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Investigating differential abundance methods in microbiome data: A benchmark study

PLoS computational biology, 2022-09, Vol.18 (9), p.e1010467-e1010467

2022

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Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

Frontiers in genetics, 2017-05, Vol.8, p.62

2017

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Simulation-based comprehensive benchmarking of RNA-seq aligners

Nature methods, 2017-02, Vol.14 (2), p.135-139

2017

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Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results

BMC bioinformatics, 2022-02, Vol.22 (Suppl 15), p.618-33, Article 618

2022

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metaSPARSim: a 16S rRNA gene sequencing count data simulator

BMC bioinformatics, 2019-11, Vol.20 (Suppl 9), p.416-416, Article 416

2019

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Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

BMC bioinformatics, 2018-09, Vol.19 (1), p.343-343, Article 343

2018

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A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

BMC genomics, 2017-08, Vol.18 (1), p.602-602, Article 602

2017

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Modeling Microbial Community Networks: Methods and Tools

Current genomics, 2021-12, Vol.22 (4), p.267-290

2021

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Cellular population dynamics shape the route to human pluripotency

Nature communications, 2023-05, Vol.14 (1), p.2829-2829, Article 2829

2023

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Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge

Scientific reports, 2023-04, Vol.13 (1), p.6303-6303, Article 6303

2023

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Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm

Bioinformatics (Oxford, England), 2022-03, Vol.38 (7), p.1920-1929

2022

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SPARSim single cell: a count data simulator for scRNA-seq data

Bioinformatics, 2020-03, Vol.36 (5), p.1468-1475

2020

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ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy

Bioinformatics (Oxford, England), 2021-11, Vol.37 (22), p.4253-4254

2021

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Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis

Microbiology spectrum, 2023-03, Vol.11 (2), p.e0294422-e0294422

2023

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Nilotinib‐induced bone marrow CD34+/lin‐Ph+ cells early clearance in newly diagnosed CP‐Chronic Myeloid Leukemia: Final report of the PhilosoPhi34 study

European journal of haematology, 2021-10, Vol.107 (4), p.436-448

2021

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MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach

Bioinformatics advances, 2022, Vol.2 (1), p.vbac092-vbac092

2022

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Investigating differential abundance methods in microbiome data: A benchmark study

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

Simulation-based comprehensive benchmarking of RNA-seq aligners

Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results

metaSPARSim: a 16S rRNA gene sequencing count data simulator

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

Modeling Microbial Community Networks: Methods and Tools

Cellular population dynamics shape the route to human pluripotency

Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge

Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment

Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm

SPARSim single cell: a count data simulator for scRNA-seq data

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy

Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis

Nilotinib‐induced bone marrow CD34+/lin‐Ph+ cells early clearance in newly diagnosed CP‐Chronic Myeloid Leukemia: Final report of the PhilosoPhi34 study

Progressive Down Regulation of JAK-STAT, Cell Cycle, and ABC Transporter Genes in CD34+/Lin- Cells of Chronic-Phase Chronic Myeloid Leukemia (CP-CML) Patients at Diagnosis Vs. 12 Months of Nilotinib Treatment Vs. Healthy Subjects

MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach

Nilotinib Deregulates Cell Cycle Checkpoints, ABC Transporters Genes and JAK-STAT Signaling Pathway of CD34+/Lin- Cells in Chronic-Phase Chronic Myeloid Leukemia (CP-CML) Patients after 12 Months of Treatment

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