List of works - Marco Pagni

A Preliminary Study on the Prediction of Human Protein Functions

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery ⬇️

A downstream mediator in the growth repression limb of the jasmonate pathway

scientific article published on 03 August 2007

A new species of genus Eulimnadia Packard, 1874 (Branchiopoda: Spinicaudata: Limnadiidae) from India with an updated key for some Indian species

scientific article

A systems genetics resource and analysis of sleep regulation in the mouse

article

Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue

scientific article published on 11 March 2020

Assay for UDPglucose 6-dehydrogenase in phosphate-starved cells: gene tuaD of Bacillus subtilis 168 encodes the UDPglucose 6-dehydrogenase involved in teichuronic acid synthesis

article

Automated annotation of microbial proteomes in SWISS-PROT.

scientific article published in February 2003

Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation

scientific article published on 11 April 2022

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

scientific article

Comparative genomics suggests primary homothallism of Pneumocystis species.

scientific article

Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host's lungs

scientific article

Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss

scientific article

Complete genome sequence of the dog commensal and human pathogen Capnocytophaga canimorsus strain 5

scientific article (publication date: October 2011)

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

article

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

scientific article published on 01 July 2019

De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient.

scientific article

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

scientific article published on 28 March 2013

Dictyostelium discoideum flotillin homologues are essential for phagocytosis and participate in plasma membrane recycling and lysosome biogenesis

Experience using web services for biological sequence analysis.

scientific article published on 11 July 2008

Expression and Immunostaining Analyses Suggest that Pneumocystis Primary Homothallism Involves Trophic Cells Displaying Both Plus and Minus Pheromone Receptors

scientific article published on 09 July 2019

Expression pattern of the Pneumocystis jirovecii major surface glycoprotein superfamily in patients with pneumonia

scientific article published on 19 June 2020

Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs.

scientific article published on 20 February 2018

Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis

scientific article

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

scientific article

Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

scientific article published on 30 April 2013

Greater topoclimatic control of above- Versus belowground communities

scientific article published on 31 August 2020

HitKeeper, a generic software package for hit list management.

scientific article published on 28 March 2007

Identification and Functional Ascertainment of the Pneumocystis jirovecii Potential Drug Targets Gsc1 and Kre6 Involved in Glucan Synthesis.

scientific article published on 17 November 2016

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models

scientific article published on 21 February 2020

Inferring gene expression networks with hubs using a degree weighted Lasso approach

article

InterPro, progress and status in 2005

scientific article

InterPro--an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: December 2000)

InterPro: an integrated documentation resource for protein families, domains and functional sites

scientific article

Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data

scientific article published on 27 December 2019

JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture.

scientific article

Linear growth and poly( -hydroxybutyrate) synthesis in response to pulse-wise addition of the growth-limiting substrate to steady-state heterotrophic continuous cultures of Aquaspirillum autotrophicum

article

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Low number of fixed somatic mutations in a long-lived oak tree.

scientific article published on 4 December 2017

Making sense of score statistics for sequence alignments

scientific article published on 01 March 2001

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii

scientific article published on 7 November 2017

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

scientific article published on 28 January 2013

MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

scientific article

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

scientific article published on 06 November 2020

Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources

scientific article published on 18 May 2009

Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing

scientific article

MyHits: a new interactive resource for protein annotation and domain identification

scientific article published on July 2004

MyHits: improvements to an interactive resource for analyzing protein sequences

scientific article published in June 2007

New genome assembly of the barn owl (Tyto alba alba)

scientific article published on 19 February 2020

Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge

scientific article published on 20 May 2019

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

scientific article

PROSITE: a documented database using patterns and profiles as motif descriptors

scientific article (publication date: September 2002)

Persistence of in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression

scientific article published on 27 February 2019

Plant species distributions along environmental gradients: do belowground interactions with fungi matter?

scientific article published on 10 December 2013

Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.

scientific article published on 08 March 2016

Predicting spatial patterns of soil bacteria under current and future environmental conditions

scientific article published on 12 March 2021

RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans

scientific article published on 22 September 2015

RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.

scientific article published on July 2016

Reconciliation of metabolites and biochemical reactions for metabolic networks ⬇️

scientific article published on November 19, 2012

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

scientific article

Specific Labeling of Diaminopimelate: A Radioassay for the Determination of the Peptidoglycan Cross-Linking Index

scientific article published on 01 December 1994

Swiss EMBnet node web server

scientific article

Teichuronic acid operon of Bacillus subtilis 168.

scientific article published in February 1999

The InterPro database, 2003 brings increased coverage and new features

scientific article (publication date: 2003)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: 2001)

The Microbe browser for comparative genomics

scientific article published on 30 April 2009

The PROSITE database, its status in 2002

scientific article (publication date: 2002)

The PROSITE database.

scientific article

The SIB Swiss Institute of Bioinformatics Semantic Web of data

scientific article published on 25 October 2023

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

scientific article (publication date: 4 January 2016)

