ALESSANDRO PALMA

PROFESSIONAL SUMMARY
Experienced scientist with a strong background in both wet-lab and computational biology. I have developed solid expertise in cell and molecular biology, functional genomics, and next-generation sequencing data analysis. My scientific interests encompass a wide range of disciplines, including cancer and neuromuscular disorders. I have cultivated a robust set of technical and transferable skills, enabling me to conduct research and manage projects effectively, both independently and as part of a team.

EDUCATION
PhD in Cell and Molecular Biology - University of Rome “Tor Vergata”, Department of Biology, Rome (Italy)
Master’s Degree in Biology (Bioinformatics) – Faculty of Science, University of Rome “Tor Vergata”, Rome (Italy)
Bachelor’s degree in Medical Biotechnologies – Faculty of Science, University of L’Aquila, L’Aquila (Italy)

WORK EXPERIENCE
05/2025-present: Assistant Professor (RTT) – Cell and Applied Biology - Sapienza University of Rome, Department of Psychology
03/2023-05/2025: Research Fellow (RTDA) – Molecular Biology - Sapienza University of Rome, Department of Biology and Biotechnologies “Charles Darwin”
08/2021-03/2023: Postdoctoral researcher – Bambino Gesù Children’s Hospital IRCCS– Rome, Department of “Onco-hematology, cell and gene therapy” and “Translational Cytogenomics Research Unit”
11/2019-07/2021: Postdoctoral researcher – Telethon Institute of Genetics and Medicine (TIGEM) – Pozzuoli (NA)

TECHNICAL SKILLS
Proficient in R programming language, working in Linux environments. Academic knowledge and use of python programming language, knowledge of mysql, php and database management systems. Excellent use of Microsoft Office Suite. Professional knowledge and use of packages for the analysis of next generation sequencing data (bulk and single-cell RNA sequencing, mass cytometry, imaging mass cytometry, proteomics, flow cytometry), using programming languages and tools.
Professional knowledge and use of the great majority of commonly used cell and molecular biology techniques, including immunofluorescence, Western Blot, mammalian cell culture, transfection/transduction, PCR/qPCR, cloning systems, bacteria cell culture, cell biology assays, nucleic acid extraction.

LANGUAGES
Italian: fluent (mother tongue)
English: proficient

AWARDS AND SCIENTIFIC SERVICE
Awards
2023: Umberto Veronesi 2023 post-doctoral fellowship. Project title: “Expanding the germline mutational spectrum of pediatric patients with high-grade glioma for improved diagnosis”.
2021: AFM-Telethon post-doctoral fellowship. Project title: “Dissecting the role of ER-phagy in Pompe Disease”.
2021:Post-doctoral fellowship. University of Naples “Federico II”, Italian Ministry of University and Research (MIUR) fellowship (POC01_0078 project, PNR 2015-2020, “Bando Proof of Concept 2018”). Project title: Molecular analysis of tissue samples isolated from mice treated with three different doses of the autophagy inducer Tat-Beclin1.

Scientific Service
2021-present: Member of the Italian National Federation of Biologists (FNOB Lazio, ID: AA_089634)
2024: Member of the grant reviewers for the “Foundation for Rare Diseases”
2023-present: Advisor for students of the bachelor’s degree in Bioinformatics (Sapienza University of Rome) and master’s degree in Bioinformatics (University of Rome “Tor Vergata”)
2023: Member of the Graduation Committee for the bachelor’s degree in Bioinformatics (“Sapienza University of Rome) and bachelor’s degree in Biotechnologies (“Sapienza” University of Rome).

Editorial Positions:
Member of the Editorial Board for The Company of Biologists – Open Biology
Member of the Editorial Board for Springer Nature – Scientific Reports (Cell Biology)
Member of the Reviewer Board of the American Journal Experts (Research Square)
Associate Editor for Frontiers in Molecular Biosciences – Molecular Diagnostics and Therapeutics
Guest Associate Editor and occasional Editor for Frontiers in Immunology – Systems Immunology
Review Editor for Frontiers in Molecular Biosciences - RNA Networks and Biology
Review Editor for Frontiers in Immunology – Systems Immunology

