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Articles by Human Technopole
Enzyme kinetics shapes the growth response of metabolic networks
Supporting information Construction of growth-optimal states, model comparison to experimental data, detailed description of the regulatory and evolutionary model, and comparison to related modeling approaches. https://doi.org/10.1371/journal.pcbi.1014642.s001 (PDF) Curated pathways (top) and sectors (bottom) of E. coli used in this study are listed by decreasing variance in log growth response (). From left to right: (1) Pathway name. (2) KEGG ID.
Competing gene regulatory networks drive naive and memory B cell differentiation
Naive and memory B cells have distinct differentiation outcomes To investigate the activation dynamics, differentiation outcomes and control of CSR in naive and memory B cells, we established an in vitro model of B cell activation. We purified human naive and memory B cells from PBMCs (Methods). To elucidate GRNs driving isotype switching, we removed B cells expressing switched antibody isotypes.
The genetic basis of the immune response to SARS-CoV-2 infection and vaccination in the Italian municipality of Vo’
Abstract Introduction: It is becoming increasingly evident that SARS-CoV-2 infection is here to stay. Therefore, understanding whether genetic variants may impact the response to the virus or vaccination is crucial. Studies on the genetic determinants of immune responses to SARS-CoV-2 have been limited by the scarcity of genetically homogenous populations and longitudinal designs that assess responses to both infection and vaccination in relation to individual genetic variation.
Best Practices in Cryo-EM Workshop
International Science Council Scientific Freedom Policy The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science. IUCr policy on Gender Equity and Diversity
Tissue-specific anti-tumor NK cell subsets identified in colorectal cancer liver metastases express candidate therapeutic targets
This record contains processed data related to article Tissue-specific anti-tumor NK cell subsets identified in colorectal cancer liver metastases express candidate therapeutic targets Abstract Liver metastases are relatively resistant to checkpoint blockade immunotherapy. The hepatic tissue has distinctive features including high numbers of NK cells.
Correction: Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA - BMC Genomics
Correction Open access Published: 01 August 2025 BMC Genomics volume 26, Article number: 714 (2025) Cite this article The Original Article was published on 01 July 2025 Correction: BMC Genomics 26, 583 (2025) https://doi.org/10.1186/s12864-025-11747-y Following publication of the original article it was reported that the Competing Interests declaration was incorrect. The original Competing Interests declaration stated: The authors declare no competing interests.
Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA - BMC Genomics
CrossWGCNA is a computational method aiming at identifying highly interacting genes across tissues or organs. It is based on the widely used WGCNA (Weighted Gene Co-expression Network Analysis) method [16] for generating scale-free biological networks based on high-throughput molecular data.
MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles - Genome Biology
Omics data is commonly represented in the form of high-dimensional, sometimes sparse, numerical matrices. In this context, dimensionality reduction becomes essential not only to make subsequent analysis feasible from a computational point of view, but also to filter out technical noise and minor sources of variability.
Voltage-gated ion channel diversity underlies neuronal excitability and nervous system evolution
Abstract All nervous systems function via electrical excitability mediated by ion channels. However, channels and excitability are both ancient, preneuronal features that many cells use to rapidly adjust behavior.
Clinical utility and implementation of polygenic risk scores for predicting cardiovascular disease: A clinical consensus statement of the ESC Council on Cardiovascular Genomics, the ESC Cardiovascular Risk Collaboration, and the European Association of Pr
Genome-wide association studies have revealed hundreds of genetic variants associated with cardiovascular diseases (CVD). Polygenic risk scores (PRS) can capture this information in a single metric and hold promise for use in CVD risk prediction. Importantly, PRS information can reflect the causally mediated risk to which the individual is exposed throughout life.
TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing
Cryo-electron tomography (cryo-ET) is emerging as the method of choice for determining the structures of biological macromolecules in situ, that is, within their native context inside cells or intact extracellular particles (Young & Villa, 2023; McCafferty et al., 2024).
Cluster-efficient pangenome graph construction with nf-core/pangenome
Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.
Protofilament-specific nanopatterns of tubulin post-translational modifications regulate the mechanics of ciliary beating
Keywords tubulin posttranslational modification motile cilia tubulin code cryo-ET U-ExM tubulin glycylation tubulin polyglutamylation Chlamydomonas cilia motility microtubule protofilaments molecular nanopatterns Introduction Cilia are thin, elongated, microtubule-based organelles with key conserved roles in organismal development and homeostasis.1,2,3,4 Their correct function relies on the precise organization of different macromolecular components along a microtubular scaffold called the...
