkman FSL (2015) Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. BMC Bioinformatics.
- Wheeler NE, Barquist L, Kingsley RA, Gardner PP (2016) A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. bioRxiv.
- Cosentino S, Larsen MV, Aarestrup FM, Lund O (2013) PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data. PLOS ONE.
Pathogen Genomics
- Chen & Shapiro (2015) The advent of genome-wide association studies for bacteria. Current Opinion in Microbiology.
- Nuccio & Bäumler (2014) Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut. mBio.
- Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput Biol.
- Barquist L, Boinett CJ, Cain AK (2013) Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA biology.
- Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Research.
- Lu et al. (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and
translational regulation. Nature Biotechnology. - Barrangou et al. (2007) CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science.
Genome annotation
- Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics.
- Gardner PP, Eldai H (2014) Annotating RNA motifs in sequences and alignments. Nucleic Acids Research.
- Washietl S, Findeiß S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N (2011) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA.
- Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z (2011) RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research.
- Cruz JA, Westhof E (2011) Sequence-based identification of 3D structural modules in RNA with RMDetect. Nature methods.
- Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research.
- Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A (2009) Rfam: updates to the RNA families database. Nucleic Acids Research.
RNA structure analysis
- Eddy SR (2014) Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. Annual review of biophysics.
- Kudla G, Murray AW , Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science.
- EP Nawrocki, SR Eddy (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol.
- Weinberg Z, Ruzzo WL (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics.
- Yao Z, Weinberg Z, Ruzzo WL (2006) CMfinder—a covariance model based RNA motif finding algorithm. Bioinformatics.
- Washietl S, Hofacker IL, Stadler PF (2005) Fast and reliable prediction of noncoding RNAs. PNAS.
- Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC bioinformatics.
- Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC bioinformatics.
- Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA.
- Rivas E, Eddy SR (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics .
Analysis of sequences
- Halvorsen M, Martin JS, Broadaway S, Laederach A (2010) Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet.
- Simons C, Pheasant M, Makunin IV, Mattick JS (2006) Transposon-free regions in mammalian genomes. Genome research.
- Eddy SR (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol.
- Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S
et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res.
RNA world
- Hoeppner MP, Gardner PP, Poole AM (2012) Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol.
- Gardner PP, Bateman A, Poole AM. (2010) SnoPatrol: how many snoRNA genes are there? Journal of Biology.
- Gardner PP, Holland BR, Moulton V, Hendy M, Penny D (2003) Optimal alphabets for an RNA world. Proceedings of the Royal Society B (Biological Sciences).
- Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. Journal of molecular evolution.
- Jeffares DC, Poole AM, Penny D (1998) Relics from the RNA world. Journal of molecular evolution.
- Orgel LE (1986) RNA catalysis and the origins of life. Journal of theoretical biology.
- Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. PNAS.
Benchmarks, controls & reproducibility
- Lindgreen S, Adair KL, Gardner PP (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports.
- Boulesteix AL, Lauer S, Eugster MJA (2013) A plea for neutral comparison studies in computational sciences. PloS ONE
- Eddy SR (2013) The ENCODE project: missteps overshadowing a success. Current biology.
- M Jelizarow, V Guillemot, A Tenenhaus, K Strimmer, AL Boulesteix (2010) Over-optimism in bioinformatics: an illustration. Bioinformatics.
- Freyhult EK, Bollback JP, Gardner PP (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research.
- Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med.
- Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research.
- Gardner PP, Giegerich R (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics.
Lab life
- Raymond ES (2000) The Cathedral and the Bazaar.
- Gardner PP and Pulakanam V (2014) Ten suggestions for selecting a research topic. Blog post.
- PLOS Computational Biology's Ten Simple Rules Series.
Classic bioinformatics and genomics
- Ray D, Kazan H, Cook KB, Weirauch MT , Najafabadi HS , Li et al. (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature.
- Eddy SR (2011) Accelerated Profile HMM Searches. PLOS Comput Biol .
- Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature.
- Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Research.
- TM Lowe, SR Eddy (1999) A computational screen for methylation guide snoRNAs in yeast. Science.
- Durbin R, Eddy S, Krogh A and Mitchison G (1998) Biological sequence analysis. Cambridge University Press.
- Lowe TM , Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids research
- Krogh A, Brown M, Mian IS, Sjölander K, Haussler D (1994) Hidden Markov models in computational biology: Applications to protein modeling. Journal of Molecular Biology.
- Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic acids research.
- Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research.
- States DJ, Gish W and Altschul SF (1991) Improved Sensitivity of Nucleic Acid Database Searches Using Application-Specific Scoring Matrices. METHODS: A Companion to Methods in Enzymology.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of molecular Biology.
- Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic acids research.
- Nussinov R, Jacobson AB (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. PNAS.