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Abstract Insider family citizens—that is, people who, according to their nationality/legal status and the possession of crucial resources for the settlement of their relatives in a foreign context—occupy an especially important place within a wide and diversified set of family relationships. Drawing on qualitative interviews with migrant women and children in mixed-status families in Italy and France, we argue that they can act as ‘membership intermediaries’ towards migrant spouses and a wider set of kin. First, facilitating non-citizen relatives’ formal incorporation in receiving countries through the provision of specially privileged forms of legality. Second, providing various resources for migrants’ informal incorporation, including housing ownership, additional income, emotional, and cultural capital. Nonetheless, the ambivalent dependencies these processes trigger can become sources of contention, heightening gender and intergenerational power imbalances in the household.

The 2020 regularisation for irregular migrant workers in Italy relied extensively on civil society actors' (CSAs) involvement to provide information, legal support and handle the bureaucratic procedures of the programme. Based on qualitative research carried out with CSAs, migrants and employers involved in the programme, the article describes the heterogeneity of the CSAs involved as well as the different politicisation routes they followed. We show that, through a series of activities – information provision, preparing and sending applications, institutional lobbying and case advocacy, civil disobedience and protest – CSAs have attempted to repoliticise the amnesty through four different avenues: solidarity, debordering, empowering and contention.

Abstract Background Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe. Results We present MALVIRUS, an easy-to-install and easy-to-use application that assists users in multiple tasks required for the analysis of a viral population, such as the SARS-CoV-2. MALVIRUS allows to: (1) construct a variant catalog consisting in a set of variations (SNPs/indels) from the population sequences, (2) efficiently genotype and annotate variants of the catalog supported by a read sample, and (3) when the considered viral species is the SARS-CoV-2, assign the input sample to the most likely Pango lineages using the genotyped variations. Conclusions Tests on Illumina and Nanopore samples proved the efficiency and the effectiveness of MALVIRUS in analyzing SARS-CoV-2 strain samples with respect to publicly available data provided by NCBI and the more complete dataset provided by GISAID. A comparison with state-of-the-art tools showed that MALVIRUS is always more precise and often have a better recall.

Abstract Background Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates. Moreover, there has been some recent evidence of back mutations in cancer: this phenomenon is currently widely ignored. Results We present a new tool, gpps, that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing each mutation to be lost at most a fixed number of times. The General Parsimony Phylogeny from Single cell (gpps) tool is open source and available at https://github.com/AlgoLab/gpps . Conclusions gpps provides new insights to the analysis of intra-tumor heterogeneity by proposing a new progression model to the field of cancer phylogeny reconstruction on Single Cell data.

The COVID-19 pandemic has unequally impacted the lives of Italian subjects. The article uses evidence from forty-seven semi-structured interviews with various migrant groups to illuminate how temporalities embedded in Italy’s migration governance shape migrants’ precarious legal status and access to welfare. The authors show that whereas migrants with secure legal status or citizenship have not engaged significantly with Italian bureaucracies, they have no easy access to welfare as it is contingent on their employment and financial status. Migrants with precarious status have been the worst hit by the pandemic’s secondary effects across several fronts. These findings have implications for policy and future research.

Summary: The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels). Here we introduce MALVA, a mapping-free method to genotype an individual from a sample of reads. MALVA is the first mapping-free tool able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variants. MALVA requires one order of magnitude less time to genotype a donor than alignment-based pipelines, providing similar accuracy. Remarkably, on indels, MALVA provides even better results than the most widely adopted variant discovery tools. : Biological Sciences; Genetics; Genomics; Bioinformatics Subject Areas: Biological Sciences, Genetics, Genomics, Bioinformatics