Author Correction: A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data - Genome Biology
Author Correction: A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data Author Correction Open access Published: 04 September 2024 Genome Biology volume 25, Article number: 239 (2024) Cite this article The Original Article was published on 19 July 2024 Correction: Genome Biol 25, 192 (2024) https://doi.org/10.1186/s13059-024-03336-1 Following publication of the original article [1], the authors identified an omission in the...
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data - Genome Biology
We compared the performances of CRISPRcleanR (CCR) [34], Chronos [39], Crispy [33], Local Drop Out (LDO), Generalized Additive Model (GAM) [40], Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) based on a maximum likelihood estimation method [41, 42], and the recent Geometric method introduced in [35], in terms of correction of biases observed in widely used large-scale CRISPR-Cas9 screening dataset.
Pangenome graph layout by Path-Guided Stochastic Gradient Descent
The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human readable graph layout: A graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph’s potential excessive size, this is a significant challenge.
Immune evasion impacts the landscape of driver genes during cancer evolution - Genome Biology
To determine the impact of immune evasion in the selective landscape of tumorigenesis, we obtained a catalog of 88 genes involved in the antigen presenting machinery or previously associated to immune evasion [18] (defined as “escape genes,” Additional file 2: Table S1). We classified 9896 TCGA patients from 31 different cancer subtypes into escaped (escape +) and non-escaped (escape −) cohorts based on the presence of a non-silent point mutation in one of these genes (Fig. 1).
In and out: Benchmarking in vitro, in vivo, ex vivo, and xenografting approaches for an integrative brain disease modeling pipeline
Associated podcast For an associated discussion of this work, listen to the latest episode of The Stem Cell Report podcast at https://www.isscr.org/podcast/s3-e9, brought to you by the ISSCR. Summary Human cellular models and their neuronal derivatives have afforded unprecedented advances in elucidating pathogenic mechanisms of neuropsychiatric diseases. Notwithstanding their indispensable contribution, animal models remain the benchmark in neurobiological research.
Cost-effectiveness of single-pill and separate-pill administration of antihypertensive triple combination therapy: a population-based microsimulation study | BMC Public Health | Full Text
The present study adhered to the reporting guideline of Consolidated Health Economic Evaluation Reporting Standards (CHEERS) [12]. Data were extracted from the Healthcare Utilization Databases of Lombardy, a region in Italy representing nearly 16% (approximately 10 million) of its population.
Deep Archetypal Analysis for interpretable multi-omic data integration based on biological principles
Abstract High-throughput multi-omic molecular profiling allows probing biological systems at unprecedented resolution. However, the integration and interpretation of high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biology using current methods is particularly difficult because they are not based on biological principles, but instead focus exclusively on a dimensionality reduction task.
Interpretable Multi-Omics Data Integration with Deep Archetypal Analysis
Abstract High-throughput multi-omics technologies offer a lens through which the concurrent states of biological systems can be viewed. However, the integration and interpretation of high-dimensional, sparse, and noisy multi-omics datasets is challenging, often requiring leveraging algorithms for dimensionality reduction. Here we introduce Deep Archetypal Analysis for the Representation of Integrated Omics (DAARIO), a framework that combines archetypal analysis with deep learning.
Resource allocation in biochemically structured metabolic networks
Abstract Microbes tune their metabolism to environmental challenges by changing protein expression levels, metabolite concentrations, and reaction rates simultaneously. Here, we establish an analytical model for microbial resource allocation that integrates enzyme biochemistry and the global architecture of metabolic networks.
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc - Genome Biology
CNAqc supports the two most popular human reference genome assemblies GRCh38 and hg19 and distinguishes between different types of allele-specific CNAs: “Simple clonal CNAs”: clonal segments including states of heterozygous diploid (AB or 1:1), monosomy loss of heterozygosity (LOH) (A or 1:0), copy-neutral loss of heterozygosity (LOH) (AA or 2:0), triploid amplification (AAB or 2:1), and tetraploid amplification (AABB or 2:2); “Complex clonal CNAs”: clonal segments with any combination of...
SARS-CoV-2 infection causes dopaminergic neuron senescence
Highlights • hPSC-derived DA neurons are susceptible to SARS-CoV-2 infection • SARS-CoV-2 infection of DA neurons triggers cellular senescence response • Several FDA-approved drugs were identified to rescue senescence of DA neurons • Cellular senescence was found in substantia nigra tissues of COVID-19 patients Summary COVID-19 patients commonly present with signs of central nervous system and/or peripheral nervous system dysfunction.
