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Posts by Collection
portfolio
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publications
Improved gap size estimation for scaffolding algorithms
Published in Bioinformatics, 2012
This paper presents a statistical model for contig gap size prediction.
BESST- Efficient scaffolding of large fragmented assemblies
Published in BMC Bioinformatics, 2014
This paper presents a de novo assembly scaffolder BESST.
Assembly scaffolding with PE-contaminated mate-pair libraries
Published in Bioinformatics, 2016
This paper presents methodology improvements to the de novo assembly scaffolder BESST.
Structural Variation Detection with Read Pair Information: An Improved Null-Hypothesis Reduces Bias
Published in Journal of Computational Biology, 2017
This paper highlights size bias in calling structural variations (specifically insertions and deletions) from mate-pair and paired-end sequencing data. The paper presents a model to correct for this bias. The model allows for fast computiation of unique optima, introducing minimal ovehead to methods that does not model this.
Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon
Published in Nature Communications, 2018
IsoCon is a tool for reconstructing transcripts from highly similar gene families with PacBio Iso-Seq data.
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm
Published in Journal of Computational Biology, 2019
This paper presents a method and its implementation to do reference-free clustering of long transcript reads into genes.
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
Published in Nature Communications, 2021
This paper presents a method and its implementation to do reference-free error correction of Oxford Nanopore cDNA sequenceing data.
software
BESST
Published:
A de novo genome assembly scaffolder.
BESST_RNA
Published:
A de novo genome assembly scaffolder using RNA-seq data.
IsoCon
Published:
IsoCon is a tool for reconstructing transcripts from highly similar gene families with PacBio Iso-Seq data.
isONclust
Published:
isONclust is a tool for reference-free clustering of long transcript reads into genes.
talks
teaching
Programming Techniques for Mathematicians (7.5hp)
Undergraduate course, Stockholm University, Department of Mathematics, 2020
Introductory course in programming techniques using Python. Fundamental computer concepts such as
Applied programming for Life Science 2 (1.5hp)
Undergraduate course, Stockholm University, Department of Mathematics, 2020
Introductory course in programming techniques using Python.
Programming Techniques for Mathematicians (7.5hp)
Undergraduate course, Stockholm University, Department of Mathematics, 2020
Introductory course in programming techniques using Python. Fundamental computer concepts such as
Applied programming for Life Science 2 (1.5hp)
Undergraduate course, Stockholm University, Department of Mathematics, 2021
Introductory course in programming techniques using Python.