% ./getref.py pmid.txt > pmid.xml
% xsltproc pubmed2bibtex.xsl pmid.xml > document.bib


@article{ukkonen,
    year={1995},
    issn={0178-4617},
    journal={Algorithmica},
    volume={14},
    number={3},
    doi={10.1007/BF01206331},
    title={On-line construction of suffix trees},
    url={http://dx.doi.org/10.1007/BF01206331},
    publisher={Springer-Verlag},
    keywords={Linear-time algorithm; Suffix tree; Suffix trie; Suffix automaton; DAWG},
    author={Ukkonen, E.},
    pages={249-260},
    language={English}
}

@book{mackay,
    author = {MacKay, David J. C.},
    title = {Information Theory, Inference \& Learning Algorithms},
    year = {2002},
    isbn = {0521642981},
    publisher = {Cambridge University Press},
    address = {New York, NY, USA},
} 

@article{WuManber1992,
    author = {Wu, Sun and Manber, Udi},
    title = {Fast Text Searching: Allowing Errors},
    journal = {Commun. ACM},
    issue_date = {Oct. 1992},
    volume = {35},
    number = {10},
    month = oct,
    year = {1992},
    issn = {0001-0782},
    pages = {83--91},
    numpages = {9},
    url = {http://doi.acm.org/10.1145/135239.135244},
    doi = {10.1145/135239.135244},
    acmid = {135244},
    publisher = {ACM},
    address = {New York, NY, USA},
    keywords = {approximate string matching, information retrieval, pattern matching, software tools, string searching},
}

@Manual{R,
  title        = {R: A Language and Environment for Statistical
                  Computing},
  author       = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address      = {Vienna, Austria},
  year         = 2014,
  url          = {http://www.R-project.org}
}

@article{pmid10673000,
    title = {{DNA uptake signal sequences in naturally transformable bacteria.}},
    author = {H O Smith and M L Gwinn and S L Salzberg},
    journal = {{Res. Microbiol.}},
    volume = {150},
    number = {9-10},
    pages = {603-16},
    year = 1999,
    abstract = {The naturally transformable bacterium Haemophilus influenzae Rd contains 1471 copies of the DNA uptake signal sequence (USS) 5'-AAGTGCGGT in its genome. Neisseria meningitidis contains 1891 copies of the USS sequence 5'-GCCGTCTGAA. The USSs are often found in the base paired stem of transcription terminators.},
    pubmed = {10673000},
    pii = {S0923-2508(99)00130-8},
    nlmuniqueid = {8907468}
}

@article{pmid16056220,
    title = {{Genome sequencing in microfabricated high-density picolitre reactors.}},
    author = {Marcel Margulies and Michael Egholm and William E Altman and Said Attiya and Joel S Bader and Lisa A Bemben and Jan Berka and Michael S Braverman and Yi-Ju Chen and Zhoutao Chen and Scott B Dewell and Lei Du and Joseph M Fierro and Xavier V Gomes and Brian C Godwin and Wen He and Scott Helgesen and Chun Heen Ho and Chun He Ho and Gerard P Irzyk and Szilveszter C Jando and Maria L I Alenquer and Thomas P Jarvie and Kshama B Jirage and Jong-Bum Kim and James R Knight and Janna R Lanza and John H Leamon and Steven M Lefkowitz and Ming Lei and Jing Li and Kenton L Lohman and Hong Lu and Vinod B Makhijani and Keith E McDade and Michael P McKenna and Eugene W Myers and Elizabeth Nickerson and John R Nobile and Ramona Plant and Bernard P Puc and Michael T Ronan and George T Roth and Gary J Sarkis and Jan Fredrik Simons and John W Simpson and Maithreyan Srinivasan and Karrie R Tartaro and Alexander Tomasz and Kari A Vogt and Greg A Volkmer and Shally H Wang and Yong Wang and Michael P Weiner and Pengguang Yu and Richard F Begley and Jonathan M Rothberg},
    journal = {{Nature}},
    volume = {437},
    number = {7057},
    year = {2005},
    month = sep,
    pages = {376-80},
    abstract = {The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.},
    pii = {nature03959},
    doi = {10.1038/nature03959},
    pubmed = {16056220},
    pmc = {PMC1464427},
    mid = {NIHMS5166},
    nlmuniqueid = {0410462}
}

