Giovanni Paternostro, M.D., Ph.D.

Giovanni Paternostro's Research Focus

Leukemia/Lymphoma, Ovarian Cancer

Our lab uses a systems biology approach to the study of complex diseases. Combined drug interventions are an increasingly common therapeutic approach to complex diseases, for example in cancer. Drugs are, however, usually developed individually and only later combined empirically in the clinic based on their known effects as single-therapy agents. We are interested in the problem of inducing selective cancer cell death. We have developed and validated search algorithms to discover optimal combinations of three or more drugs that would be infeasible to identify by fully combinatorial searches. In our procedure the optimization is not carried out in silico, but directly in an in vivo high-throughput system, where the response to therapeutic combinations is used as information to guide the system toward improved combinations using an iterative algorithm. System-wide molecular measurements (for example metabolomics and transcriptomics) and models can also be incorporated in these algorithms. It is useful to view the information processing by our experimental cellular systems as biological computations, since the algorithms we use are indeed often derived from algorithms that are implemented in silico in other scientific fields.

We also use the fruit fly (Drosophila) to study cardiac and metabolic alterations caused by aging and hypoxia, using high-throughput physiological measurements, NMR metabolomics and models of metabolism.

Our multi-disciplinary team is composed of biomedical and computational scientists, and we have close collaborations with physicists, engineers and bioengineers.

Giovanni Paternostro's Bio

Giovanni Paternostro earned his Ph.D. in Biochemistry from the University of Oxford, England, in 1997. He has obtained his M.D. and Board Certification in Cardiology from the University of Rome, Italy. After postdoctoral training at the Imperial College School of Medicine, Hammersmith Hospital, London and at Sanford Burnham Prebys he was promoted to Research Investigator in 2001 and to Assistant Professor in 2003. In 2001 he was nominated member of the Whitaker Institute for Biomedical Engineering, UC San Diego. His research has been recognized by the 2002 Society for Geriatric Cardiology Basic Science Award and by the Ellison Medical Foundation New Scholar in Aging Award. Dr. Paternostro now holds adjunct faculty positions at Sanford Burnham Prebys Medical Discovery Institute and at the Department of Bioengineering, UC San Diego. His lab is located at Sanford Burnham Prebys.


CMSN Accessory

Publications

Integrating metabolomics and phenomics with systems models of cardiac hypoxia.

Feala JD, Coquin L, Paternostro G, McCulloch AD

Prog Biophys Mol Biol 2008 Jan-Apr ;96(1-3):209-25

Selective control of the apoptosis signaling network in heterogeneous cell populations.

Calzolari D, Paternostro G, Harrington PL Jr, Piermarocchi C, Duxbury PM

PLoS One 2007 Jun 20 ;2(6):e547

Show All Select Publications

Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters.

Domanskyi S, Szedlak A, Hawkins NT, Wang J, Paternostro G, Piermarocchi C

BMC Bioinformatics 2019 Jul 1 ;20(1):369

Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems.

Szedlak A, Sims S, Smith N, Paternostro G, Piermarocchi C

PLoS Comput Biol 2017 Nov ;13(11):e1005849

High-throughput screening and bioinformatic analysis to ascertain compounds that prevent saturated fatty acid-induced β-cell apoptosis.

Lee SH, Cunha D, Piermarocchi C, Paternostro G, Pinkerton A, Ladriere L, Marchetti P, Eizirik DL, Cnop M, Levine F

Biochem Pharmacol 2017 Aug 15 ;138:140-149

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks.

Szedlak A, Smith N, Liu L, Paternostro G, Piermarocchi C

PLoS Comput Biol 2016 Jun ;12(6):e1005009

Combinations of Kinase Inhibitors Protecting Myoblasts against Hypoxia.

Kang Y, Tierney M, Ong E, Zhang L, Piermarocchi C, Sacco A, Paternostro G

PLoS One 2015 ;10(6):e0126718

Control of asymmetric Hopfield networks and application to cancer attractors.

Szedlak A, Paternostro G, Piermarocchi C

PLoS One 2014 ;9(8):e105842

Show All Publications