The elusive roles of bacterial glutathione S-transferases: new lessons from genomes.

scientific article

The relationship between kinetics of substrate-limited transitions and steady-state growth in continuous cultures ofAquaspirillum autotrophicum limited by pyruvate

article

The salivary microbiome for differentiating individuals: proof of principle

scientific article

Time-resolved RNA-seq profiling of the infection of Dictyostelium discoideum by Mycobacterium marinum reveals an integrated host response to damage and stress

scholarly article published 27 March 2019

Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria

scientific article published on 10 March 2020

Updates in Rhea - an expert curated resource of biochemical reactions

scientific article

Updates in Rhea - an expert curated resource of biochemical reactions

scientific article published on 15 December 2016

Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum

scientific article published on 01 June 2020

Vps13F links bacterial recognition and intracellular killing in Dictyostelium

scientific article

mmsearch: a motif arrangement language and search program

scientific article

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

scientific article published on 16 March 2013

trEST, trGEN and Hits: access to databases of predicted protein sequences.

scientific article

trome, trEST and trGEN: databases of predicted protein sequences

scientific article published on January 2004

List of works by Marco Pagni

A Preliminary Study on the Prediction of Human Protein Functions

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery ⬇️

A downstream mediator in the growth repression limb of the jasmonate pathway

A new species of genus Eulimnadia Packard, 1874 (Branchiopoda: Spinicaudata: Limnadiidae) from India with an updated key for some Indian species

A systems genetics resource and analysis of sleep regulation in the mouse

Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue

Assay for UDPglucose 6-dehydrogenase in phosphate-starved cells: gene tuaD of Bacillus subtilis 168 encodes the UDPglucose 6-dehydrogenase involved in teichuronic acid synthesis

Automated annotation of microbial proteomes in SWISS-PROT.

Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

Comparative genomics suggests primary homothallism of Pneumocystis species.

Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host's lungs

Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss

Complete genome sequence of the dog commensal and human pathogen Capnocytophaga canimorsus strain 5

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis

De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient.

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

Dictyostelium discoideum flotillin homologues are essential for phagocytosis and participate in plasma membrane recycling and lysosome biogenesis

Experience using web services for biological sequence analysis.

Expression and Immunostaining Analyses Suggest that Pneumocystis Primary Homothallism Involves Trophic Cells Displaying Both Plus and Minus Pheromone Receptors

Expression pattern of the Pneumocystis jirovecii major surface glycoprotein superfamily in patients with pneumonia

Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs.

Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

Greater topoclimatic control of above- Versus belowground communities

HitKeeper, a generic software package for hit list management.

Identification and Functional Ascertainment of the Pneumocystis jirovecii Potential Drug Targets Gsc1 and Kre6 Involved in Glucan Synthesis.

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models

Inferring gene expression networks with hubs using a degree weighted Lasso approach

InterPro, progress and status in 2005

InterPro--an integrated documentation resource for protein families, domains and functional sites

InterPro: an integrated documentation resource for protein families, domains and functional sites

Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data

JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture.

Linear growth and poly( -hydroxybutyrate) synthesis in response to pulse-wise addition of the growth-limiting substrate to steady-state heterotrophic continuous cultures of Aquaspirillum autotrophicum

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Low number of fixed somatic mutations in a long-lived oak tree.

Making sense of score statistics for sequence alignments

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii

Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources

Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing

MyHits: a new interactive resource for protein annotation and domain identification

MyHits: improvements to an interactive resource for analyzing protein sequences

New genome assembly of the barn owl (Tyto alba alba)

Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

PROSITE: a documented database using patterns and profiles as motif descriptors

Persistence of in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression

Plant species distributions along environmental gradients: do belowground interactions with fungi matter?

Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.

Predicting spatial patterns of soil bacteria under current and future environmental conditions

RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans

RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.

Reconciliation of metabolites and biochemical reactions for metabolic networks ⬇️

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

Specific Labeling of Diaminopimelate: A Radioassay for the Determination of the Peptidoglycan Cross-Linking Index

Swiss EMBnet node web server

Teichuronic acid operon of Bacillus subtilis 168.

The InterPro database, 2003 brings increased coverage and new features

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

The Microbe browser for comparative genomics

The PROSITE database, its status in 2002

The PROSITE database.

The SIB Swiss Institute of Bioinformatics Semantic Web of data

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The elusive roles of bacterial glutathione S-transferases: new lessons from genomes.

The relationship between kinetics of substrate-limited transitions and steady-state growth in continuous cultures ofAquaspirillum autotrophicum limited by pyruvate

The salivary microbiome for differentiating individuals: proof of principle

Time-resolved RNA-seq profiling of the infection of Dictyostelium discoideum by Mycobacterium marinum reveals an integrated host response to damage and stress

Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria

Updates in Rhea - an expert curated resource of biochemical reactions

Updates in Rhea - an expert curated resource of biochemical reactions

Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum