Josep Gregori
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View article: Deep Sequencing Analysis of Hepatitis C Virus Subtypes and Resistance-Associated Substitutions in Genotype 4 Patients Resistant to Direct-Acting Antiviral (DAA) Treatment in Egypt
Deep Sequencing Analysis of Hepatitis C Virus Subtypes and Resistance-Associated Substitutions in Genotype 4 Patients Resistant to Direct-Acting Antiviral (DAA) Treatment in Egypt Open
Egypt has the highest global prevalence of hepatitis C virus (HCV), with genotype 4 (G4) in over 94% of cases. Direct-acting antivirals (DAAs) yield sustained virologic response (SVR) rates above 95%. Second-generation DAAs are recommended…
View article: Viral Quasispecies Inference from Single Observations—Mutagens as Accelerators of Quasispecies Evolution
Viral Quasispecies Inference from Single Observations—Mutagens as Accelerators of Quasispecies Evolution Open
RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for unde…
View article: Deep Sequencing Reveals Dual Evolution of SARS‐CoV‐2: Insights Into Defective Genomes From Wuhan‐Hu‐1 Variants to Omicron Subvariants
Deep Sequencing Reveals Dual Evolution of SARS‐CoV‐2: Insights Into Defective Genomes From Wuhan‐Hu‐1 Variants to Omicron Subvariants Open
SARS‐CoV‐2 has evolved from early variants dominating the first (B.1.5, B.1.1) and second (B.1.177) pandemic waves, which exhibited a higher frequency of minority mutants with deletions leading to Defective Viral Genomes (DVGs) in the spik…
View article: Methods for Quasispecies Single Observations Comparative Analysis
Methods for Quasispecies Single Observations Comparative Analysis Open
The study of viral quasispecies structure and diversity poses distinct challenges when comparing samples, particularly in scenarios involving single observations from individual biosamples collected at different time points or under varyin…
View article: Association of Liver Damage and Quasispecies Maturity in Chronic HCV Patients: The Fate of a Quasispecies
Association of Liver Damage and Quasispecies Maturity in Chronic HCV Patients: The Fate of a Quasispecies Open
Viral diversity and disease progression in chronic infections, and particularly how quasispecies structure affects antiviral treatment, remain key unresolved issues. Previous studies show that advanced liver fibrosis in long-term viral inf…
View article: In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications
In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications Open
The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic a…
View article: Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation
Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation Open
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5′ end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencin…
View article: Virus Quasispecies Rarefaction: Subsampling with or without Replacement?
Virus Quasispecies Rarefaction: Subsampling with or without Replacement? Open
In quasispecies diversity studies, the comparison of two samples of varying sizes is a common necessity. However, the sensitivity of certain diversity indices to sample size variations poses a challenge. To address this issue, rarefaction …
View article: In-Host HEV Quasispecies Evolution Shows the Limits of Mutagenic Antiviral Treatments
In-Host HEV Quasispecies Evolution Shows the Limits of Mutagenic Antiviral Treatments Open
Here, we report the in-host hepatitis E virus (HEV) quasispecies evolution in a chronically infected patient who was treated with three different regimens of ribavirin (RBV) for nearly 6 years. Sequential plasma samples were collected at d…
View article: Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater
Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater Open
Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking…
View article: Fitness-Dependent, Mild Mutagenic Activity of Sofosbuvir for Hepatitis C Virus
Fitness-Dependent, Mild Mutagenic Activity of Sofosbuvir for Hepatitis C Virus Open
The concept of a mild mutagen was coined to describe a minor mutagenic activity exhibited by some nucleoside analogues that potentiated their efficacy as antiretroviral agents. In the present study, we report the mild mutagen activity of s…
View article: Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater
Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater Open
This dataset contains the FASTQ files used in the paper Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater. The FASTQ files are classified in 2 different folders: MinION and MiSeq. Inside …
View article: Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater
Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater Open
This dataset contains the FASTQ files used in the paper Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater. The FASTQ files are classified in 2 different folders: MinION and MiSeq. Inside …
View article: Table S1 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S1 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Clinical characteristics of patients
View article: Table S2 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S2 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
List of differentially secreted proteins between the 2D and 3D secretomes of SW48 parental cells
View article: Table S1 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S1 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Clinical characteristics of patients
View article: Table S4 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S4 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Gene ontology description of the 301 G12V unique proteins shown in Figure 2B
View article: Data from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Data from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Purpose: The lack of secreted biomarkers measurable by noninvasive tests hampers the development of effective targeted therapies against cancer. Our hypothesis is that cetuximab (an anti-EGFR mAb) induces a specific secretome in col…
View article: Supplementary Figures 1-20 from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer
Supplementary Figures 1-20 from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer Open
Supplementary Figures 1-20
View article: Table S4 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S4 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Gene ontology description of the 301 G12V unique proteins shown in Figure 2B
View article: Table S6 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S6 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
List of differentially secreted proteins between the EGF_cetuximab and EGF secretomes of SW48 parental cells in 2D
View article: Table S2 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S2 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
List of differentially secreted proteins between the 2D and 3D secretomes of SW48 parental cells
View article: Data from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer
Data from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer Open
Purpose:The study of the cancer secretome suggests that a fraction of the intracellular proteome could play unanticipated roles in the extracellular space during tumorigenesis. A project aimed at investigating the invasive secretome led us…
View article: SupplementaryMaterial from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
SupplementaryMaterial from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
It contains supplementary Experimental Procedures and Suppl. figures
View article: Table S3 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S3 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Gene ontology description of the 28 G12V unique proteins shown in Figure 2B
View article: Data from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Data from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Purpose: The lack of secreted biomarkers measurable by noninvasive tests hampers the development of effective targeted therapies against cancer. Our hypothesis is that cetuximab (an anti-EGFR mAb) induces a specific secretome in col…
View article: Supplementary Figures 1-20 from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer
Supplementary Figures 1-20 from Extracellular HMGA1 Promotes Tumor Invasion and Metastasis in Triple-Negative Breast Cancer Open
Supplementary Figures 1-20
View article: Table S5 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S5 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
List of differentially secreted proteins between the EGF_cetuximab and EGF secretomes of SW48 parental cells in 3D
View article: Table S6 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S6 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
List of differentially secreted proteins between the EGF_cetuximab and EGF secretomes of SW48 parental cells in 2D
View article: Table S3 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer
Table S3 from Circulating pEGFR Is a Candidate Response Biomarker of Cetuximab Therapy in Colorectal Cancer Open
Gene ontology description of the 28 G12V unique proteins shown in Figure 2B