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Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation

An evaluation framework isolates perturbation-specific effects in perturbation datasets.

Ramon Viñas Torné
Maciej Wiatrak
Maria Brbić
ResearchOpen Access25 Aug 2025
Nature Biotechnology

P: 1-10
Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis

Here, the authors investigate the proteome trajectory of human iPSCs differentiating into hepatic stellate cells (diHSCs) and identify RORA as a key transcription factor that governs metabolic reprogramming essential for diHSCs’ commitment, identity, and quiescent phenotype.

Raquel A. Martínez García de la Torre
Julia Vallverdú
Pau Sancho-Bru
ResearchOpen Access10 Feb 2025
Nature Communications

Volume: 16, P: 1-19
Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

Pandemic cholera was reintroduced to Argentina in 1992, leading to epidemic spread. Here, the authors use whole genome sequencing to show how, over 6 years, epidemic cholera was caused by invariant 7PET lineage Vibrio cholerae, against a background of sporadic disease caused by diverse local strains.

Matthew J. Dorman
Daryl Domman
Nicholas R. Thomson
ResearchOpen Access01 Oct 2020
Nature Communications

Volume: 11, P: 1-12
Pilot case control evaluation of artificial intelligence assisted orthodontic monitoring and pediatric patient perception

Ana Martínez Gil-Ortega
Patricia Cintora-López
Marta Macarena Paz-Cortés
ResearchOpen Access18 Nov 2025
Scientific Reports

Volume: 15, P: 1-10
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

The microbiota of cesarean-born infants can be partially restored to that of vaginally born infants immediately after birth.

Maria G Dominguez-Bello
Kassandra M De Jesus-Laboy
Jose C Clemente
Research01 Feb 2016
Nature Medicine

Volume: 22, P: 250-253
Bis-naphthopyrone pigments protect filamentous ascomycetes from a wide range of predators

It is thought that fungi protect themselves from predators by the production of toxic compounds. Here, Xu et al. show that a wide range of animal predators avoid feeding on Fusarium fungi, and this depends on fungal production of a bis-naphthopyrone pigment that is not toxic to the predators.

Yang Xu
Maria Vinas
Petr Karlovsky
ResearchOpen Access08 Aug 2019
Nature Communications

Volume: 10, P: 1-12
Reconciling global-model estimates and country reporting of anthropogenic forest CO₂ sinks

The model–inventory discrepancy in net land-use carbon emissions mainly results from conceptual differences in estimating anthropogenic forest sinks. A revised disaggregation of global land model results allows greater comparability with inventories.

Giacomo Grassi
Jo House
Sönke Zaehle
Research24 Sept 2018
Nature Climate Change

Volume: 8, P: 914-920
Music compensates for altered gene expression in age-related cognitive disorders

Alberto Gómez-Carballa
Laura Navarro
Antonio Salas
ResearchOpen Access02 Dec 2023
Scientific Reports

Volume: 13, P: 1-15
3D and 2D aromatic units behave like oil and water in the case of benzocarborane derivatives

2D/2D fusion of aromatic halves leading to a global aromatic is found in many polycyclic aromatic hydrocarbons, whereas 2D/3D aromaticity is difficult to achieve. Here the authors report a computational chemistry investigation showing that 3D/2D aromatic combination is not possible.

Jordi Poater
Clara Viñas
Francesc Teixidor
ResearchOpen Access04 Jul 2022
Nature Communications

Volume: 13, P: 1-8
The cognitive and psychiatric subacute impairment in severe Covid-19

Pedro J. Serrano-Castro
Francisco J. Garzón-Maldonado
Fernando Rodríguez de Fonseca
ResearchOpen Access03 Mar 2022
Scientific Reports

Volume: 12, P: 1-13
Craniofacial and three-dimensional palatal analysis in cleft lip and palate patients treated in Spain

María José Viñas
Francesca Galiotto-Barba
Elena Martínez-Sanz
ResearchOpen Access06 Nov 2022
Scientific Reports

Volume: 12, P: 1-13
Influence of historical land use and modern agricultural expansion on the spatial and ecological divergence of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) in Brazil

Vitor A. C. Pavinato
Andrew P. Michel
Maria I. Zucchi
Research20 Nov 2017
Heredity

Volume: 120, P: 25-37
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

María-Eugenia Guazzaroni
Florian-Alexander Herbst
Manuel Ferrer
ResearchOpen Access26 Jul 2012
The ISME Journal

Volume: 7, P: 122-136
Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

Sort-assisted single-cell chromatin immunocleavage (sortChIC) combines single-cell histone modification profiling with fluorescence-activated cell sorting (FACS), enabling the study of rare cell populations. H3K4me1/H3K4me3, H3K9me3 and H3K27me3 profiling of blood suggest a model of lineage-shared repressive and cell type-specific active chromatin.

