| 1. |
- Ekim, Baris, et al.
(author)
-
Efficient mapping of accurate long reads in minimizer space with mapquik
- 2023
-
In: Genome Research. - 1088-9051 .- 1549-5469. ; 33:7, s. 1188-1197
-
Journal article (peer-reviewed)abstract
- DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g., Pacific Biosciences [PacBio] HiFi) to a reference genome, which poses challenges in terms of accuracy and computational resources when using cutting-edge read mapping approaches that are designed for all types of alignments. A natural idea would be to optimize efficiency with longer seeds to reduce the probability of extraneous matches; however, contiguous exact seeds quickly reach a sensitivity limit. We introduce mapquik, a novel strategy that creates accurate longer seeds by anchoring alignments through matches of k consecutively sampled minimizers (k-min-mers) and only indexing k-min-mers that occur once in the reference genome, thereby unlocking ultrafast mapping while retaining high sensitivity. We show that mapquik significantly accelerates the seeding and chaining steps-fundamental bottlenecks to read mapping-for both the human and maize genomes with >96% sensitivity and near-perfect specificity. On the human genome, for both real and simulated reads, mapquik achieves a 37x speedup over the state-of-the-art tool minimap2, and on the maize genome, mapquik achieves a 410x speedup over minimap2, making mapquik the fastest mapper to date. These accelerations are enabled from not only minimizer-space seeding but also a novel heuristic O(n) pseudochaining algorithm, which improves upon the long-standing O(nlogn) bound. Minimizer-space computation builds the foundation for achieving real-time analysis of long-read sequencing data.
|
|
| 2. |
- Lasaviciute, Gintare, 1990-, et al.
(author)
-
Human Bone Marrow Mesenchymal Stromal Cell-Derived CXCL12, IL-6 and GDF-15 and Their Capacity to Support IgG-Secreting Cells in Culture Are Divergently Affected by Doxorubicin
- 2021
-
In: Hemato. - : MDPI AG. - 2673-6357. ; 2:1, s. 154-166
-
Journal article (peer-reviewed)abstract
- Various subsets of bone marrow mesenchymal stromal cells (BM MSCs), including fibroblasts, endothelial, fat and reticular cells, are implicated in the regulation of the hematopoietic microenvironment and the survival of long-lived antibody-secreting cells (ASCs). Nowadays it is widely acknowledged that vaccine-induced protective antibody levels are diminished in adults and children that are treated for hematological cancers. A reason behind this could be damage to the BM MSC niche leading to a diminished pool of ASCs. To this end, we asked whether cell cytotoxic treatment alters the capacity of human BM MSCs to support the survival of ASCs. To investigate how chemotherapy affects soluble factors related to the ASC niche, we profiled a large number of cytokines and chemokines from in vitro-expanded MSCs from healthy donors or children who were undergoing therapy for acute lymphoblastic leukemia (ALL), following exposure to a widely used anthracycline called doxorubicin (Doxo). In addition, we asked if the observed changes in the measured soluble factors after Doxo exposure impacted the ability of the BM niche to support humoral immunity by co-culturing Doxo-exposed BM MSCs with in vitro-differentiated ASCs from healthy blood donors, and selective neutralization of cytokines. Our in vitro results imply that Doxo-induced alterations in BM MSC-derived interleukin 6 (IL-6), CXCL12 and growth and differentiation factor 15 (GDF-15) are not sufficient to disintegrate the support of IgG-producing ASCs by the BM MSC niche, and that serological memory loss may arise during later stages of ALL therapy.
|
|
| 3. |
- Marschall, Tobias, et al.
(author)
-
Computational pan-genomics : status, promises and challenges
- 2018
-
In: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 19:1, s. 118-135
-
Journal article (peer-reviewed)abstract
- Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
|
|
| 4. |
- Sahlin, Kristoffer, et al.
(author)
-
Assembly scaffolding with PE-contaminated mate-pair libraries
- 2016
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:13, s. 1925-1932
-
Journal article (peer-reviewed)abstract
- Motivation: Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-end libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problems is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed before, in relation to integrated scaffolders, but solutions rely on the orientation being observable, e.g. by finding the junction adapter sequence in the reads. This is not always possible, making orientation and insert size of a read pair stochastic. To our knowledge, there is neither previous work on modeling PE-contamination, nor a study on the effect PE-contamination has on scaffolding quality. Results: We have addressed PE-contamination in an update to our scaffolder BESST. We formulate the problem as an integer linear program which is solved using an efficient heuristic. The new method shows significant improvement over both integrated and stand-alone scaffolders in our experiments. The impact of modeling PE-contamination is quantified by comparing with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in an increased number of misassemblies, more conservative scaffolding and inflated assembly sizes.
|
|
| 5. |
- Sahlin, Kristoffer, 1984-, et al.
(author)
-
Genome scaffolding with PE-contaminated mate-pair libraries
- 2015
-
Other publication (other academic/artistic)abstract
- Scaffolding is often an essential step in a genome assembly process,in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed in previous work on integrated scaffolders in end-to-end assemblers such as Allpaths-LG and MaSuRCA but the methods relies on the fact that the orientation is observable, \emph{e.g.}, by finding the junction adapter sequence in the reads. This is not always the case, making orientation and insert size of a read pair stochastic. Furthermore, work on modeling PE-contamination has so far been disregarded in stand-alone scaffolders and the effect that PE-contamination has on scaffolding quality has not been examined before. We have addressed PE-contamination in an update of our scaffolder BESST. We formulate the problem as an Integer Linear Program (ILP) and use characteristics of the problem, such as contig lengths and insert size, to efficiently solve the ILP using a linear amount (with respect to the number of contigs) of Linear Programs. Our results show significant improvement over both integrated and standalone scaffolders. The impact of modeling PE-contamination is quantified by comparison with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in increased number of misassemblies, more conservative scaffolding, and inflated assembly sizes. The model is implemented in BESST. Source code and usage instructions are found at https://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.
|
|
| 6. |
- Willink, Beatriz, 1988-, et al.
(author)
-
The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies
- 2024
-
In: Nature Ecology & Evolution. - 2397-334X. ; 8:1, s. 83-97
-
Journal article (peer-reviewed)abstract
- Sex-limited morphs can provide profound insights into the evolution and genomic architecture of complex phenotypes. Inter-sexual mimicry is one particular type of sex-limited polymorphism in which a novel morph resembles the opposite sex. While inter-sexual mimics are known in both sexes and a diverse range of animals, their evolutionary origin is poorly understood. Here, we investigated the genomic basis of female-limited morphs and male mimicry in the common bluetail damselfly. Differential gene expression between morphs has been documented in damselflies, but no causal locus has been previously identified. We found that male mimicry originated in an ancestrally sexually dimorphic lineage in association with multiple structural changes, probably driven by transposable element activity. These changes resulted in similar to 900 kb of novel genomic content that is partly shared by male mimics in a close relative, indicating that male mimicry is a trans-species polymorphism. More recently, a third morph originated following the translocation of part of the male-mimicry sequence into a genomic position similar to 3.5 mb apart. We provide evidence of balancing selection maintaining male mimicry, in line with previous field population studies. Our results underscore how structural variants affecting a handful of potentially regulatory genes and morph-specific genes can give rise to novel and complex phenotypic polymorphisms.
|
|