@article{pmid18660515,
    title = {{Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.}},
    author = {Juliane C Dohm and Claudio Lottaz and Tatiana Borodina and Heinz Himmelbauer},
    journal = {{Nucleic Acids Res.}},
    volume = {36},
    number = {16},
    year = {2008},
    month = sep,
    pages = {e105},
    abstract = {Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A > C transversion being among the most frequent and C > G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.},
    pii = {gkn425},
    doi = {10.1093/nar/gkn425},
    pubmed = {18660515},
    pmc = {PMC2532726},
    nlmuniqueid = {0411011}
}

@article{pmid18809713,
    title = {{Dissecting T cell lineage relationships by cellular barcoding.}},
    author = {Koen Schepers and Erwin Swart and Jeroen W J van Heijst and Carmen Gerlach and Maria Castrucci and Daoud Sie and Mike Heimerikx and Arno Velds and Ron M Kerkhoven and Ramon Arens and Ton N M Schumacher},
    journal = {{J. Exp. Med.}},
    volume = {205},
    number = {10},
    year = {2008},
    month = sep,
    pages = {2309-18},
    abstract = {T cells, as well as other cell types, are composed of phenotypically and functionally distinct subsets. However, for many of these populations it is unclear whether they develop from common or separate progenitors. To address such issues, we developed a novel approach, termed cellular barcoding, that allows the dissection of lineage relationships. We demonstrate that the labeling of cells with unique identifiers coupled to a microarray-based detection system can be used to analyze family relationships between the progeny of such cells. To exemplify the potential of this technique, we studied migration patterns of families of antigen-specific CD8(+) T cells in vivo. We demonstrate that progeny of individual T cells rapidly seed independent lymph nodes and that antigen-specific CD8(+) T cells present at different effector sites are largely derived from a common pool of precursors. These data show how locally primed T cells disperse and provide a technology for kinship analysis with wider utility.},
    pii = {jem.20072462},
    doi = {10.1084/jem.20072462},
    pubmed = {18809713},
    pmc = {PMC2556794},
    nlmuniqueid = {2985109R}
}

@article{pmid19023044,
    title = {{Real-time DNA sequencing from single polymerase molecules.}},
    author = {John Eid and Adrian Fehr and Jeremy Gray and Khai Luong and John Lyle and Geoff Otto and Paul Peluso and David Rank and Primo Baybayan and Brad Bettman and Arkadiusz Bibillo and Keith Bjornson and Bidhan Chaudhuri and Frederick Christians and Ronald Cicero and Sonya Clark and Ravindra Dalal and Alex Dewinter and John Dixon and Mathieu Foquet and Alfred Gaertner and Paul Hardenbol and Cheryl Heiner and Kevin Hester and David Holden and Gregory Kearns and Xiangxu Kong and Ronald Kuse and Yves Lacroix and Steven Lin and Paul Lundquist and Congcong Ma and Patrick Marks and Mark Maxham and Devon Murphy and Insil Park and Thang Pham and Michael Phillips and Joy Roy and Robert Sebra and Gene Shen and Jon Sorenson and Austin Tomaney and Kevin Travers and Mark Trulson and John Vieceli and Jeffrey Wegener and Dawn Wu and Alicia Yang and Denis Zaccarin and Peter Zhao and Frank Zhong and Jonas Korlach and Stephen Turner},
    journal = {{Science}},
    volume = {323},
    number = {5910},
    year = {2009},
    month = jan,
    pages = {133-8},
    abstract = {We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.},
    pii = {1162986},
    doi = {10.1126/science.1162986},
    pubmed = {19023044},
    nlmuniqueid = {0404511}
}

