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Hire Dr. Matteo C.

Italy

USD 50 /hr

Professional Bioinformatician & High-Throughput Data Analyst | Expert in R and Linux | Advanced Training Experience

Profile Summary

Professional bioinformatician for 3 years, I have specialized in working as a service and support to research. My services covered all aspects of scientific projects from the experimental design to the final drafting of the manuscript. My background in molecular biology (MSc) and biotechnology allows me to communicate efficiently with biologists, medics, and technicians, translate biological and medical research needs into bioinformatics pipelines and translate back methods and results in a prompt and efficient manner. I am thrilled about working on new biology topics. I have already worked on cancer, cardiological diseases, neurodegeneration, and dementia: I am a fast learner and can easily find connections between the different topics I have worked on to give you a broader picture. My Ph.D. in bioinformatics and direct working experience ensures the quality of the analysis that is coupled with biological knowledge. I specialize in the analysis of a wide range of different high-throughput sequencing data. mRNAs, miRNAs, circRNAs, genomic variants (both germline or somatic), ChIP-Seq, Superenahncers, microbial communities (metabarcoding and metagenomics) are all data types I have previously analyzed with success and on which I have published peer-reviewed literature. From raw data to the final interpretation, I can do QC, basic or personalized analysis, results interpretation, annotation and database query. I can provide code review, build specialized pipelines or write helper scripts to smooth your operations and ease the burden on you bioinformaticians. I have years of experience as a trainer for international advanced courses in high-throughput data analysis (EMBL - Heidelberg, MBC - Torino) and can provide personalized training sessions for your biologists on specific bioinformatics topics.

Subject Matter Expertise

• ★ Next Generation Sequencing (NGS)
• ★ Bioinformatics
• ☆ Genetics
• ☆ Exome Sequencing
• ☆ ChIP-Seq
• ☆ Data Science
• ☆ Data Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Non-Alzheimer's Dementia
• ☆ Alzheimer's Disease
• ☆ Cardiovascular Disease
• ☆ Cancer Research
• ☆ Research
• ☆ Technical & Scientific Writing

Services

• Writing
• Research
• Data & AI

Writing Technical Writing, Newswriting

Research Systematic Literature Review, Secondary Data Collection

Data & AI Statistical Analysis, Algorithm Design-Non ML, Data Visualization

Work Experience

Bioinformatician

IRCCS Fatebenefratelli, Brescia, Italy

July 2018 - Present

Researcher

IRCCS Centro S Giovanni di Dio Fatebenefratelli

July 2018 - Present

Bioinformatician

IRCCS San Donato, San Donato Milanese, Italy

February 2016 - February 2018

Researcher

IRCCS Policlinico San Donato

February 2016 - February 2018

Education

Ph.D. in Complex Systems for Life Sciences

University of Torino

January 2013 - January 2016

PhD in Complex Systems for Life Sciences (Natural Sciences)

Università degli Studi di Torino

January 2013 - January 2016

MSc in Cellular and Molecular Biology

University of Torino

October 2010 - October 2012

MSc in Cellular and Molecular Biology (Natural Sciences)

Università degli Studi di Torino

September 2010 - October 2012

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

(2019). Dysregulation of Circular RNAs in Myotonic Dystrophy Type 1 .

(2019). Dysregulation of circular RNAs in myotonic dystrophy type 1 . International Journal of Molecular Sciences. 20. (8).

(2019). The missing heritability of sporadic frontotemporal dementia: New insights from rare variants in neurodegenerative candidate genes . International Journal of Molecular Sciences. 20. (16).

(2018). Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases . Journal of cellular and molecular medicine.

(2018). High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2 . Cell death & disease.

(2018). High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2 . Cell death & disease.

(2018). High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2 . Cell Death and Disease. 9. (7).

Carrara, M., Fuschi, P., Ivan, C., Martelli, F.(2018). Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases . Journal of Cellular and Molecular Medicine. 22. (11). p. 5176-5187.

