List of works - Nuno A. Fonseca

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

scientific article published on 01 September 2019

A pipelined data-parallel algorithm for ILP

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies

scientific article published on 16 September 2011

A user guide for the online exploration and visualization of PCAWG data

scientific article published on 07 July 2020

ADOPS - Automatic Detection Of Positively Selected Sites

scientific article

ADOPS--Automatic Detection Of Positively Selected Sites

scientific article published on 24 July 2012

AND Parallelism for ILP: The APIS System

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins

scientific article

Amino acid pairing at the N- and C-termini of helical segments in proteins

scientific article published on 01 January 2008

An S-RNase-based gametophytic self-incompatibility system evolved only once in eudicots

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

ArrayExpress update - from bulk to single-cell expression data

scientific article published on 01 January 2019

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design

article

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

article

BIORED - A Genetic Algorithm for Pattern Detection in Biosequences

Boosting the Detection of Transposable Elements Using Machine Learning

scholarly article by Tiago Loureiro et al published 2013 in Advances in Intelligent Systems and Computing

Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases

scholarly article by Max Pereira et al published 2009 in Lecture Notes in Computer Science

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

scientific article published on 18 June 2015

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

article

Conceptual Clustering of Multi-Relational Data

Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus

scientific article published on 19 May 2015

DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida)

scientific article published on 02 August 2021

Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation

scientific article published on January 2013

Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)

scientific article (publication date: 28 June 2010)

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

scientific article

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

scientific article

Expression Atlas update: from tissues to single cells

scientific article published on 01 January 2020

Expression Atlas: gene and protein expression across multiple studies and organisms.

scientific article

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci

scientific article published on 06 August 2020

Gene classification based on amino acid motifs and residues: the DLX (distal-less) test case

scientific article

Genomic basis for RNA alterations in cancer

scientific article published on 05 February 2020

Gramene 2016: comparative plant genomics and pathway resources

scientific article

Gramene 2018: unifying comparative genomics and pathway resources for plant research

scientific article

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

scientific article published on 05 February 2020

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

scientific article

ILP :- Just Trie It

Improving the efficiency of inductive logic programming systems

Improving the performance of Transposable Elements detection tools

scientific article published on 14 November 2013

Improving the performance of Transposable Elements detection tools.

scientific article published in December 2013

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

scientific article

Interactive Discriminative Mining of Chemical Fragments

LogCHEM: Interactive Discriminative Mining of Chemical Structure

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

scientific article published on 25 May 2014

Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

scientific article published in 2021

On Applying Tabling to Inductive Logic Programming

article by Ricardo Rocha et al published 2005 in Lecture Notes in Computer Science

On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites

article

Online resources for PCAWG data exploration, visualization, and discovery

scholarly article published 14 July 2017

Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems

Parallel ILP for distributed-memory architectures

article by Nuno A. Fonseca et al published 19 December 2008 in Machine Learning

Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach

Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model

scientific article (publication date: May 2013)

Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish

scientific article published in March 2010

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

scientific article published on 16 June 2010

Predicting Malignancy from Mammography Findings and Surgical Biopsies

scientific article

Predicting malignancy from mammography findings and image-guided core biopsies

scientific article published on January 2015

Predicting the secondary structure of proteins using machine learning algorithms.

scientific article published in January 2012

Protein evolution of ANTP and PRD homeobox genes

scientific article

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

scholarly article by Bruno Cavadas et al published 2017 in Advances in Intelligent Systems and Computing

RNA-Seq gene profiling--a systematic empirical comparison

scientific article

RNase-Based Gametophytic Self-Incompatibility Evolution: Questioning the Hypothesis of Multiple Independent Recruitments of the S-Pollen Gene

scientific article published on 4 June 2009

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison

scientific article published on 19 March 2022

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions

scientific article published in April 2012

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions

scientific article

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

scientific article published on 20 March 2020

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

scientific article published on 07 July 2020

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data.

scientific article

The number, age, sharing and relatedness of S-locus specificities in Prunus

scientific article published in February 2008

Tools for mapping high-throughput sequencing data

scientific article

Transcription factor activities enhance markers of drug sensitivity in cancer.

scientific article published on 11 December 2017

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

scientific article published on 17 July 2020

List of works by Nuno A. Fonseca

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

A pipelined data-parallel algorithm for ILP

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies

A user guide for the online exploration and visualization of PCAWG data

ADOPS - Automatic Detection Of Positively Selected Sites

ADOPS--Automatic Detection Of Positively Selected Sites

AND Parallelism for ILP: The APIS System

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins

Amino acid pairing at the N- and C-termini of helical segments in proteins

An S-RNase-based gametophytic self-incompatibility system evolved only once in eudicots

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

ArrayExpress update - from bulk to single-cell expression data

Assemblathon 1: a competitive assessment of de novo short read assembly methods

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

BIORED - A Genetic Algorithm for Pattern Detection in Biosequences

Boosting the Detection of Transposable Elements Using Machine Learning

Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

Conceptual Clustering of Multi-Relational Data

Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus

DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida)

Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation

Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Expression Atlas update: from tissues to single cells

Expression Atlas: gene and protein expression across multiple studies and organisms.

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci

Gene classification based on amino acid motifs and residues: the DLX (distal-less) test case

Genomic basis for RNA alterations in cancer

Gramene 2016: comparative plant genomics and pathway resources

Gramene 2018: unifying comparative genomics and pathway resources for plant research

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

ILP :- Just Trie It

Improving the efficiency of inductive logic programming systems

Improving the performance of Transposable Elements detection tools

Improving the performance of Transposable Elements detection tools.

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

Interactive Discriminative Mining of Chemical Fragments

LogCHEM: Interactive Discriminative Mining of Chemical Structure

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

On Applying Tabling to Inductive Logic Programming

On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites

Online resources for PCAWG data exploration, visualization, and discovery

Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems

Parallel ILP for distributed-memory architectures

Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach

Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model

Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

Predicting Malignancy from Mammography Findings and Surgical Biopsies

Predicting malignancy from mammography findings and image-guided core biopsies

Predicting the secondary structure of proteins using machine learning algorithms.

Protein evolution of ANTP and PRD homeobox genes

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

RNA-Seq gene profiling--a systematic empirical comparison

RNase-Based Gametophytic Self-Incompatibility Evolution: Questioning the Hypothesis of Multiple Independent Recruitments of the S-Pollen Gene

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-Seq data.

The number, age, sharing and relatedness of S-locus specificities in Prunus

Tools for mapping high-throughput sequencing data

Transcription factor activities enhance markers of drug sensitivity in cancer.

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

Tumour gene expression signature in primary melanoma predicts long-term outcomes

Two independent modes of chromatin organization revealed by cohesin removal

Visually Guiding and Controlling the Search While Mining Chemical Structures

k-RNN