Miguel Madrid-Mencía

Invention: ML Pipeline for Genome-Wide Association Studies (Patent)

Thu, 11 Apr 2024 00:00:00 +0000

Co-authored patent US20240120024A1 for a machine learning approach that significantly improves causal gene identification in GWAS. Assignee: Illumina Inc.

Machine learning pipeline for genome-wide association studies

Thu, 11 Apr 2024 00:00:00 +0000

A machine learning approach to predict causal genes from GWAS summary statistics, substantially improving identification precision and recall. Assignee: Illumina Inc.

Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs

Mon, 01 Apr 2024 00:00:00 +0000

CDA overexpression in pancreatic adenocarcinoma resolves replicative stress at forks and correlates with resistance to DNA-damaging chemotherapy.

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Mon, 08 Nov 2021 00:00:00 +0000

STAG2 loss-of-function links cohesin variant distribution to a basal transcriptional shift in bladder cancer, offering new insights into tumor suppressor mechanisms.

Low replicative stress triggers cell-type specific inheritable advanced replication timing

Fri, 07 May 2021 00:00:00 +0000

Low replicative stress induces inheritable advances in replication timing at specific chromosomal domains, with potential impacts on cellular identity and gene expression.

GEMDeCan: Tumor Immune Microenvironment Deconvolution

Fri, 09 Apr 2021 00:00:00 +0000

Snakemake pipelines for tumor immune microenvironment deconvolution from RNA-seq and DNA methylation data, applied to 7,000+ TCGA samples and 166 immunotherapy patients.

Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies

Mon, 07 Dec 2020 00:00:00 +0000

A Boolean model of macrophage polarization extended to tumor microenvironment conditions, predicting potential regulators such as STAT1 and EGF as immunotherapy targets.

Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

Mon, 01 Jun 2020 00:00:00 +0000

Open-source software for flow cytometry-like visualization and exploration of pre-processed multi-omics single cell datasets.

GARDEN-NET & ChAseR: 3D Chromatin Interaction Networks

Thu, 07 May 2020 00:00:00 +0000

R package and web-based visualization tool for the analysis and integration of epigenomic data within 3D chromatin networks. Published in Nucleic Acids Research.

Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

Thu, 07 May 2020 00:00:00 +0000

First-author. An R package and web-based visualization tool for the representation, analysis, and integration of epigenomic data in the context of 3D chromatin interaction networks.

OpenEBench Embeddable Benchmarking Widget

Tue, 01 May 2018 00:00:00 +0000

Sole-author d3.js radial arc widget for the ELIXIR European scientific benchmarking platform, embeddable on any scientific tool website.

DoriTool: a bioinformatics integrative tool for post-association functional annotation

Tue, 19 Sep 2017 00:00:00 +0000

An integrative bioinformatics pipeline for post-association functional annotation, combining data from multiple functional tools to maximize reproducibility and reduce researcher workload.

AQuAS: Health System Observatory Visualization Platform

Sat, 01 Jul 2017 00:00:00 +0000

Interactive geospatial platform for the Catalan Agency for Health Quality and Evaluation to visualize and analyze regional health system indicators.

Structure-PPi v2.0

Sun, 01 May 2016 00:00:00 +0000

Module for annotating cancer-related single-nucleotide variants at protein-protein interfaces, integrating Appris, Interactome3D, and COSMIC.

Computer Vision adapted to Optical Coherence Tomographies (Bachelor's Thesis)

Wed, 01 Jul 2015 00:00:00 +0000

Automated image processing algorithm using Python and OpenCV to measure uvea thickness and monitor uveitis evolution in OCT scans.

CV

Mon, 01 Jan 0001 00:00:00 +0000

Expertise

Mon, 01 Jan 0001 00:00:00 +0000

Travailler avec moi

Mon, 01 Jan 0001 00:00:00 +0000

Cette page s’adresse aux recruteurs et responsables RH. Si vous êtes arrivé ici depuis un message LinkedIn ou une plateforme, vous êtes au bon endroit.

Ce que je cherche
#

Un CDI en France, en hybride ou full remote
Backend cloud-native ou bioinformatique / génomique
Une équipe avec une vraie autonomie et un rythme soutenable

Ce qui compte pour moi, c’est comment vous travaillez, pas les technologies. La culture d’équipe, la stabilité et l’organisation passent avant le stack.

Working with me

Mon, 01 Jan 0001 00:00:00 +0000

This page is for recruiters and hiring managers. If you reached it from a job platform or a direct message — you’re in the right place.

What I’m looking for
#

French CDI, hybrid or remote
Backend cloud-native or bioinformatics / genomics
A team with real autonomy and a sustainable pace

I care more about how you work than what you use. Stack and frameworks are secondary, team dynamics, engineering culture, and long-term stability are what I evaluate first.

Miguel Madrid-Mencía

Invention: ML Pipeline for Genome-Wide Association Studies (Patent)

Machine learning pipeline for genome-wide association studies

Cytidine deaminase resolves replicative stress and protects pancreatic cancer from DNA-targeting drugs

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Low replicative stress triggers cell-type specific inheritable advanced replication timing

GEMDeCan: Tumor Immune Microenvironment Deconvolution

Insights on TAM formation from a Boolean model of macrophage polarization based on in vitro studies

Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

GARDEN-NET & ChAseR: 3D Chromatin Interaction Networks

Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

OpenEBench Embeddable Benchmarking Widget

DoriTool: a bioinformatics integrative tool for post-association functional annotation

AQuAS: Health System Observatory Visualization Platform

Structure-PPi v2.0

Computer Vision adapted to Optical Coherence Tomographies (Bachelor's Thesis)

CV

Expertise

Travailler avec moi

Ce que je cherche #

Working with me

What I’m looking for #

Ce que je cherche
#

What I’m looking for
#