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Strain level microbial detection and quantification with applications to single cell metagenomics.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33869-7
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- Publication type:
- Article
Computational pharmacogenotype extraction from clinical next-generation sequencing.
- Published in:
- Frontiers in Oncology, 2023, p. 1, doi. 10.3389/fonc.2023.1199741
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- Publication type:
- Article
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. W1, p. W494, doi. 10.1093/nar/gku370
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- Publication type:
- Article
taveRNA: a web suite for RNA algorithms and applications.
- Published in:
- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W325, doi. 10.1093/nar/gkm303
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- Publication type:
- Article
Personalized copy number and segmental duplication maps using next-generation sequencing.
- Published in:
- Nature Genetics, 2009, v. 41, n. 10, p. 1061, doi. 10.1038/ng.437
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- Publication type:
- Article
DeeZ: reference-based compression by local assembly.
- Published in:
- Nature Methods, 2014, v. 11, n. 11, p. 1082, doi. 10.1038/nmeth.3133
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- Publication type:
- Article
mrsFAST: a cache-oblivious algorithm for short-read mapping.
- Published in:
- 2010
- By:
- Publication type:
- Letter
Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks.
- Published in:
- GigaScience, 2019, v. 8, n. 4, p. N.PAG, doi. 10.1093/gigascience/giz024
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- Publication type:
- Article
Robustness of Massively Parallel Sequencing Platforms.
- Published in:
- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0138259
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- Publication type:
- Article
smyRNA: A Novel Ab Initio ncRNA Gene Finder.
- Published in:
- PLoS ONE, 2009, v. 4, n. 5, p. 1, doi. 10.1371/journal.pone.0005433
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- Publication type:
- Article
Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10737-5
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- Publication type:
- Article
Manipulating multiple sequence alignments via MaM and WebMaM.
- Published in:
- Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w295, doi. 10.1093/nar/gki406
- By:
- Publication type:
- Article
A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression.
- Published in:
- Algorithms for Molecular Biology, 2019, v. 14, n. 1, p. N.PAG, doi. 10.1186/s13015-019-0152-9
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- Publication type:
- Article
Sparsification of RNA structure prediction including pseudoknots.
- Published in:
- Algorithms for Molecular Biology, 2010, v. 5, p. 39, doi. 10.1186/1748-7188-5-39
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- Publication type:
- Article
Fast prediction of RNA-RNA interaction.
- Published in:
- Algorithms for Molecular Biology, 2010, v. 5, p. 1
- By:
- Publication type:
- Article
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.
- Published in:
- PLoS Computational Biology, 2011, v. 7, n. 5, p. 1, doi. 10.1371/journal.pcbi.1001138
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- Publication type:
- Article
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data.
- Published in:
- PLoS Computational Biology, 2007, v. 3, n. 9, p. 1807, doi. 10.1371/journal.pcbi.0030181
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- Publication type:
- Article
Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution.
- Published in:
- PLoS Computational Biology, 2007, v. 3, n. 7, p. e118, doi. 10.1371/journal.pcbi.0030118
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- Publication type:
- Article
Poly-gene fusion transcripts and chromothripsis in prostate cancer.
- Published in:
- Genes, Chromosomes & Cancer, 2012, v. 51, n. 12, p. 1144, doi. 10.1002/gcc.21999
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- Publication type:
- Article
Biomolecular network motif counting and discovery by color coding.
- Published in:
- Bioinformatics, 2008, v. 24, n. 13, p. i241, doi. 10.1093/bioinformatics/btn163
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- Publication type:
- Article
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
- Published in:
- Bioinformatics, 2008, v. 24, n. 13, p. i32, doi. 10.1093/bioinformatics/btn173
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- Publication type:
- Article
Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 7, p. e38, doi. 10.1093/nar/gkz067
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- Publication type:
- Article
Optimal compressed representation of high throughput sequence data via light assembly.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02480-6
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- Publication type:
- Article
ReMixT: clone-specific genomic structure estimation in cancer.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1267-2
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- Publication type:
- Article
Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.
