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Quantitative Cell Biology · IBFG · CSIC

Dr. Alfonso
Fernández-Álvarez

Meiotic Chromosome Dynamics · Telomeres & Centromeres · Quantitative Imaging

Institute of Functional Biology and Genomics (IBFG) · CSIC / University of Salamanca

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I'm Alfonso
Fernández-Álvarez

I am a Tenured Scientist (Científico Titular) at CSIC, leading the Nuclear Dynamics, Telomeres & Reproduction group at the Institute of Functional Biology and Genomics (IBFG, CSIC/USAL) in Salamanca, Spain. Our lab focuses on quantitative cell biology of meiotic chromosome dynamics, using fission yeast Schizosaccharomyces pombe as a primary model organism.

I obtained my PhD in Genetics (2011, cum laude, Extraordinary Award) from Universidad Pablo de Olavide, Seville, working on protein glycosylation in the plant pathogen Ustilago maydis. I then trained as an EMBO Long-Term Fellow at the London Research Institute (Cancer Research UK, 2011–2014) and as Senior Postdoc at the NIH (Bethesda, 2014–2018), in both cases in the lab of Dr. Julie Cooper, specialising in telomere biology and live-cell quantitative imaging. I returned to Spain in 2018 as a Ramón y Cajal Fellow at CABD (Seville) before joining IBFG as CSIC Tenured Scientist in December 2021.

A hallmark of my research is the integration of experimental cell biology with quantitative and computational approaches, including unsupervised machine-learning analysis of chromosome trajectories. This has led to the open-access platform ChroMo for automated analysis of chromosome dynamics.

🧬 Meiosis 🔬 Chromosome Dynamics 🫧 Telomeres & Centromeres 💻 Bioinformatics 🍄 Fission Yeast 🤖 Quantitative Imaging & ML

Research Lines

Our lab combines genetics, quantitative live-cell microscopy and bioinformatics to understand how chromosomes segregate faithfully during meiosis.

🔄

Self-assembled meiotic spindle dynamics

We study how the meiotic spindle forms and functions in S. pombe and how its dynamic properties ensure faithful chromosome segregation. We use live-cell fluorescence microscopy combined with quantitative image analysis in real time.

Active
Funding: AEI Plan Estatal · CSIC / USAL (PID2021-127232NB-I00; PID2024-162761NB-I00)
🫧

Telomeres & centromeres in meiosis: the telomere bouquet

We explore the molecular identity, plasticity and mechanics of telomere bouquet formation and dissolution. Our 2025 Nature Communications paper showed that centromere positioning orchestrates bouquet formation and the onset of meiotic differentiation.

Active
Funding: AEI Plan Estatal · CSIC / USAL (PID2024-162761NB-I00)
💻

Computational analysis of chromosome movements

We develop unsupervised machine-learning algorithms to identify patterns in meiotic chromosome trajectories. This line gave rise to ChroMo, an open-access web platform for automated analysis of chromosome dynamics.

Active
Funding: AEI Plan Estatal · EMBO Short-Term & Scientific Exchange Grants
🧬

Expanding to new model organisms

We are extending our quantitative approaches to budding yeast and C. elegans to address nuclear organisation during gametogenesis from a comparative and biomedically relevant perspective, including implications for female fertility.

Active
Funding: AEI Plan Estatal · EMBO Scientific Exchange Grant (2025–2026)

Scientific Publications

Full list of 24 peer-reviewed articles. # = corresponding author. Also available on PubMed, Google Scholar and ORCID.

