Research Explorer

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Researcher

Jim Clauwaert

Awards & Distinctions

20 Results

2024

Deep learning decodes new sites of RNA translation in medulloblastoma

Jim ClauwaertGerben MenschaertJohn Prensner

Deep learning to decode sites of RNA translation in normal and cancerous tissues

Jim ClauwaertZahra McVeyRamneek GuptaIan YannuzziGerben MenschaertJohn R. Prensner

Multimodal deregulation of imprinted gene HM13 : a pan-cancer study

Floris VoorthuijzenCedric StroobandtJeroen GalleLouis CoussementJim ClauwaertTine GoovaertsRyan EnglanderOlga AnczukowGerben MenschaertWim Van Criekinge et al.

2023

RIBO-former: applying attention-based neural networks for precise delineation of translated open reading frames using ribosome profiling data.

Jim ClauwaertZahra McVeyRamneek GuptaJohn PrensnerGerben Menschaert

RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames

Jim ClauwaertZahra McVeyRamneek GuptaGerben Menschaert

TIS transformer : remapping the human proteome using deep learning

Jim ClauwaertZahra McVeyRamneek GuptaGerben Menschaert

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

2022

CpG transformer for imputation of single-cell methylomes

Gaetan De WaeleJim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BIOINFORMATICS

Novel transformer networks for improved sequence labeling in genomics

Jim ClauwaertWillem Waegeman

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

ProD : a tool for predictive design of tailored promoters in Escherichia coli

Friederike MeyJim ClauwaertMaarten Van BremptMichiel StockJo MaertensWillem WaegemanMarjan De Mey

Bookchapter in Prokaryotic gene regulation : methods and protocols

2021

Explainability in transformer models for functional genomics

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in BRIEFINGS IN BIOINFORMATICS

Improving the performance of machine learning models for biotechnology : the quest for deus ex machina

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

A1 Journal Article in BIOTECHNOLOGY ADVANCES

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

Lecture / Speech

2020

An in-depth evaluation of annotated transcription start sites in E. coli using deep learning

Jim ClauwaertWillem Waegeman

Deep learning techniques for genome processing and annotation tasks in prokaryotes

Jim ClauwaertWillem WaegemanMarjan De MeyGerben Menschaert

Predictive design of sigma factor-specific promoters

Maarten Van BremptJim ClauwaertFriederike MeyMichiel StockJo MaertensWillem WaegemanMarjan De Mey

A1 Journal Article in NATURE COMMUNICATIONS

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike MeyJim ClauwaertKirsten Van HuffelWillem WaegemanMarjan De Mey

2019

DeepRibo : a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns

Jim ClauwaertGerben MenschaertWillem Waegeman

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2018

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data

Jim ClauwaertGerben MenschaertWillem Waegeman

DeepRibo : precise gene annotation of prokaryotes using deep learning and ribosome profiling data, validated with mass spectrometry data

Jim ClauwaertGerben MenschaertWillem Waegeman

2017

The use of shallow convolutional neural networks in predicting promotor strength in Eschericha coli

Jim ClauwaertMichiel StockMarjan De MeyWillem Waegeman