Abstract Background While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computationally feasible. This latter task, which is adequate for many transcriptome analyses, is usually achieved by aligning the reads to a reference genome, followed by comparing the alignments with a gene annotation, often implicitly represented by a graph: the splicing graph. Results We present ASGAL (Alternative Splicing Graph ALigner): a tool for mapping RNA-Seq data to the splicing graph, with the specific goal of detecting novel splicing events, involving either annotated or unannotated splice sites. ASGAL takes as input the annotated transcripts of a gene and a RNA-Seq sample, and computes (1) the spliced alignments of each read in input, and (2) a list of novel events with respect to the gene annotation. Conclusions An experimental analysis shows that ASGAL allows to enrich the annotation with novel alternative splicing events even when genes in an experiment express at most one isoform. Compared with other tools which use the spliced alignment of reads against a reference genome for differential analysis, ASGAL better predicts events that use splice sites which are novel with respect to a splicing graph, showing a higher accuracy. To the best of our knowledge, ASGAL is the first tool that detects novel alternative splicing events by directly aligning reads to a splicing graph. Availability Source code, documentation, and data are available for download at http://asgal.algolab.eu.

Abstract Background Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome. These long reads are also characterized by a high error rate, an issue which may be mitigated, however, with larger sets of reads, when this error rate is uniform across genome positions. Unfortunately, current state-of-the-art dynamic programming approaches designed for long reads deal only with limited coverages. Results Here, we propose a new method for assembling haplotypes which combines and extends the features of previous approaches to deal with long reads and higher coverages. In particular, our algorithm is able to dynamically adapt the estimated number of errors at each variant site, while minimizing the total number of error corrections necessary for finding a feasible solution. This allows our method to significantly reduce the required computational resources, allowing to consider datasets composed of higher coverages. The algorithm has been implemented in a freely available tool, HapCHAT: Haplotype Assembly Coverage Handling by Adapting Thresholds. An experimental analysis on sequencing reads with up to 60 × coverage reveals improvements in accuracy and recall achieved by considering a higher coverage with lower runtimes. Conclusions Our method leverages the long-range information of sequencing reads that allows to obtain assembled haplotypes fragmented in a lower number of unphased haplotype blocks. At the same time, our method is also able to deal with higher coverages to better correct the errors in the original reads and to obtain more accurate haplotypes as a result. Availability HapCHAT is available at http://hapchat.algolab.euunder the GNU Public License (GPL).

The problem of finding the maximum number of vertex-disjoint uni-color paths in an edge-colored graph has been recently introduced in literature, motivated by applications in social network analysis. In this paper we investigate the approximation and parameterized complexity of the problem. First, we show that, for any constant ε > 0, the problem is not approximable within factor c1-ε, where c is the number of colors, and that the corresponding decision problem is W[1]-hard when parametrized by the number of disjoint paths. Then, we present a fixed-parameter algorithm for the problem parameterized by the number and the length of the disjoint paths.

Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a characterization of the class of circular languages generated by circular splicing systems is still an open problem. In this paper we solve this problem for complete systems, which are special finite circular splicing systems. We show that a circular language L is generated by a complete system if and only if the set Lin(L) of all words corresponding to L is a pure unitary language generated by a set closed under the conjugacy relation. The class of pure unitary languages was introduced by A. Ehrenfeucht, D. Haussler, G. Rozenberg in 1983, as a subclass of the class of context-free languages, together with a characterization of regular pure unitary languages by means of a decidable property. As a direct consequence, we characterize (regular) circular languages generated by complete systems. We can also decide whether the language generated by a complete system is regular. Finally, we point out that complete systems have the same computational power as finite simple systems, an easy type of circular splicing system defined in the literature from the very beginning, when only one rule is allowed. From our results on complete systems, it follows that finite simple systems generate a class of context-free languages containing non-regular languages, showing the incorrectness of a longstanding result on simple systems.

The article explores the experiences of separation and reunification by children of migrant mothers in Italy by analysing 32 qualitative interviews conducted with adolescents who had rejoined their mothers at different points in their lives. We show that international migration causes children to face multiple shifts in the configuration of their family ties due to the geographical dislocations and re-locations to which these ties are subject. The way in which children interpret and adjust to these changes depends on factors such as the timing of the family migration process and the frequency of transnational family practices, which are affected by more or less abrupt discontinuities in family life after their mothers’ and their own departure.