CV
Simone Bianco
Contact Information
Permanent address: via Berardi, 44 – 74100 Taranto (Italy)
Present address: 682 28th ave, San Francisco, CA 94121
Work address: IBM Almaden Research Center, 650 Harry rd, San Jose, CA 95120
Tel: 408-927-1811
Fax: 408-927-3215
Email address: sbianco@us.ibm.com
Personal webpage: http://researcher.ibm.com/researcher/view.php?person=ussbianco
Research Interests and Accomplishments
I am an expert in dynamical systems theory, and its application to problems of
biological interests. My current research focuses on studying the evolution of
RNA viruses from a mathematical modeling standpoint. I make extensive use of
methods from physics and mathematics to investigate the impact of viral
populations dynamics and its interaction with the host on the evolution of the
virus.
I have contributed to build mathematical models for the spread of dengue fever
and ebola with realistic strain to strain interactions. My work has produced
several research publications on peer-reviewed scientific journals.
I have also worked, and have published, in statistical physics, condensed matter
theory, geophysics, neuroscience, and financial mathematics.
Education

Ph.D. in Physics, Center for Nonlinear Science, Department of Physics,
University of North Texas, May 2007.
Dissertation: “Complexity as aging non-Poisson renewal processes”.
Supervisor: Professor P. Grigolini.
Work supported by the Welch Foundation for Basic Research in Chemistry and
the Army Research Office.
M.S. in Physical and Astrophysical Sciences, University of Pisa (Italy),
July 2004.
Dissertation: “La correlazione seriale nel mercato italiano dei futures”
(Serial correlation in
the Italian futures market).
Supervisors: Professor R. Reno'
Professor T. Del Prete


B.S. in Physics, University of Pisa (Italy), January 2004.
Dissertation: “La correlazione seriale nel mercato italiano dei futures”
(Serial correlation in the Italian futures market).
Supervisors: Professor R. Reno'
Professor T. Del Prete
Present position
Research Staff Member, IBM Almaden Research Center, since April 2014. Full time
position (40 hrs/wk). My research duties include devising new techniques to
understand the evolution of viral populations. I have devised a new method to
understand the appearance of coupled mutations in RNA viruses like poliovirus,
HIV or Ebola. Moreover, I have worked on a new mathematical model to understand
the spread of Ebola virus. My effort has brought a publication on the subject
where for the first time it has been estimated an upper time for hospitalization
to be able to prevent the spread of the disease. I am also currently working on
using computational genomics to assess the quality and safety of food products.
The aim is to devise new methods to be used by industrial partners in order to
increase the safety of the food at processing plants.
Past positions held

Associate Specialist I, Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco, from June 2013. Full
time position (40 hrs/wk). My research duties include investigating the
early development of cancer through a morphological analysis of cancer
cells. I have developed a new detection method based on subtle changes of
the cell morphology during the neoplastic transformation, and I have used
this method to assess the stage of development of early carcinomas.
Moreover, I have studied the the evolution of RNA viruses through the
analysis of high throughput genetic data. I have build a mathematical
model to predict the evolution of RNA viruses under different level of
genetic robustness, and I have assessed the interplay between population
diversity and probability of viral evolution in a new environment.
Finally, I have devised a new method of association between viral
mutations to understand the coupling between mutations. This method is
aimed at finding the pathways which are responsible for the adaptation of
the virus to a new environment, to tackle the difficult problem of drug
resistance and drug escape.



Postdoctoral research associate of Professor Chao Tang, Department of
Bioengineering and Therapeutic Sciences, University of California San
Francisco, from September 2010 to May 2013. Full time position (40
hrs/wk). Work funded by the NSF, NIH and UCSF QB3. My research duties
include investigating the early development of cancer through a
morphological analysis of cancer cells. I have developed a new detection
method based on subtle changes of the cell morphology during the
neoplastic transformation, and I have used this method to assess the stage
of development of early carcinomas. Moreover, I have studied the the
evolution of RNA viruses through the analysis of high throughput genetic
data. I have build a mathematical model to predict the evolution of RNA
viruses under different level of genetic robustness, and I have assessed
the interplay between population diversity and probability of viral
evolution in a new environment. Finally, I have devised a new method of
association between viral mutations to understand the coupling between
mutations. This method is aimed at finding the pathways which are
responsible for the adaptation of the virus to a new environment, to
tackle the difficult problem of drug resistance and drug escape.
Postdoctoral research associate of Professor Leah B. Shaw, Department of
Applied Sciences, The College of William and Mary, from September 2007 to
August 2010. Full time position (40 hrs/wk). Work funded by the Jeffries
foundation and the ARO. My research duties included modeling the diffusion
of multistrain diseases, especially dengue fever, through complex
analytical and computational methods. I have expanded these models to
include geographic heterogeneity and have studied the effect of asymmetry
in the social and epidemiological parameters of the model on the disease
dynamics. Furthermore, I have devised new analytical methods based on
large fluctuation theory to predict the extinction probabilities of
diseases in a finite population, and used these methods to compute both
extinction trajectories and most probable paths to extinction.
Postdoctoral research associate of Professor Paolo Grigolini, Department
of Physics and Center for Nonlinear Science, University of North Texas,
from June 2007 to August 2007. Research duties included working on a
computational algorithm to describe the signal emitted by a human brain.
The aim of the work was to devise a new diagnostic method of
neuropathologies based on non-invasive techniques of data analysis.
Teaching Experience