@article{pmid19561594,
    title = {{Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.}},
    author = {Debashish Ray and Hilal Kazan and Esther T Chan and Lourdes Peña Castillo and Sidharth Chaudhry and Shaheynoor Talukder and Benjamin J Blencowe and Quaid Morris and Timothy R Hughes},
    journal = {{Nat. Biotechnol.}},
    volume = {27},
    number = {7},
    year = {2009},
    month = jul,
    pages = {667-70},
    abstract = {Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation, require significant time and labor investment. Here we introduce RNAcompete, a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4 and YB1). RNAcompete identified expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than are conventional motif models. We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.},
    pii = {nbt.1550},
    doi = {10.1038/nbt.1550},
    pubmed = {19561594},
    nlmuniqueid = {9604648}
}

@article{pmid21148542,
    title = {{SlideSort: all pairs similarity search for short reads.}},
    author = {Kana Shimizu and Koji Tsuda},
    journal = {{Bioinformatics}},
    volume = {27},
    number = {4},
    year = {2011},
    month = feb,
    pages = {464-70},
    abstract = {Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses.},
    pii = {btq677},
    doi = {10.1093/bioinformatics/btq677},
    pubmed = {21148542},
    pmc = {PMC3035798},
    nlmuniqueid = {9808944}
}

@article{pmid21576222,
    title = {{Sequence-specific error profile of Illumina sequencers.}},
    author = {Kensuke Nakamura and Taku Oshima and Takuya Morimoto and Shun Ikeda and Hirofumi Yoshikawa and Yuh Shiwa and Shu Ishikawa and Margaret C Linak and Aki Hirai and Hiroki Takahashi and Md Altaf-Ul-Amin and Naotake Ogasawara and Shigehiko Kanaya},
    journal = {{Nucleic Acids Res.}},
    volume = {39},
    number = {13},
    year = {2011},
    month = jul,
    pages = {e90},
    abstract = {We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.},
    pii = {gkr344},
    doi = {10.1093/nar/gkr344},
    pubmed = {21576222},
    pmc = {PMC3141275},
    nlmuniqueid = {0411011}
}

@article{pmid21810899,
    title = {{SEED: efficient clustering of next-generation sequences.}},
    author = {Ergude Bao and Tao Jiang and Isgouhi Kaloshian and Thomas Girke},
    journal = {{Bioinformatics}},
    volume = {27},
    number = {18},
    year = {2011},
    month = sep,
    pages = {2502-9},
    abstract = {Similarity clustering of next-generation sequences (NGS) is an important computational problem to study the population sizes of DNA/RNA molecules and to reduce the redundancies in NGS data. Currently, most sequence clustering algorithms are limited by their speed and scalability, and thus cannot handle data with tens of millions of reads.},
    pii = {btr447},
    doi = {10.1093/bioinformatics/btr447},
    pubmed = {21810899},
    pmc = {PMC3167058},
    nlmuniqueid = {9808944}
}

@article{pmid22942077,
    title = {{Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.}},
    author = {Zechen Chong and Jue Ruan and Chung-I Wu},
    journal = {{Bioinformatics}},
    volume = {28},
    number = {21},
    year = {2012},
    month = nov,
    pages = {2732-7},
    abstract = {The innovation of restriction-site associated DNA sequencing (RAD-seq) method takes full advantage of next-generation sequencing technology. By clustering paired-end short reads into groups with their own unique tags, RAD-seq assembly problem is divided into subproblems. Fast and accurately clustering and assembling millions of RAD-seq reads with sequencing errors, different levels of heterozygosity and repetitive sequences is a challenging question.},
    pii = {bts482},
    doi = {10.1093/bioinformatics/bts482},
    pubmed = {22942077},
    nlmuniqueid = {9808944}
}

