Pierre Lindenbaum
Bioinformatician
Nantes, Pays de la Loire, France
Summary
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Rockstar🎓
Top SchoolPierre Lindenbaum is a veteran bioinformatician with 17+ years applying software engineering to genomics and next-generation sequencing, currently researching cardiac disease genetics at UMR1087 in Nantes. He brings deep hands-on expertise in Java, C/C++, shell scripting, databases and open-source Unix tools, and has materially improved cornerstone bioinformatics projects such as samtools/htsjdk, Picard and samtools through refactoring, feature additions and testing. Comfortable as both developer and system architect, he designs robust back-end utilities (including CRAM/BAM/VCF handling and text-based alignment viewers) and has led bioinformatics teams and platform development in industry and academic settings. Trained to PhD level in virology and bioinformatics, he pairs molecular biology insight with pragmatic engineering to solve complex sequencing data problems. Notably, his long-term maintenance of jvarkit and contributions to widely used HTS libraries reflect a commitment to reproducible, production-grade open-source tools.
17 years of coding experience
9 years of employment as a software developer
PhD, virology, bioinformatics, PhD, virology, bioinformatics at Université Paris Sud (Paris XI)
French, English
Stackoverflow
34,862reputation
5.2mreached
467answers
211questions
mysql
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swing
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Github Skills (43)
file-rename10
biom10
bam10
testing10
curses10
c1110
java10
c1710
javas10
xml10
bioinformatics10
java-api10
mysql9
xslt9
data-structure9
Programming languages (25)
Github contributions (5)
lindenb/jvarkit
May 2013 - Jan 2023
Java utilities for Bioinformatics
Role in this project:
Back-end Developer
Back-end DeveloperContributions:11 releases, 3023 commits, 10 PRs in 9 years 10 months
Contributions summary:Pierre's commits focus on enhancing and refactoring the underlying components of the jvarkit project. They've made improvements to functionalities related to data processing and analysis, with specific changes in the VCF module. These modifications cover several areas within the project, suggesting an effort to improve overall code quality and modularity.
sciencesystems-biologybiologynext-generation-sequencinggenomics
samtools/samtools
Jan 2013 - Aug 2022
Tools (written in C using htslib) for manipulating next-generation sequencing data
Role in this project:Back-end Developer & System Architect
Back-end Developer & System ArchitectContributions:1 review, 14 commits, 9 PRs in 9 years 8 months
Contributions summary:Pierre appears to be focused on enhancing the `samtools` project, which involves tools for next-generation sequencing data. The contributions involve adding features and modifying existing functionality within the `bam_tview` module, specifically by implementing a text-based user interface with curses, and refactoring the html component. The user's work includes refactoring and extending the core functionality of the project with the goal of supporting various display options of the alignment data.
next-generationsequencing-datanext-generation-sequencinggenomicssequencing
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