(2017). Central role of the p53 pathway in the noncoding-RNA response to oxidative stress . Aging.

(2017). Increased BACE1-AS long noncoding RNA and β-amyloid levels in heart failure . Cardiovascular research.

Greco, S., Zaccagnini, G., Fuschi, P., Greco, S., Zaccagnini, G., Fuschi, P., Voellenkle, C., Carrara, M., Sadeghi, I., Bearzi, C., et al.(2017). Increased BACE1-AS long noncoding RNA and β-amyloid levels in heart failure . Cardiovascular Research. 113. (5). p. 453-463.

Fuschi, P., Carrara, M., Voellenkle, C., Fuschi, P., Carrara, M., Voellenkle, C., Garcia-Manteiga, J.M., Righini, P., Maimone, B., Sangalli, E., et al.(2017). Central role of the p53 pathway in the noncoding-RNA response to oxidative stress . Aging. 9. (12). p. 2559-2586.

(2015). YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers . Molecular cell.

Galli GG, Carrara M, Yuan WC, Valdes-Quezada C, Gurung B, Pepe-Mooney B, Zhang T, Geeven G, Gray NS, de Laat W, Calogero RA, Camargo FD, Molecular cell, 2015, vol. 60, no. 2, pp. 328-337 .

(2015). Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis . BMC bioinformatics.

Carrara M, Lum J, Cordero F, Beccuti M, Poidinger M, Donatelli S, Calogero RA, Zolezzi F, BMC bioinformatics, 2015, vol. 16 Suppl 9, pp. S2 .

(2015). YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers . Molecular Cell. 60. (2). p. 328-337.

Carrara, M., Lum, J., Cordero, F., Beccuti, M., Poidinger, M., Donatelli, S., Calogero, R.A., Zolezzi, F.(2015). Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis . BMC Bioinformatics. 16.

Beccuti M, Carrara M, Cordero F, Lazzarato F, Donatelli S, Nadalin F, Policriti A, Calogero RA, Bioinformatics (Oxford, England), 2014, vol. 30, no. 24, pp. 3556-3557 .

Pazienza V, Pomara C, Cappello F, Calogero R, Carrara M, Mazzoccoli G, Vinciguerra M, American journal of physiology. Heart and circulatory physiology, 2014, vol. 307, no. 7, pp. H939-44 .

Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD, PLoS genetics, 2014, vol. 10, no. 9, pp. e1004566 .

Tremblay AM, Missiaglia E, Galli GG, Hettmer S, Urcia R, Carrara M, Judson RN, Thway K, Nadal G, Selfe JL, Murray G, Calogero RA, De Bari C, Zammit PS, Delorenzi M, Wagers AJ, Shipley J, Wackerhage H, Camargo FD, Cancer cell, 2014, vol. 26, no. 2, pp. 273-287 .

Galli GG, Multhaupt HA, Carrara M, de Lichtenberg KH, Christensen IB, Linnemann D, Santoni-Rugiu E, Calogero RA, Lund AH, Oncogene, 2014, vol. 33, no. 25, pp. 3342-3350 .

(2014). Characterization of a genetic mouse model of lung cancer: A promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers . BMC Genomics. 15.

Galli, G.G., Multhaupt, H.A., Carrara, M., De Lichtenberg, K.H., Galli, G.G., Multhaupt, H.A., Carrara, M., De Lichtenberg, K.H., Christensen, I.B.J., Linnemann, D., et al.(2014). Prdm5 suppresses Apc Min-driven intestinal adenomas and regulates monoacylglycerol lipase expression . Oncogene. 33. (25). p. 3342-3350.

Riccardo F, Arigoni M, Buson G, Zago E, Iezzi M, Longo D, Carrara M, Fiore A, Nuzzo S, Bicciato S, Nanni P, Landuzzi L, Cavallo F, Calogero R, Quaglino E, BMC genomics, 2014, vol. 15 Suppl 3, pp. S1 .

