“Come is a science and technology enthusiast thriving on hard computational problems. His personal commitment to radically change the way computing and informatics are used in life science is impressive. He possesses a clear vision of the direction and inspiration that brings teams and projects to success. As a thought leader he consistently get acceptance and support even for controversial ideas. Come is truly a technical expert with a flair for effective and elegant solutions taking full advantage of the latest advances in technology, whether it is software or hardware.”
Come Raczy
San Diego County, California, United States
3K followers
500+ connections
About
• Over 20 years experience leading small- and medium-sized teams (up to 20) of software…
Contributions
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How do you analyze the complexity of a distributed algorithm?
In computer science, the complexity of an algorithm is an indication of the amount of a given resource required to run it, usually established as a function of the input size. For centralized algorithms, the resources of interest are time (or number of operations on bits) and space. For distributed algorithms, communication (number or volume of messages between nodes) is also an important resource. Depending on the situation, focus can be on worst case complexity, or on average complexity. Additional complexity measures, including semantic complexity (how difficult is it to understand the algorithm), and Kolmogorov complexity (length of the minimal implementation), focus more on development and maintenance of the code than on execution.
Activity
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We're building an AI Research Assistant at Potato. It can now plan and run computational experiments - see demo video 🤯 Reach out if you want to…
We're building an AI Research Assistant at Potato. It can now plan and run computational experiments - see demo video 🤯 Reach out if you want to…
Liked by Come Raczy
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35X35cm _ ink on paper _ 2024 #encre #xieyi #shuimo #dessin #design #morsure_dencre #calligraphy #calligraphie #書法 #書道 #水彩画 #水彩畫 #sumi_e…
35X35cm _ ink on paper _ 2024 #encre #xieyi #shuimo #dessin #design #morsure_dencre #calligraphy #calligraphie #書法 #書道 #水彩画 #水彩畫 #sumi_e…
Liked by Come Raczy
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@Illumina Connected Software is here to power your next innovations and solutions. From work in human genetics and drug discovery, rare disease and…
@Illumina Connected Software is here to power your next innovations and solutions. From work in human genetics and drug discovery, rare disease and…
Liked by Come Raczy
Experience
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Self-employed
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Education
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University of Lille 1
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Defined an efficient method to compute smooth time optimal controls for differentially flat systems.
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Concepts and fundamental principles in key management disciplines, and how to apply them to improve decision-making within your organisation.
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Implemented operations on usual data structures (lists, trees, etc.) for massively parallel synchronous computers.
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Implemented the signal processing software for a multi-probe microwave radiometric imaging system.
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Licenses & Certifications
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Certified ScrumMaster
Scrum Alliance
Issued
Publications
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k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.
Nucleic Acids Research
k-SLAM is a highly efficient algorithm for the characterization of metagenomic data. Unlike other ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identification and variant calling in addition to accurate taxonomic classification. A k-mer based method provides greater taxonomic accuracy than other classifiers and a three orders of magnitude speed increase over alignment based approaches. The use of alignments to find variants and genes along with their…
k-SLAM is a highly efficient algorithm for the characterization of metagenomic data. Unlike other ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identification and variant calling in addition to accurate taxonomic classification. A k-mer based method provides greater taxonomic accuracy than other classifiers and a three orders of magnitude speed increase over alignment based approaches. The use of alignments to find variants and genes along with their taxonomic origins enables novel strains to be characterized. k-SLAM's speed allows a full taxonomic classification and gene identification to be tractable on modern large data sets. A pseudo-assembly method is used to increase classification accuracy by up to 40% for species which have high sequence homology within their genus.
Other authorsSee publication -
Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platforms
Bioinformatics/Oxford University Press
An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high memory hardware (>48GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is 4-5 times faster than BWA+GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on…
An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high memory hardware (>48GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is 4-5 times faster than BWA+GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware.
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Projects
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DRAGMAP
DRAGEN open source mapper: pure software implementation of the embedded FPGA implementation running on Illumina sequencers
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Isaac aligner
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Languages
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French
Native or bilingual proficiency
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English
Full professional proficiency
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Spanish
Limited working proficiency
Recommendations received
4 people have recommended Come
Join now to viewMore activity by Come
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I am looking forward to speaking tomorrow (2 July) at the Privacy Laws & Business International Conference in Cambridge, UK, on EU perspectives on AI…
I am looking forward to speaking tomorrow (2 July) at the Privacy Laws & Business International Conference in Cambridge, UK, on EU perspectives on AI…
Liked by Come Raczy
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Leave no gene behind with #DRAGEN. At @Illumina, we are committed to improving the detection of variants in difficult medically relevant genes such…
Leave no gene behind with #DRAGEN. At @Illumina, we are committed to improving the detection of variants in difficult medically relevant genes such…
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Bravo à George Drettakis et à son équipe GraphDeco d'Inria de l'Université Côte d’Azur pour cette avancée spectaculaire dans la reconstruction 3D qui…
Bravo à George Drettakis et à son équipe GraphDeco d'Inria de l'Université Côte d’Azur pour cette avancée spectaculaire dans la reconstruction 3D qui…
Liked by Come Raczy
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DRAGEN v4.3 is here! bringing our best #multigenomemapping with a prebuilt pangenome containing 128 diverse samples and the ability to build your…
DRAGEN v4.3 is here! bringing our best #multigenomemapping with a prebuilt pangenome containing 128 diverse samples and the ability to build your…
Liked by Come Raczy
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I’m looking for a way to get into machine learning. I’ve studied it extensively for the past year, so I know the basics. I can’t get one interview…
I’m looking for a way to get into machine learning. I’ve studied it extensively for the past year, so I know the basics. I can’t get one interview…
Liked by Come Raczy
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Illumina Connected Insights version 4.0 is out! Now supporting variant interpretation for somatic oncology assays at scale, enabling - powerful…
Illumina Connected Insights version 4.0 is out! Now supporting variant interpretation for somatic oncology assays at scale, enabling - powerful…
Liked by Come Raczy
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Call me a neuro nerd, but pose estimation using deep learning is one of the coolest technologies out there. Allows you to deeply quantify animal…
Call me a neuro nerd, but pose estimation using deep learning is one of the coolest technologies out there. Allows you to deeply quantify animal…
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