2025
Research Article · PLoS Genetics
PP6 phosphatase and Elongator contribute to kinesin 5-dependent spindle assembly by controlling microtubule regulators levels
Marín L, Castro-Sangrador J, Hoya M, Tello S, Coll PM, Encinar Del Dedo J, Fernández-Álvarez A, Ribas JC, Tran PT, Rincon SA
PLoS Genetics · 2025; 21(10):e1011596
2025
Research Article · Nature Communications
Centromere positioning orchestrates telomere bouquet formation and the initiation of meiotic differentiation
Jiménez-Martín A, Pineda-Santaella A, Martín-García R, Esteban-Villafañe R, Matarrese A, Pinto-Cruz J, Camacho-Cabañas S, León-Periñán D, Terrizzano A, Daga RR, Braun S, Fernández-Álvarez A#
Nature Communications · Jan 2025; 16(1):837
2024
Protocol · Methods in Molecular Biology
Identifying Chromosome Movement Patterns During Meiosis Using ChroMo
Pinto-Cruz J, Correas M, Mendoza-Madrigal R, León-Periñán D, Fernández-Álvarez A#
Methods in Molecular Biology · 2024; 2818:271–288
2023
Review · Frontiers in Cell and Developmental Biology
Beyond tradition: exploring the non-canonical functions of telomeres in meiosis
Fernández-Álvarez A#
Frontiers in Cell and Developmental Biology · Nov 2023; 11:1278571
2023
Protocol · STAR Protocols
Analyzing self-assembled spindle dynamics in fission yeast meiosis using in vivo fluorescence imaging
Pineda-Santaella A, Martín-García R, Fernández-Álvarez A#
STAR Protocols · Dec 2023; 4(4):102655
2022
Research Article · Molecular Biology of the Cell
The Rabl chromosome configuration masks a kinetochore reassembly mechanism in yeast mitosis
Jiménez-Martín A, Pineda-Santaella A, Pinto-Cruz J, León-Periñán D, García-Sánchez S, Delgado-Gestoso D, Marín-Toral L, Fernández-Álvarez A#
Molecular Biology of the Cell · May 2022; 33(5):br8
2021
Research Article · Journal of Cell Science
Loss of kinesin-8 improves the robustness of the self-assembled spindle in Schizosaccharomyces pombe
Pineda-Santaella A, Fernández-Castillo N, Jiménez-Martín A, Macías-Cabeza MDC, Sánchez-Gómez Á, Fernández-Álvarez A#
Journal of Cell Science · Aug 2021; 134(16):jcs253799
2021
Research Article · Cells
ChroMo, an Application for Unsupervised Analysis of Chromosome Movements in Meiosis
León-Periñán D, Fernández-Álvarez A#
Cells · Aug 2021; 10(8):2013
2021
Research Article · Journal of Fungi
Structural, Evolutionary, and Functional Analysis of the Protein O-Mannosyltransferase Family in Pathogenic Fungi
Pejenaute-Ochoa MD, Santana-Molina C, Devos DP, Ibeas JI, Fernández-Álvarez A#
Journal of Fungi · Apr 2021; 7(5):328
2019
Research Article · PLoS Pathogens
N-glycosylation of the protein disulfide isomerase Pdi1 ensures full Ustilago maydis virulence
Marín-Menguiano M, Moreno-Sánchez I, Barrales RR, Fernández-Álvarez A#, Ibeas JI#
PLoS Pathogens · Nov 2019; 15(11):e1007687
2019
Research Article · Chromosoma
Spindle assembly without spindle pole body insertion into the nuclear envelope in fission yeast meiosis
Pineda-Santaella A, Fernández-Álvarez A#
Chromosoma · Sep 2019; 128(3):267–277
2017
Research Article · Cell Cycle
The functionally elusive RabI chromosome configuration directly regulates nuclear membrane remodeling at mitotic onset
Fernández-Álvarez A, Cooper JP
Cell Cycle · Aug 2017; 16(15):1392–1396
2017
Review · Trends in Cell Biology
Chromosomes Orchestrate Their Own Liberation: Nuclear Envelope Disassembly
Fernández-Álvarez A, Cooper JP
Trends in Cell Biology · Apr 2017; 27(4):255–265
2016
Research Article · Developmental Cell
Mitotic Nuclear Envelope Breakdown and Spindle Nucleation Are Controlled by Interphase Contacts between Centromeres and the Nuclear Envelope
Fernández-Álvarez A#, Bez C, O'Toole ET, Morphew M, Cooper JP#
Developmental Cell · Dec 2016; 39(5):544–559
2015
Research Article · Nature Cell Biology
The telomere bouquet regulates meiotic centromere assembly
Klutstein M, Fennell A, Fernández-Álvarez A, Cooper JP
Nature Cell Biology · Apr 2015; 17(4):458–469
2015
Research Article · Journal of Cell Biology
Telomeres and centromeres have interchangeable roles in promoting meiotic spindle formation
Fennell A*, Fernández-Álvarez A*, Tomita K, Cooper JP (* co-first author)
Journal of Cell Biology · Feb 2015; 208(4):415–428
2015
Research Article · PLoS Pathogens
The Hos2 Histone Deacetylase Controls Ustilago maydis Virulence through Direct Regulation of Mating-Type Genes
Elías-Villalobos A, Fernández-Álvarez A, Moreno-Sánchez I, Helmlinger D, Ibeas JI
PLoS Pathogens · Aug 2015; 11(8):e1005134
2013
Research Article · Plant Cell
Endoplasmic reticulum glucosidases and protein quality control factors cooperate to establish biotrophy in Ustilago maydis
Fernández-Álvarez A, Elías-Villalobos A, Jiménez-Martín A, Marín-Menguiano M, Ibeas JI
Plant Cell · Nov 2013; 25(11):4676–4690
2012
Research Article · PLoS Pathogens
Identification of O-mannosylated virulence factors in Ustilago maydis
Fernández-Álvarez A, Marín-Menguiano M, Lanver D, Jiménez-Martín A, Elías-Villalobos A, Pérez-Pulido AJ, Kahmann R, Ibeas JI
PLoS Pathogens · Mar 2012; 8(3):e1002563
2011
Research Article · PLoS Pathogens
The general transcriptional repressor Tup1 is required for dimorphism and virulence in a fungal plant pathogen
Elías-Villalobos A, Fernández-Álvarez A, Ibeas JI
PLoS Pathogens · Sep 2011; 7(9):e1002235
2011
Research Article · Plant Cell
The DNA damage response signaling cascade regulates proliferation of the phytopathogenic fungus Ustilago maydis in planta
de Sena-Tomás C, Fernández-Álvarez A, Holloman WK, Pérez-Martín J
Plant Cell · Apr 2011; 23(4):1654–1665
2010
Research Article · Fungal Genetics and Biology
Protein glycosylation in the phytopathogen Ustilago maydis: From core oligosaccharide synthesis to the ER glycoprotein quality control system, a genomic analysis
Fernández-Álvarez A, Elías-Villalobos A, Ibeas JI
Fungal Genetics and Biology · Sep 2010; 47(9):727–735
2010
Research Article · Plant Signaling & Behavior
The requirement for protein O-mannosylation for Ustilago maydis virulence seems to be linked to intrinsic aspects of the infection process rather than an altered plant response
Fernández-Álvarez A, Elías-Villalobos A, Ibeas JI
Plant Signaling & Behavior · Apr 2010; 5(4):412–414
2009
Research Article · Plant Cell
The O-mannosyltransferase PMT4 is essential for normal appressorium formation and penetration in Ustilago maydis
Fernández-Álvarez A, Elías-Villalobos A, Ibeas JI
Plant Cell · Oct 2009; 21(10):3397–3412

