selected publications
- Blackbird: structural variant detection using synthetic and low-coverage long-reads. 2024 GET IT
- Automatic ploidy prediction and quality assessment of human blastocysts using time-lapse imaging. Nature communications. 2024 Academic Article GET IT
- cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. Bioinformatics (Oxford, England). 2024 Academic Article GET IT
- Automatic Ploidy Prediction and Quality Assessment of Human Blastocyst Using Time-Lapse Imaging. 2023 GET IT
- Ariadne: synthetic long read deconvolution using assembly graphs. Genome biology. 2023 Academic Article GET IT
- Back in 3D-a report on Genome Informatics 2022. Genome biology. 2023 Academic Article GET IT
- Cue: a deep-learning framework for structural variant discovery and genotyping. Nature methods. 2023 Academic Article GET IT
- A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. The Lancet. Digital health. 2023 Academic Article GET IT
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Nucleic acids research. 2022 Academic Article GET IT
- Weakly-supervised tumor purity prediction from frozen H&E stained slides. EBioMedicine. 2022 Academic Article GET IT
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System-wide transcriptome damage and tissue identity loss in COVID-19 patients.
Cell reports. Medicine.
2022
Academic Article
GET IT
Times cited: 29 - coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. Bioinformatics (Oxford, England). 2021 Academic Article GET IT
- A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 2021 Academic Article GET IT
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Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.
Bioinformatics (Oxford, England).
2021
Academic Article
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Times cited: 24 -
A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion.
Journal of magnetic resonance imaging : JMRI.
2021
Academic Article
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Times cited: 54 -
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
Nature communications.
2021
Academic Article
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Times cited: 90 - gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC bioinformatics. 2020 Academic Article GET IT
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Precision medicine and artificial intelligence: overview and relevance to reproductive medicine.
Fertility and sterility.
2020
Information Resource
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Times cited: 4 -
Predictive modeling in reproductive medicine: Where will the future of artificial intelligence research take us?.
Fertility and sterility.
2020
Information Resource
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Times cited: 3 -
A robust benchmark for detection of germline large deletions and insertions.
Nature biotechnology.
2020
Academic Article
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Times cited: 34 -
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.
Nature medicine.
2020
Academic Article
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Times cited: 153 -
VALOR2: characterization of large-scale structural variants using linked-reads.
Genome biology.
2020
Academic Article
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Times cited: 11 -
Meltos: multi-sample tumor phylogeny reconstruction for structural variants.
Bioinformatics (Oxford, England).
2020
Academic Article
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Times cited: 9 -
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
Genome research.
2019
Academic Article
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Times cited: 51 -
BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples.
BMC bioinformatics.
2019
Academic Article
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Times cited: 10 -
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.
Genome research.
2019
Academic Article
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Times cited: 41 -
The tech for the next decade: promises and challenges in genome biology.
Genome biology.
2019
Conference Paper
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Times cited: 2 - Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization. NPJ digital medicine. 2019 Academic Article GET IT
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Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.
Genome research.
2018
Academic Article
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Times cited: 14 -
Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.
Current protocols in bioinformatics.
2018
Academic Article
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Times cited: 6 -
Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images.
EBioMedicine.
2017
Academic Article
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Times cited: 252 -
Fast and scalable inference of multi-sample cancer lineages.
Genome biology.
2015
Academic Article
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Times cited: 159 -
Characterization of structural variants with single molecule and hybrid sequencing approaches.
Bioinformatics (Oxford, England).
2014
Academic Article
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Times cited: 46 -
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Bioinformatics (Oxford, England).
2014
Academic Article
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Times cited: 83 -
Detecting independent and recurrent copy number aberrations using interval graphs.
Bioinformatics (Oxford, England).
2014
Academic Article
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Times cited: 22 -
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Nature communications.
2014
Academic Article
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Times cited: 295 -
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
Bioinformatics (Oxford, England).
2013
Academic Article
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Times cited: 32 -
An integrated map of genetic variation from 1,092 human genomes.
Nature.
2012
Academic Article
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Times cited: 6065 -
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.
The Journal of pathology.
2012
Academic Article
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Times cited: 156 -
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.
The Journal of pathology.
2012
Academic Article
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Times cited: 63 -
Mirroring co-evolving trees in the light of their topologies.
Bioinformatics (Oxford, England).
2012
Academic Article
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Times cited: 1 -
Simultaneous structural variation discovery among multiple paired-end sequenced genomes.
Genome research.
2011
Academic Article
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Times cited: 53 -
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinformatics (Oxford, England).
2011
Academic Article
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Times cited: 28 -
Mapping copy number variation by population-scale genome sequencing.
Nature.
2011
Academic Article
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Times cited: 877 -
Alu repeat discovery and characterization within human genomes.
Genome research.
2010
Academic Article
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Times cited: 82 -
A map of human genome variation from population-scale sequencing.
Nature.
2010
Academic Article
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Times cited: 5281 -
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinformatics (Oxford, England).
2010
Academic Article
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Times cited: 162 -
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Bioinformatics (Oxford, England).
2010
Academic Article
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Times cited: 83 -
smyRNA: a novel Ab initio ncRNA gene finder.
PloS one.
2009
Academic Article
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Times cited: 11 -
Biomolecular network motif counting and discovery by color coding.
Bioinformatics (Oxford, England).
2008
Academic Article
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Times cited: 174 -
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
Bioinformatics (Oxford, England).
2008
Academic Article
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Times cited: 16