Reviewer Positions:
• Wiley – Clinical and Translational Medicine
• Wiley – Advanced Science
• Wiley – Mediators of Inflammation
• Wiley – The FASEB Journal
• Wiley - Immunity inflammation and disease
• Cell Press - Cell Genomics
• Cell Press – Helyion
• Cell Press – STAR Protocols
• BMC - Biology Direct
• BMC - Journal of Hematology & Oncology
• BMC - Infectious Diseases
• BMC - Bioinformatics
• BMC - Neurology
• Taylor & Francis – RNA biology
• Taylor & Francis – All Life
• Taylor & Francis – Cell Adhesion & Migration
• Frontiers in Molecular Biosciences
• Frontiers in Cell and Developmental Biology
• Frontiers in Bioinformatics
• Frontiers in Pharmacology
• Frontiers in Immunology
• Nature - Scientific Reports
• Nature - Oncogenesis
• Nature - Communications Biology
• Springer Nature – Cellular and Molecular Life Sciences
• Springer Nature – Discover Oncology
• Springer Nature – Journal of Neuroinflammation
• Elsevier – Gene
• Elsevier - Biochemical and Biophysical Research Communications
• Elsevier - Computational and Structural Biotechnology Journal
• Elsevier - Immunobiology
• BMJ - Journal for ImmunoTherapy of Cancer

COURSES AND CERTIFICATIONS
02/2024: John Hopkins University, (online course) “Design and Interpretation of Clinical Trials”.
01/2024: The National Institutes of Health, (online course) “Introduction to the Principles and Practice of Clinical Research 2023-2024”.
08/2021: Elsevier, (online course) “Certified peer reviewer Course”.
05/2019: Telethon Institute of Genetics and Medicine – Pozzuoli (Naples), “Single-Cell RNA Sequencing and Data Analysis”.
05/2019: Fondazione Santa Lucia IRCCS – CNR – Rome, “The use of statistics in biomedical research and applications of the R software (advanced course)”.

CONFERENCES AND SEMINARS
Oct 2024: “Non-coding RNA World 2024: Exploring Mechanisms, Designing Medicines”, Basel (Switzerland). Abstract titles:

1. “The lncRNA Charme, an evolutionary conserved regulator of muscle differentiation and pathology”
2. “The role of the long non-coding RNA Charme in the phenotype and function of resident cardiac mesenchymal stromal cells”
3. “Targeting the MYC-dependent long non-coding RNA MB3 regulates the TGF-β and OTX2 pathways in Group 3 Medulloblastoma”
Jun 2024: “SIBBM 2024 conference – The time of Molecular Biology: development, homeostasis and aging” – Trento (Italy). Abstract title: “The nuclear lncRNA Charme plays an evolutionarily conserved role in the epigenetic regulation of muscle differentiation”

Mar 2024: “Cold Spring Harbor Laboratory Meeting - Regulatory & Non-Coding RNAs”, Cold Spring Harbor, NY (USA). Abstract title: “Neuromuscular interplay and lncRNAs - A synaptic liaison”

Feb 2024: “EMBO workshop 2024. The new cardiobiology” (Heidelberg, Germany). Abstract title: “From mouse to human: how RNA epigenetic influences cardiomyocytes maturation to prevent cardiac hyperplasia”

Jun 2023: “SIBBM 2023 conference – Frontiers in Molecular Biology” – Bari (Italy). Abstract title: “Integration of transcriptomic data to dissect the role of long non coding RNAs in amyotrophic lateral sclerosis”.

Jun 2023: “BITS 2023 conference” – Bari (Italy) Abstract title: “Integration of transcriptomic data to dissect the role of long non coding RNAs in amyotrophic lateral sclerosis”.

Feb 2023: Seminar at “Sapienza University of Rome” – (Italy). Title: “Data- and network-based approaches in basics and translational research: an example from muscle circuitries”

June 2022: “The 20th International Symposium on Pediatric Neuro-Oncology ISPNO 2022” – Hamburg (Germany). Abstract titles:

1. “Unraveling and Targeting the stem-regulatory network driving invasion in Diffuse hemispheric glioma, H3G34-mutant”
2. “Inter and Intra-tumor Heterogeneity of Pediatric-type Diffuse High-Grade Glioma Revealed by High-Dimensional Single-Cell Proteomics”
3. “Abrogation of exosome biogenesis significantly affects cell motility in heterogenous sub-populations of paediatric-type diffuse high-grade glioma”
October 2018: “IIM meeting 2018: pathogenesis and therapies of neuromuscular diseases” – Assisi (Italy). Presentation title: “Myo-REG: a new web portal for exploring inter- and intra-cellular interactions in muscle regeneration”.