Peter Zeller
Jake Yeung
Alexander van Oudenaarden
ResearchOpen Access20 Dec 2022
Nature Genetics

Volume: 55, P: 333-345
Pro-inflammatory Ca⁺⁺-activated K⁺ channels are inhibited by hydroxychloroquine

María Eugenia Schroeder
Sofía Russo
Marcelo Hill
ResearchOpen Access15 May 2017
Scientific Reports

Volume: 7, P: 1-7
Using population-based data to evaluate the impact of adherence to endocrine therapy on survival in breast cancer through the web-application BreCanSurvPred

Rebeca Font
Maria Buxó
Ramon Clèries
ResearchOpen Access16 May 2022
Scientific Reports

Volume: 12, P: 1-13
Visual simulators replicate vision with multifocal lenses

Maria Vinas
Clara Benedi-Garcia
Susana Marcos
ResearchOpen Access07 Feb 2019
Scientific Reports

Volume: 9, P: 1-11
Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa

Pamela Sánchez-Vendizú
Gideon Erkenswick
Mrinalini Watsa
ResearchOpen Access01 Oct 2025
Scientific Data

Volume: 12, P: 1-15
Orderly progression through S-phase requires dynamic ubiquitylation and deubiquitylation of PCNA

Vanesa Álvarez
Laura Viñas
Avelino Bueno
ResearchOpen Access06 May 2016
Scientific Reports

Volume: 6, P: 1-14
MAP kinase ERK5 modulates cancer cell sensitivity to extrinsic apoptosis induced by death-receptor agonists

Sergio Espinosa-Gil
Saska Ivanova
José Miguel Lizcano
ResearchOpen Access02 Nov 2023
Cell Death & Disease

Volume: 14, P: 1-17
HCV-coinfection is related to an increased HIV-1 reservoir size in cART-treated HIV patients: a cross-sectional study

Maria Rosa López-Huertas
Claudia Palladino
María Luisa Gaspar
ResearchOpen Access03 Apr 2019
Scientific Reports

Volume: 9, P: 1-10
Clockwise rotation of perspective view improves spatial recognition of complex environments in aging

Joaquín Castillo-Escamilla
Isabel Carmona
José Manuel Cimadevilla
ResearchOpen Access05 Nov 2022
Scientific Reports

Volume: 12, P: 1-12
Vision is protected against blue defocus

Clara Benedi-Garcia
Maria Vinas
Susana Marcos
ResearchOpen Access11 Jan 2021
Scientific Reports

Volume: 11, P: 1-9
Multifocal acceptance score to evaluate vision: MAS-2EV

Xoana Barcala
Maria Vinas
Carlos Dorronsoro
ResearchOpen Access14 Jan 2021
Scientific Reports

Volume: 11, P: 1-15
Brewers’ spent hop revalorization for the production of high added-value cosmetics ingredients with elastase inhibition capacity

Maria Paredes-Ramos
Enma Conde Piñeiro
Jose M. Lopez Vilariño
ResearchOpen Access21 Dec 2022
Scientific Reports

Volume: 12, P: 1-9
The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes

María Velasco-Galilea
Miriam Piles
Juan P. Sánchez
ResearchOpen Access30 Sept 2021
Scientific Reports

Volume: 11, P: 1-18

Search

Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation

Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis

Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

Pilot case control evaluation of artificial intelligence assisted orthodontic monitoring and pediatric patient perception

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

Bis-naphthopyrone pigments protect filamentous ascomycetes from a wide range of predators

Reconciling global-model estimates and country reporting of anthropogenic forest CO₂ sinks

Music compensates for altered gene expression in age-related cognitive disorders

3D and 2D aromatic units behave like oil and water in the case of benzocarborane derivatives

The cognitive and psychiatric subacute impairment in severe Covid-19

Craniofacial and three-dimensional palatal analysis in cleft lip and palate patients treated in Spain

Influence of historical land use and modern agricultural expansion on the spatial and ecological divergence of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) in Brazil

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

Pro-inflammatory Ca⁺⁺-activated K⁺ channels are inhibited by hydroxychloroquine

Using population-based data to evaluate the impact of adherence to endocrine therapy on survival in breast cancer through the web-application BreCanSurvPred

Visual simulators replicate vision with multifocal lenses

Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa

Orderly progression through S-phase requires dynamic ubiquitylation and deubiquitylation of PCNA

MAP kinase ERK5 modulates cancer cell sensitivity to extrinsic apoptosis induced by death-receptor agonists

HCV-coinfection is related to an increased HIV-1 reservoir size in cART-treated HIV patients: a cross-sectional study

Clockwise rotation of perspective view improves spatial recognition of complex environments in aging

Vision is protected against blue defocus

Multifocal acceptance score to evaluate vision: MAS-2EV

Brewers’ spent hop revalorization for the production of high added-value cosmetics ingredients with elastase inhibition capacity

The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes

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