Compartmentalizing damaged DNA: A double-edged sword
A recent publication in Nature by Arnould et al.describes a novel chromatin compartment, termed “damaged” or “D compartment,” that facilitates the repair of DNA double-strand breaks but also increases the risk of potentially oncogenic translocation formation.
A super-pangenome of the North American wild grape species - Genome Biology
Several plant tissues (see corresponding sections below) were collected for sequencing of DNA, RNA, and full-length transcripts, Bionano next-generation mapping, and flow cytometry. All plant material intended for nucleic acid extraction was immediately frozen upon collection and ground in liquid nitrogen. Most of the samples were collected from accessions maintained in the vineyards by the Foundation Plant Services at the University of California, Davis (Additional File 1: Table S1).
Cancer Evolution: A Multifaceted Affair
This content is only available via PDF. This open access article is distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License .
CHARR efficiently estimates contamination from DNA sequencing data
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Adapting cardiovascular risk prediction models to different populations: the need for recalibration
This editorial refers to ‘Recommendations for statin management in primary prevention: disparities among international risk scores’, by G.B.J. Mancini et al., https://doi.org/10.1093/eurheartj/ehad539.
Phenotypic noise and plasticity in cancer evolution
Highlights Cancer cells change phenotype through cancer evolution; some phenotype changes are caused by underlying genetic mutations, but many are due to non-genetic mechanisms. We suggest separating non-genetic phenotype changes into two distinct mechanisms: changes induced by microenvironmental stimuli (that we term ‘phenotypic plasticity’) and changes induced by stochastic cell-intrinsic effects (that we term ‘phenotypic noise’).
Opportunities and tradeoffs in single-cell transcriptomic technologies
Highlights Different single-cell sequencing approaches have unique strengths and weaknesses, with cellular throughput and transcript coverage being generally anticorrelated. Characterization of rearranged V(D)J sequences in lymphocytes is a valuable complement to single-cell analysis of adaptive immune responses. Single-cell transcriptomics start to go beyond gene-level quantification and incorporate differential transcription start site and isoform usage in a cell-state-specific manner.
RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity
Highlights • RAGE activation in monocytes strongly correlates with COVID-19 severity at admission • Patients’ healing is associated with deactivation of the RAGE pathway • RAGE and the S1-RBD of SARS-CoV-2 interact directly in silico and in vitro • RAGE is involved in monocyte permissiveness to SARS-CoV-2 entry Summary The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of...
Anatomically compliant modes of variations: New tools for brain connectivity
Conclusions In the present work, we proposed to extend the use of SF-PCA method, previously validated for FC maps computed over the cortical surface, for the analysis of grey matter volume data. The FC maps considered refer to two separate fMRI sessions: one resting-state and one during a task based on the switching paradigm. The adequacy of the proposed approach is assessed through classification performance and compliance of the extracted features with previous findings.
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
Citation: Patruno L, Milite S, Bergamin R, Calonaci N, D’Onofrio A, Anselmi F, et al. (2023) A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput Biol 19(11): e1011557. https://doi.org/10.1371/journal.pcbi.1011557 Editor: Teresa M. Przytycka, National Library of Medicine, UNITED STATES Received: August 14, 2023; Accepted: September 30, 2023; Published: November 2, 2023 Copyright: © 2023 Patruno et al.
Enhancers dysfunction in the 3D genome of cancer cells
Principles of 3D genome organization and functions The spatial organization of eukaryotic genomes within the cell nucleus meets the necessity to fit very long DNA molecules into relatively small nuclei with an average diameter of 10 µm (Sun et al., 2000; Piovesan et al., 2019). This physical constraint has represented an increasing challenge for eukaryotes during evolution as genomes became larger and more complex (Fedoroff, 2012).
Intracellular traffic and polarity in brain development
Martina Polenghi1 Elena Taverna1* 1Neurogenomics Research Centre, Human Technopole, Italy The final, formatted version of the article will be published soon. Receive an email when it is updated Neurons forming the human brain are generated during embryonic development by neural stem and progenitor cells via a process called neurogenesis.