(2014). Chimera: A Bioconductor package for secondary analysis of fusion products . Bioinformatics. 30. (24). p. 3556-3557.

Pazienza, V., Pomara, C., Cappello, F., Calogero, R., Carrara, M., Mazzoccoli, G., Vinciguerra, M.(2014). The TRPA1 channel is a cardiac target of mIGF-1/SIRT1 signaling . American Journal of Physiology - Heart and Circulatory Physiology. 307. (7). p. H939-H944.

Popovic, R., Martinez-Garcia, E., Giannopoulou, E.G., Popovic, R., Martinez-Garcia, E., Giannopoulou, E.G., Zhang, Q., Zhang, Q., Ezponda, T., Shah, M.Y., et al.(2014). Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation . PLoS Genetics. 10. (9).

(2014). The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation . Cancer Cell. 26. (2). p. 273-287.

Galli GG, Carrara M, Francavilla C, de Lichtenberg KH, Olsen JV, Calogero RA, Lund AH, Molecular and cellular biology, 2013, vol. 33, no. 22, pp. 4504-4516 .

(2013). Genomic and proteomic analyses of prdm5 reveal interactions with insulator binding proteins in embryonic stem cells . Molecular and Cellular Biology. 33. (22). p. 4504-4516.

Carrara M, Beccuti M, Cavallo F, Donatelli S, Lazzarato F, Cordero F, Calogero RA, BMC bioinformatics, 2013, vol. 14 Suppl 7, pp. S2 .

Carrara, M., Beccuti, M., Cavallo, F., Donatelli, S., Carrara, M., Beccuti, M., Cavallo, F., Donatelli, S., Lazzarato, F., Cordero, F., et al.(2013). State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? . BMC Bioinformatics. 14. (SUPPL7).

Carrara, M., Beccuti, M., Lazzarato, F., Cavallo, F., Cordero, F., Donatelli, S., Calogero, R.A.(2013). State-of-the-art fusion-finder algorithms sensitivity and specificity . BioMed Research International. 2013.

Bolasco G, Calogero R, Carrara M, Banchaabouchi MA, Bilbao D, Mazzoccoli G, Vinciguerra M, Aging, 2012, vol. 4, no. 6, pp. 402-416 .

Bolasco, G., Calogero, R., Carrara, M., Bolasco, G., Calogero, R., Carrara, M., Al Banchaabouchi, M., Bilbao, D., Mazzoccoli, G., Vinciguerra, M.(2012). Cardioprotective mIGF-1/SIRT1 signaling induces hypertension, leukocytosis and fear response in mice . Aging. 4. (6). p. 402-416.

(2012). Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone . PLoS Genetics. 8. (5).

Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele A. Calogero, 2013, 'State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity', <i>BioMed Research International</i>, vol. 2013, no. 16 .

Giorgio Giacomo Galli, Kristian Honnens de Lichtenberg, Matteo Carrara, Wolfgang Hans, Manuela Wuelling, Bettina Mentz, Hinke Arnolda Multhaupt, Cathrine Kolster Fog, Klaus Thorleif Jensen, Juri Rappsilber, Andrea Vortkamp, Les Coulton, Helmut Fuchs, Valérie Gailus-Durner, Martin Hrabě de Angelis, Raffaele Adolfo Calogero, John Robert Couchman, Anders Henrik Lund, Marshall S. Horwitz, 2012, 'Prdm5 Regulates Collagen Gene Transcription by Association with RNA Polymerase II in Developing Bone', <i>PLoS Genetics</i>, vol. 8, no. 5 .

CONFERENCE PAPER

(2012). Digging in the RNA-seq garbage: Evaluating the characteristics of unmapped RNA-seq reads in normal tissues . Proceedings - 2012 6th International Conference on Complex, Intelligent, and Software Intensive Systems, CISIS 2012. p. 588-591.