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Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells.
- Published in:
- Nature Biotechnology, 2024, v. 42, n. 8, p. 1254, doi. 10.1038/s41587-023-01949-8
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- Article
Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications.
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- Frontiers in Oncology, 2024, p. 1, doi. 10.3389/fonc.2023.1310054
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- Publication type:
- Article
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions.
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- Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-023-03159-6
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- Article
GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers.
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- Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01259-3
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- Publication type:
- Article
Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.
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- NAR Cancer, 2023, v. 5, n. 3, p. 1, doi. 10.1093/narcan/zcad034
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- Publication type:
- Article
Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing.
- Published in:
- Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-29575-z
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- Publication type:
- Article
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.
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- Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01178-3
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- Article
Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS.
- Published in:
- Cancers, 2023, v. 15, n. 1, p. 228, doi. 10.3390/cancers15010228
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- Article
KmerKeys: a web resource for searching indexed genome assemblies and variants.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. W1, p. W448, doi. 10.1093/nar/gkac266
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- Article
Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-13569-4
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- Article
A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images.
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- NPJ Precision Oncology, 2022, v. 6, n. 1, p. 1, doi. 10.1038/s41698-022-00252-0
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- Publication type:
- Article
Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02554-1
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- Article
Characterization of the consensus mucosal microbiome of colorectal cancer.
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- NAR Cancer, 2021, v. 3, n. 4, p. 1, doi. 10.1093/narcan/zcab049
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- Publication type:
- Article
Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.
- Published in:
- Nature Biotechnology, 2021, v. 39, n. 10, p. 1259, doi. 10.1038/s41587-021-00911-w
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- Article
Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8.
- Published in:
- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00958-z
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- Publication type:
- Article
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.
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- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00882-2
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- Article
The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing.
- Published in:
- 2020
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- Publication type:
- Letter
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.
- Published in:
- Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-00747-0
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- Publication type:
- Article
Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.
- Published in:
- Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-61643-6
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- Publication type:
- Article
scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data.
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- Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1862-5
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- Publication type:
- Article
Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.
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- Nucleic Acids Research, 2019, v. 47, n. 19, p. e115, doi. 10.1093/nar/gkz661
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- Publication type:
- Article
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 8, p. 3846, doi. 10.1093/nar/gkz169
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- Publication type:
- Article
A functional CRISPR/Cas9 screen identifies kinases that modulate FGFR inhibitor response in gastric cancer.
- Published in:
- Oncogenesis, 2019, v. 8, n. 5, p. N.PAG, doi. 10.1038/s41389-019-0145-z
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- Publication type:
- Article
Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model.
- Published in:
- Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-019-40809-x
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- Publication type:
- Article
A robust targeted sequencing approach for low input and variable quality DNA from clinical samples.
- Published in:
- NPJ Genomic Medicine, 2018, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41525-017-0041-4
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- Publication type:
- Article
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
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- GigaScience, 2018, v. 7, n. 7, p. N.PAG, doi. 10.1093/gigascience/giy081
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- Article
Identification of large rearrangements in cancer genomes with barcode linked reads.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 4, p. e19, doi. 10.1093/nar/gkx1193
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- Publication type:
- Article
Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.
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- Nucleic Acids Research, 2017, v. 45, n. 19, p. 1, doi. 10.1093/nar/gkx712
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- Publication type:
- Article
Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes.
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- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4141-4
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- Publication type:
- Article
Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.
- Published in:
- Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0447-8
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- Publication type:
- Article
CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis.
- Published in:
- Nature Communications, 2017, v. 8, n. 2, p. 14291, doi. 10.1038/ncomms14291
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- Publication type:
- Article
A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
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- Nucleic Acids Research, 2016, v. 44, n. 15, p. 1, doi. 10.1093/nar/gkw481
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- Article
Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.
- Published in:
- Scientific Reports, 2015, p. 16178, doi. 10.1038/srep16178
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- Publication type:
- Article
The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations.
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- Genome Medicine, 2015, v. 7, p. 1, doi. 10.1186/s13073-015-0226-3
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- Publication type:
- Article
Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy.
- Published in:
- PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0136720
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- Publication type:
- Article
Allele-specific copy number profiling by next-generation DNA sequencing.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 4, p. 1, doi. 10.1093/nar/gku1252
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- Publication type:
- Article
Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.
- Published in:
- Genome Biology, 2014, v. 15, n. 7, p. 28, doi. 10.1186/s13059-014-0428-9
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- Publication type:
- Article
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.
- Published in:
- BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-290
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- Publication type:
- Article
Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture.
- Published in:
- Nature Medicine, 2014, v. 20, n. 7, p. 769, doi. 10.1038/nm.3585
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- Publication type:
- Article
A programmable method for massively parallel targeted sequencing.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. 10, p. e88, doi. 10.1093/nar/gku282
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- Publication type:
- Article
RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.
- Published in:
- BMC Research Notes, 2013, v. 6, n. 1, p. 1, doi. 10.1186/1756-0500-6-206
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- Article
Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis.
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- BMC Medical Genomics, 2013, v. 6, n. 1, p. 1, doi. 10.1186/1755-8794-6-54
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- Publication type:
- Article
Performance comparison of whole-genome sequencing platforms.
- Published in:
- Nature Biotechnology, 2012, v. 30, n. 6, p. 562, doi. 10.1038/nbt0612-562e
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- Publication type:
- Article
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.
- Published in:
- Nucleic Acids Research, 2012, p. D1137, doi. 10.1093/nar/gkr973
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- Publication type:
- Article
Performance comparison of whole-genome sequencing platforms.
- Published in:
- Nature Biotechnology, 2012, v. 30, n. 1, p. 78, doi. 10.1038/nbt.2065
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- Publication type:
- Article
Ultrasensitive detection of rare mutations using next-generation targeted resequencing.
- Published in:
- Nucleic Acids Research, 2012, v. 40, n. 1, p. 1, doi. 10.1093/nar/gkr861
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- Publication type:
- Article
A cross-sample statistical model for SNP detection in short-read sequencing data.
- Published in:
- Nucleic Acids Research, 2012, v. 40, n. 1, p. 1, doi. 10.1093/nar/gkr851
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- Publication type:
- Article
Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
- Published in:
- Nature Biotechnology, 2011, v. 29, n. 11, p. 1024, doi. 10.1038/nbt.1996
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- Article
A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing.
- Published in:
- PLoS ONE, 2011, v. 6, n. 6, p. 1, doi. 10.1371/journal.pone.0021088
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- Publication type:
- Article
Detecting simultaneous changepoints in multiple sequences.
- Published in:
- Biometrika, 2010, v. 97, n. 3, p. 631, doi. 10.1093/biomet/asq025
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- Publication type:
- Article