@article{pmid23060610,
    title = {{CD-HIT: accelerated for clustering the next-generation sequencing data.}},
    author = {Limin Fu and Beifang Niu and Zhengwei Zhu and Sitao Wu and Weizhong Li},
    journal = {{Bioinformatics}},
    volume = {28},
    number = {23},
    year = {2012},
    month = dec,
    pages = {3150-2},
    abstract = {CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.},
    pii = {bts565},
    doi = {10.1093/bioinformatics/bts565},
    pubmed = {23060610},
    pmc = {PMC3516142},
    nlmuniqueid = {9808944}
}

@article{pmid23253355,
    title = {{RRM-RNA recognition: NMR or crystallography…and new findings.}},
    author = {Gerrit M Daubner and Antoine Cléry and Frédéric H-T Allain},
    journal = {{Curr. Opin. Struct. Biol.}},
    volume = {23},
    number = {1},
    year = {2013},
    month = feb,
    pages = {100-8},
    abstract = {To characterize protein-RNA recognition at the molecular level, structural biology has turned out to be an indispensable approach. Detailed and direct insights into the mechanism of RNA binding and specificity have emerged from protein-RNA structures, especially from the most abundant RNA recognition motif (RRM). Although this protein domain has a very conserved α-β fold, it can recognize a large number of different RNA sequences and shapes and can be involved in a multitude of biological processes. Here, we report on recent single and multiple RRM-RNA structures and point out those features that provide novel insights into the mechanism of RNA recognition by RRMs. We further outline inherent problems to both NMR spectroscopy and X-ray crystallography methods and review recent strategies that emphasize the need to use both methodologies for more rapid and accurate structure determinations.},
    pii = {S0959-440X(12)00190-X},
    doi = {10.1016/j.sbi.2012.11.006},
    pubmed = {23253355},
    nlmuniqueid = {9107784}
}

@article{pmid23562324,
    title = {{Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.}},
    author = {Shatakshi Pandit and Yu Zhou and Lily Shiue and Gabriela Coutinho-Mansfield and Hairi Li and Jinsong Qiu and Jie Huang and Gene W Yeo and Manuel Ares and Xiang-Dong Fu},
    journal = {{Mol. Cell}},
    volume = {50},
    number = {2},
    year = {2013},
    month = apr,
    pages = {223-35},
    abstract = {SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins, SRSF1 (SF2/ASF) and SRSF2 (SC35), using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.},
    pii = {S1097-2765(13)00204-9},
    doi = {10.1016/j.molcel.2013.03.001},
    pubmed = {23562324},
    pmc = {PMC3640356},
    mid = {NIHMS455011},
    nlmuniqueid = {9802571}
}

@article{pmid23953119,
    title = {{Chromatin position effects assayed by thousands of reporters integrated in parallel.}},
    author = {Waseem Akhtar and Johann de Jong and Alexey V Pindyurin and Ludo Pagie and Wouter Meuleman and Jeroen de Ridder and Anton Berns and Lodewyk F A Wessels and Maarten van Lohuizen and Bas van Steensel},
    journal = {{Cell}},
    volume = {154},
    number = {4},
    year = {2013},
    month = aug,
    pages = {914-27},
    abstract = {Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.},
    pii = {S0092-8674(13)00889-1},
    doi = {10.1016/j.cell.2013.07.018},
    pubmed = {23953119},
    nlmuniqueid = {0413066}
}

@article{pmid5420325,
    title = {{A general method applicable to the search for similarities in the amino acid sequence of two proteins.}},
    author = {S B Needleman and C D Wunsch},
    journal = {{J. Mol. Biol.}},
    volume = {48},
    number = {3},
    year = {1970},
    month = mar,
    pages = {443-53},
    pubmed = {5420325},
    pii = {0022-2836(70)90057-4},
    nlmuniqueid = {2985088R}
}