Better Research Software Tools to Elevate the Rate of Scientific Discovery or why we need to invest in research software engineering
Joran Deschamps1* Damian Dalle Nogare1 Florian Jug1* 1Human Technopole, Italy The final, formatted version of the article will be published soon. Receive an email when it is updated You just subscribed to receive the final version of the article The maintenance problem and its technical and social causes Two major determinants for the widespread adoption of a tool are its usability and its maintenance over time [7,8].
Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR
Abstract Specificity in protein–DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5′-phosphate (PLP) biosynthesis.
Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression
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Adherence to antidiabetic drug therapy and reduction of fatal events in elderly frail patients - Cardiovascular Diabetology
References Zoungas S, Arima H, Gerstein HC, Holman RR, Woodward M, Reaven P, Hayward RA, Craven T, Coleman RL, Chalmers J. Effects of intensive glucose control on microvascular outcomes in patients with type 2 diabetes: a meta-analysis of individual participant data from randomised controlled trials. Lancet Diabetes Endocrinol. 2017;5:431–7.
Learning high-order interactions for polygenic risk prediction
Loading metrics Open Access Peer-reviewed Research Article Abstract Within the framework of precision medicine, the stratification of individual genetic susceptibility based on inherited DNA variation has paramount relevance. However, one of the most relevant pitfalls of traditional Polygenic Risk Scores (PRS) approaches is their inability to model complex high-order non-linear SNP-SNP interactions and their effect on the phenotype (e.g. epistasis).
Mendelian randomisation identifies priority groups for prophylactic EBV vaccination - BMC Infectious Diseases
In order to perform an MR on the association between the acquisition of EBV infection and different putative risk factors, we undertook the following steps, each of which are laid out in separate sections of the methods. (1) Identify a population of interest for the analysis within which (2) EBV serostatus (as a proxy for infection) had been tested for and (3) which had been genotyped. (4) Identify the putative risk factors of interest for EBV infection from the published literature.
A wholistic view on the study of cell biology of brain development and evolution
Felipe Mora-Bermúdez1, Giuseppe Testa2 and Elena Taverna2* 1Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society, Germany 2Human Technopole, Italy Provisionally accepted: The final, formatted version of the article will be published soon.
The length of FOXE1 polyalanine tract in congenital hypothyroidism: evidence for a pathogenic role from familial, molecular and cohort studies
Elisa S. Grassi1, Giuditta Rurale2, Tiziana de Filippis2, Davide Gentilini2, 3, Erika Carbone2, Francesca Coscia4, Sarah Uraghi5, Martyn Bullock6, Roderick Clifton-Bligh6, Abhinav K.
Unbiased pangenome graphs
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Obesity and cardiovascular disease: mechanistic insights and management strategies. A joint position paper by the World Heart Federation and World Obesity Federation
See the editorial comment for this article ‘Obesity and cardiovascular disease: beyond body weight and energy balance’, by Katharina Lechner and Ronald M. Krauss, https://doi.org/10.1093/eurjpc/zwac220.
Using genetic variation to disentangle the complex relationship between food intake and health outcomes
Results in context Previous MR studies have mainly focused on specific food groups such as coffee, alcohol and milk consumption while none has comprehensively investigated the role of different food groups on health outcomes. Here we have expanded this approach to encompass a wide range of specific foods and dietary patterns allowing to compare results across the different traits and giving us more insight in the interpretation of the results.
Dangerous RNA links pave the way to glioblastoma
Deforzh et al. investigated a common mechanism of HOXD/miR-10b genes’ derepression in glioblastoma and revealed the coordinated activity of two lncRNAs, HOXD-embedded HOXD-AS2 and distant enhancer-associated LINC01116, in CTCF/cohesin binding, chromatin topology, and astrocyte transformation. The work shed light on the molecular mechanisms of gliomagenesis.
EZH2-Mediated H3K27me3 Targets Transcriptional Circuits of Neuronal Differentiation
Impact Factor 4.677 | CiteScore 5.4 More on impact › TABLE OF CONTENTS 1Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy 2Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy 3Human Technopole, Milan, Italy 4Department of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland The Polycomb Repressive Complex 2 (PRC2) plays important roles in the epigenetic regulation of cellular development...
CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories
Highlights • CHD8-mutant cerebral organoids recapitulate a macrocephaly-like phenotype • Proliferation and differentiation dynamics are affected by CHD8 mutations • CHD8 haploinsufficiency disrupts neurodevelopmental trajectories • mRNA processing in post-mitotic neurons is altered in CHD8 mutants Summary Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD).
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