July 2017: “ISW 2017:2nd interdisciplinary signaling workshop” – Visegràd (Hungary). Abstract title: “Myo-REG: a new web portal for exploring inter- and intra-cellular interactions in muscle regeneration”

June 2017: “BITS meeting 2017” (Bioinformatics Italian Society) – Cagliari (Italy). Abstract title: “Myo-REG: a new web portal for exploring inter- and intra-cellular interactions in muscle regeneration”.

Sept 2016: “The modularity of signaling proteins and network” – Seefeld (Austria). Abstract title: “SIGNOR a database of causal relationships between biological entities”.

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PUBLICATIONS
Publications as a prominent author
1. The Landscape of SPP1+ Macrophages Across Tissues and Diseases: A Comprehensive Review
A. Palma. Immunology. 2025; doi: 10.1111/imm.13952
2. Genome biology of long non-coding RNAs in humans: a virtual karyotype
A. Palma, et al. Computational and Structural Biotechnology Journal. 2025; doi: 10.1016/j.csbj.2025.01.026
3. SPP1 macrophages across diseases: a call for reclassification?
A. Palma, et al. The FASEB Journal. 2025; doi: 10.1096/fj.202403227R
4. Signaling regulation of FAM134-dependent ER-phagy in cells
A. Palma, A. Reggio. Journal of Cellular Physiology. 2024; doi: 10.1002/jcp.31492
5. Macrophages and autophagy: partners in crime
A. Vitaliti, A. Reggio, A. Palma. The FEBS Journal. 2024; doi: 10.1111/febs.17305
6. Integration of single-cell datasets depicts profiles of macrophages and fibro/adipogenic progenitors in dystrophic muscle
A. Vitaliti, A. Reggio, A. Palma. Experimental Cell Research. 2024 Aug 5;442(1):114197. doi: 10.1016/j.yexcr.2024.114197
7. Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis
A. Palma, M. Ballarino. bioRxiv. 2024 doi: 10.1101/2024.03.18.585481. (in revision on Helyion)
8. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs
M. Ballarino, A. Palma. Computational and Structural Biotechnology Journal. 2023, 09, 21. doi: 10.1016/j.csbj.2023.09.041
9. Integrating Patient-Specific Information into Logic Models of Complex Diseases: Application to Acute Myeloid Leukemia
A. Palma, M. Iannuccelli, et al. Journal of Personalized Medicine. 2021 11(2), 117; doi: 10.3390/jpm11020117
10. Adipogenesis of Skeletal Muscle Fibro/Adipogenic Progenitors is Controlled by the WNT5a/GSK3/β-Catenin Axis
A. Reggio*, M. Rosina*, A. Palma*, et al. Cell Death and Differentiation. 2020 Oct;27(10):2921-2941. doi: 10.1038/s41418-020-0551-y
11. Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration
A. Palma, et al. Frontiers in Physiology September 2019. doi: 10.3389/fphys.2019.01216
12. Gene regulatory network modeling of macrophage differentiation corroborates the continuum hypothesis of polarization states
A. Palma, et al. Frontiers in Physiology 2018; 9: 1659. doi: 10.3389/fphys.2018.01659