Our Lab

We are a young, dynamic group at IBFG (CSIC/USAL) in Salamanca, combining experimental cell biology with quantitative and computational approaches.

🔬
Alfonso Fernández-Álvarez
Principal Investigator
Tenured Scientist (CSIC) · Group leader since 2021
🧪
Rebeca Martín García
Lab Technician (M3)
CSIC Technical Staff · Lab management & strain library
🎓
Sergio Camacho Cabañas
PhD Student
Meiotic chromosome dynamics in S. pombe
🎓
Rodrigo Esteban Villafañe
PhD Student
Co-supervised with Dr. Pedro San Segundo
🎓
Camino Villadangos Benavides
PhD Student
Telomere bouquet & nuclear organisation during meiosis
🎓
Javier Nuevo Aparicio
PhD Student
Quantitative approaches to chromosome segregation
👨‍🔬
Alberto Jiménez Martín
Postdoc · Juan de la Cierva (2021–2024)
→ Hospital Virgen del Rocío · AI & Clinical Data Sciences
🏆
Alberto Pineda Santaella
PhD, USAL 2024 · Cum Laude · International Mention
→ Marie Curie Postdoc · Oliferenko Lab, London
🏆
Sabas García Sánchez
PhD, USAL 2025 · Cum Laude · International Mention
→ Postdoctoral researcher in Spain
🌍
Antonia Terrizzano · Alix Matarrese · Ritisha Akilan
International Students · Université Paris IV (2021–2025)
→ Graduate research training in nuclear dynamics

Get in Touch

Open to scientific collaborations, enquiries about our research, Master's and PhD projects, and postdoctoral applications.

Address
IBFG · C/ Zacarías González 2
37007 Salamanca, Spain
Download CV (PDF)