- Published in:
- BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-963
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- Publication type:
- Article
IDENTIFYING UNIFORMLY MUTATED SEGMENTS WITHIN REPEATS.
- Published in:
- Journal of Bioinformatics & Computational Biology, 2004, v. 2, n. 4, p. 657, doi. 10.1142/S0219720004000788
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- Publication type:
- Article
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem.
- Published in:
- Bioinformatics, 2020, v. 36, p. i169, doi. 10.1093/bioinformatics/btaa464
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- Publication type:
- Article
Identification of conserved evolutionary trajectories in tumors.
- Published in:
- Bioinformatics, 2020, v. 36, p. i427, doi. 10.1093/bioinformatics/btaa453
- By:
- Publication type:
- Article
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.
- Published in:
- Bioinformatics, 2019, v. 35, n. 1, p. 20, doi. 10.1093/bioinformatics/bty544
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- Publication type:
- Article
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS.
- Published in:
- Bioinformatics, 2017, v. 33, n. 6, p. 871, doi. 10.1093/bioinformatics/btw758
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- Publication type:
- Article
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
- Published in:
- Bioinformatics, 2017, v. 33, n. 1, p. 26, doi. 10.1093/bioinformatics/btw536
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- Publication type:
- Article
CoLoRMap: Correcting Long Reads by Mapping short reads.
- Published in:
- Bioinformatics, 2016, v. 32, n. 17, p. i545, doi. 10.1093/bioinformatics/btw463
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- Publication type:
- Article
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.
- Published in:
- Bioinformatics, 2015, v. 31, n. 12, p. i27, doi. 10.1093/bioinformatics/btv232
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- Publication type:
- Article
Clonality inference in multiple tumor samples using phylogeny.
- Published in:
- 2015
- By:
- Publication type:
- Product Review
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
- Published in:
- Bioinformatics, 2014, v. 30, n. 5, p. 644, doi. 10.1093/bioinformatics/btt591
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- Publication type:
- Article
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
- Published in:
- Bioinformatics, 2012, v. 28, n. 23, p. 3051, doi. 10.1093/bioinformatics/bts593
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- Publication type:
- Article
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
- Published in:
- Bioinformatics, 2012, v. 28, n. 12, p. i179, doi. 10.1093/bioinformatics/bts214
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- Publication type:
- Article
Mirroring co-evolving trees in the light of their topologies.
- Published in:
- Bioinformatics, 2012, v. 28, n. 9, p. 1202, doi. 10.1093/bioinformatics/bts109
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- Publication type:
- Article
Sensitive and fast mapping of di-base encoded reads.
- Published in:
- 2012
- By:
- Publication type:
- Correction Notice
Sensitive and fast mapping of di-base encoded reads.
- Published in:
- Bioinformatics, 2011, v. 27, n. 14, p. 1915, doi. 10.1093/bioinformatics/btr303
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- Publication type:
- Article
Optimally discriminative subnetwork markers predict response to chemotherapy.
- Published in:
- Bioinformatics, 2011, v. 27, n. 13, p. i205, doi. 10.1093/bioinformatics/btr245
- By:
- Publication type:
- Article
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
- Published in:
- Bioinformatics, 2011, v. 27, n. 11, p. 1481, doi. 10.1093/bioinformatics/btr184
- By:
- Publication type:
- Article
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
- Published in:
- Bioinformatics, 2010, v. 26, n. 13, p. 1608, doi. 10.1093/bioinformatics/btq249
- By:
- Publication type:
- Article
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
- Published in:
- Bioinformatics, 2010, v. 26, n. 12, p. i350, doi. 10.1093/bioinformatics/btq216
- By:
- Publication type:
- Article
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
- Published in:
- Bioinformatics, 2010, v. 26, n. 10, p. 1277, doi. 10.1093/bioinformatics/btq152
- By:
- Publication type:
- Article
A partition function algorithm for interacting nucleic acid strands.
- Published in:
- Bioinformatics, 2009, v. 25, n. 12, p. i365, doi. 10.1093/bioinformatics/btp212
- By:
- Publication type:
- Article