Publications as a collaborator
13. Long noncoding RNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyocyte differentiation by splicing regulation
G. Buonaiuto, et al. Nature Communications, 2025 Aug 23. doi: 10.1038/s41467-025-62754-2
14. Effect of the cardiac long non-coding RNA Charme depletion on the maturation and paracrine signaling of resident cardiac fibroblasts
E. Floris, et al. Cell Death and Disease – IN PRESS
15. A circuit involving the lncRNA MB3 and the driver genes MYC and OTX2 inhibits apoptosis in Group 3 Medulloblastoma by regulating the TGF-β pathway via HMGN5
A. Grandioso, et al. bioRxiv 2024, 10.1101/2024.10.21.619459 (in revision for Cell Death and Disease)
16. Sestrin2 drives ER-phagy in response to protein misfolding
C. De Leonibus, M. Maddaluno, et al. Developmental Cell. 2024 Aug 19;59(16):2035-2052.e10. doi: 10.1016/j.devcel.2024.07.004
17. Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas
G. Pericoli, et al. Cell & Bioscience. 2023 Nov 13;13(1):207. doi: 10.1186/s13578-023-01166-5
18. A New Insight into MYC Action: Control of RNA Polymerase II Methylation and Transcription Termination
F. Scagnoli, et al. Biomedicines. 2023, 11(2), 412; doi: 10.3390/biomedicines11020412
19. An Update on Circular RNA in Pediatric Cancers
A. Galardi, et al. Biomedicines. 2023, 11, 36. Doi: 10.3390/ biomedicines11010036
20. Inter and Intra-tumour Heterogeneity of Paediatric-type Diffuse High-Grade Glioma Revealed by Single-Cell Mass Cytometry
L. L. Petrilli, et al. Frontiers in Oncology. 2022 Dec 08. doi: 10.3389/fonc.2022.1016343
21. Phosphorylation of FAM134C by CK2 controls starvation induced ER-phagy
G. Di Lorenzo, F. Iavarone, et al. Science Advances. 2022 Sep 2;8(35):eabo1215. doi: 10.1126/sciadv.abo1215
22. Ejection of damaged mitochondria and their removal by macrophages ensure efficient thermogenesis in brown adipose tissue
M. Rosina, et al. Cell metabolism. 2022 Apr 5;34(4):533-548.e12. doi: 10.1016/j.cmet.2022.02.016
23. Crosstalk between cilia and autophagy: implication for human diseases
M. Morleo, et al. Autophagy. 2022 May 25;1-20. doi: 10.1080/15548627.2022.2067383
24. MAPK15 Protects from Oxidative Stress-Dependent Cellular Senescence by Inducing the Mitophagic Process
L. Franci, et al. Aging Cell. 2022 Jun 1;e13620. doi: 10.1111/acel.13620
25. Skeletal Muscle Subpopulation Rearrangements upon Rhabdomyosarcoma Development through Single-Cell Mass Cytometry
L. L. Petrilli, et al. Journal of Clinical Medicine. 2021, 10(4), 823; doi: 10.3390/jcm10040823
26. SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
G. Giuliani, et al. Cell Death and Disease. 2021 12, 122. doi: 10.1038/s41419-021-03408-1
27. Regulation of autophagosome biogenesis by OFD1-mediated selective autophagy
M. Morleo, et al. EMBO Journal. 2020 Dec 28;e105120. doi: 10.15252/embj.2020105120
28. High-Dimensional Single-Cell Quantitative Profiling of Skeletal Muscle Cell Population Dynamics during Regeneration
L. L. Petrilli, F. Spada, et al. Cells. 2020 Jul 18;9(7):1723. doi: 10.3390/cells9071723
29. SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update
L. Licata, et al. Nucleic Acids Research. 2020 Jan 8;48(D1):D504-D510. doi: 10.1093/nar/gkz949
30. Metabolic reprogramming of Fibro/Adipogenic Progenitors facilitates muscle regeneration
A. Reggio, M. Rosina, et al. Life Sci Alliance. 2020 Feb 4;3(3):e202000646. doi: 10.26508/lsa.202000660
31. Janus effect of glucocorticoids on differentiation of muscle fibro/adipogenic progenitors
A. Cerquone Perpetuini, et al. Scientific Reports. 2020; 10: 5363 doi: 10.1038/s41598-020-62194-6
32. Critical nodes reveal peculiar features of human essential genes and protein interactome
A. Celestini, et al. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. doi: 10.1109/BIBM47256.2019.8983221
33. CancerGeneNet: linking driver genes to cancer hallmarks
M. Iannuccelli, E. Micarelli, et al. Nucleic Acids Research. 2019 Oct 10. doi: 10.1093/nar/gkz871
34. Statistical ensemble of gene regulatory networks of macrophage differentiation
F. Castiglione, et al. BMC Bioinformatics. 2016; 17(Suppl 19): 506. doi: 10.1186/s12859-016-1363-4