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DEPARTMENT
CELLULAR, COMPUTATIONAL AND INTEGRATIVE BIOLOGY - CIBIO
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Home | Research | Laboratories | Cancer Biology & Genomics | Laboratory of Bioinformatics and Computational Genomics

Laboratory of Bioinformatics and Computational Genomics

  • Programs
  • Laboratories
    • Cancer Biology & Genomics
      • Armenise-Harvard Cancer Biology & Genetics
      • Armenise-Harvard Laboratory of Brain Disorders and Cancer
      • Bioinformatics and Computational Genomics
      • Biotechnology and nanomedicine
      • Cell Biology and Molecular Genetics
      • Chromatin Biology & Epigenetics
      • Computational and Functional Oncology
      • Experimental Cancer Biology
      • Genomic Screening
      • Radiobiology
      • Metabolism of Cell Growth and Neuronal Survival
      • Molecular Cancer Genetics
      • Protein Crystallography and Structure-based Drug Design
      • RNA Regulatory Networks
      • Stem Cells and Cancer Genomics
      • Translational Genomics
      • Transcriptional Networks
    • Cell and Molecular Biology
      • Armenise-Harvard Laboratory of Cell Division
      • Biophysics and Translational Cardiology
      • Chromosome Segregation Biology
      • Computational Modeling
      • Dulbecco Telethon Prions and Amyloids
      • Molecular and Cellular Neurobiology
      • Molecular Virology
      • Molecular and Cellular Ophthalmology
      • RNA and Disease Data Science
      • RNA Biology and Biotechnology
      • Virus-Cell Interaction
    • Microbiology and Synthetic Biology
      • Armenise-Harvard Synthetic and Reconstructive Biology
      • Artificial Biology
      • Bacterial Genetics & Physiology
      • Computational Metagenomics
      • Microbial Genomics
      • Synthetic and Structural Vaccinology
    • Neurobiology & Development
      • Armenise-Harvard Axonal Neurobiology
      • Dulbecco Telethon Biology of Synapses
      • Dulbecco Telethon Stem Cells and Regenerative Medicine
      • Neural Development and Regeneration
      • NeuroEpigenetics
      • Neurogenomic Biomarkers
      • Stem Cell Biology
      • Transcriptional Neurobiology
      • Translational Neurogenetics
      • Synaptic Plasticity
  • Core Facilities
  • Recent publications

Overview

3D representation of a DNA filament The main focus of the laboratory is the development of novel approaches to understand the biological mechanisms that underlie cancer genesis, cancer evolution and cancer treatment resistance. We design and combine bioinformatics approaches, computational strategies and algorithms for the analysis of next generation sequencing and high-density array data, and systems biology methods. We are particularly interested in exploiting our analyses to identify prognostic and predictive cancer biomarkers.

 

Research Directions

  • Determinants of cancers
    Regulatory regions mediate a variety of cellular processes at the transcriptional, post-transcriptional, and post-translational levels. Inherited polymorphisms and somatic aberrations within regulatory elements can affect regulatory mechanisms impacting gene expression and were shown to increase cancer susceptibility and to drive progression. We design and implement novel computational strategies to understand the intricate links between inherited polymorphisms and somatic events.

  • Liquid biopsies
    Plasma DNA contains circulating tumor DNA (ctDNA) released from widespread tumor cells, that potentially uncovers full cancer heterogeneity. We design ad-hoc assays and develop advanced computational methods to generate and analyze next generation sequencing data obtained from plasma DNA.

  • Allele-specific expression in cancer
    Allele-specific expression (ASE) is a common phenomenon observed in human cells where transcription originates predominantly from one allele. Although many studies showed that ASE is essential for cellular programming a development as well as for the diversity of cellular phenotypes, limited studies have explored the role and impact of ASE in cancer genesis and progression. We analyze genomes of thousands of patients’ cancer cells to deeply investigate ASE phenomena in cancer and identify cancer specific ASE genes and cancer specific ASE patterns.

Group members

  • Alessandro Romanel, PI
  • Samuel Valentini, PhD student
  • Davide Dalfovo, PhD student
  • Riccardo Scandino, PhD student
  • Tecla Venturelli, Master student QCB
  • Filippo Gastaldello, Bachelor student DISI
  • Christopher Porterfield, Bachelor student STB

Grants

  • 2019-2022, Ministero della Salute, Ricerca Finalizzata
  • 2018-2022, AIRC MFAG

Selected publications

S. Valentini, F. Gandolfi, M. Carolo, D. Dalfovo, L. Pozza, A. Romanel. Polympact: exploring functional relations among common human genetic variants. Nucleic Acids Research, 2022. S. Valentini*, C. Marchioretti*, A. Bisio*, A. Rossi, S. Zaccara, A. Romanel#, A. Inga#. TranSNPs: a class of functional SNPs affecting mRNA translation potential revealed by fraction-based allelic imbalance. iScience, 2021. D. Dalfovo, S. Valentini, A. Romanel. Exploring functionally annotated transcriptional consensus regulatory elements with CONREL. Database: The Journal of Biological Databases and Curation, 2020. N. Casiraghi*, F. Orlando*, Y. Ciani, J. Xiang, A. Sboner, O. Elemento, G. Attard, H. Beltran, F. Demichelis#, A. Romanel#. ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA. Bioinformatics, 2020. S. Valentini, T. Fedrizzi, F. Demichelis, A. Romanel. PaCBAM: fast and scalable processing of whole exome and targeted sequencing data. BMC Genomics, 20:1018, 2019. A. Romanel. Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data. Cancer Bioinformatics, Methods in Molecular Biology, Springer 1878:125-137, 2019. A. Romanel*, S. Garritano*, B. Stringa, M. Blattner, D. Dalfovo, D. Chakravarty, D. Soong, K.A. Cotter, G. Petris, P. Dhingra, P. Gasperini, A. Cereseto, O. Elemento, A. Sboner, E. Khurana, A. Inga, M.A. Rubin, F. Demichelis. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nature Communications, 8:48, 2017. A. Romanel, T. Zhang, O. Elemento, F. Demichelis. EthSEQ: ethnicity annotation from whole exome sequencing data. Bioinformatics 33(15):2402-2404, 2017. A. Romanel*, D. Gasi Tandefelt*, V. Conteduca, A. Jayaram, N. Casiraghi, D. Wetterskog, S. Salvi, D. Amadori, Z. Zafeiriou, P. Rescigno, D. Bianchini, G. Gurioli, V. Casadio, S. Carreira, J. Goodall, A. Wingate, R. Ferraldeschi, N. Tunariu, P. Flohr, U. De Giorgi, J.S. de Bono, F. Demichelis#, G. Attard#. Plasma AR and abiraterone-resistant prostate cancer. Science Translational Medicine 7 312re10, 2015. A. Romanel, S. Lago, D. Prandi, A. Sboner, F. Demichelis. ASEQ: fast allele-specific studies from next-generation sequencing data. BMC Medical Genomics 8(1):9, 2015.

Alessandro Romanel, PI
via Sommarive n. 9, 38123 Povo (TN)
Ph. 
+390461285217
Fax 
+39 0461 283937
alessandro.romanel [at] unitn.it