Biology 404 - 04 – Introduction to Biological Data Analysis, The College
of William and Mary, Fall 2009.
Biology 404 - 09 – MATLAB for Biology, The College of William and Mary,
Fall 2009.
Skills



Computer skills: Advanced knowledge of Fortran 77,
numerical simulation of dynamical systems and time
Laboratory/experimental experience: proficiency in
disk confocal microscope for image acquisition.
Language skills: Italian (native), English (spoken
TOEFL 2004)
C and C++, for
series analysis.
the use of spinning
and written fluency,
Professional Services
Referee for International Review of Economics and Finance, Physical Biology,
Chaos, Solitons and Fractals, Malaria Journal, New Journal of Physics,
Fluctuation and Noise Letters.
Invited guest editor for a 2014 special supplement of the Journal of
Environmental Health Insights on Disease Dynamics.
Named 2013 Most Valuable Reviewer by Chaos, Solitons and Fractals (Elsevier,
Holland).
Invited committee member for the 2015 AAAI-W3PHI conference.
Grant reviewer for the National Science Foundation.
Scholarships/ Honors
2013 - Most Valuable Reviewer, Chaos, Solitons and Fractals
2009 - HHMI Biomathematics Program Scholarship
2008 - ISI Epiwork (Epidemic Workshop) postdoctoral award
2008 - SIAM Life Science 2008 postdoctoral travel award
2006/2007 - USC (University Scholarship Committee) Scholarship for Continuing
Students
2005/2006 - Robert B. Toulouse Academic Achievement Scholarship
Spring 2005 - Craig B. Raupe Scholarship for Professional Development
2004/2005 - Robert B. Toulouse Academic Achievement Scholarship
Contributed Talks and Poster Presentations

“Understanding cellular architecture in cancer cells”, talk held at the
first winter Qbio conference, Honolulu, HI, February 20, 2013

“Cellular architecture in cancer cells”, talk help at the APS March
meeting 2011, Dallas, TX, March 16, 2011.

“Understanding the emergence of traveling waves in the spread of dengue
fever”, talk held at the 2010 APS March meeting, Portland, OR, March 1419, 2010.

“Stochastic disease extinction in multistrain disease with interacting
strains”, talk held at the 2009 APS March meeting, Pittsburgh, PA, March
15-19, 2009.

"Understanding Multistrain Disease Interactions: Cross Immunity and
Antibody-Dependent Enhancement", talk held at the workshop "Facing the
challenge of infectious diseases - Integrating mathematical modeling,
computational thinking and ICT applications", ISI Foundation, Torino,
Italy, October 13-17, 2008.

“Modeling Multistrain Interactions: Cross Immunity and Antibody-Dependent
Enhancement”, poster presentation at the Virginia Tech Dean's Forum on
Infectious Diseases, Blacksburg, VA, September 28-29, 2008.

“Modeling Multistrain Interactions: Cross Immunity and Antibody-Dependent
Enhancement”, talk held at the 2008 SIAM Conference on Life Science,
Montreal, Canada, August 4 -7 2008.

“Epidemics with Multistrain Interactions: Cross Immunity and AntibodyDependent Enhancement”, talk held at the 2008 APS March meeting, New
Orleans, March 10-14, 2008. This talk has been highlighted among the most
interesting of its session on the APS News journal (“The Econophysics of
Epidemics”, APS News, pag. 7, March 2008).

“A fluctuating environment as a source of periodic modulation”, poster
presentation at the 373rd WE Heraeus-Stiftung Seminar” Anomalous
transport: experimental results and theoretical challenges", Physikzentrum
Bad-Honnef, Germany, July 12-16, 2006.

“Dynamics of intraday serial correlation in the Italian Futures market”,
talk held at the Third Symposium SPIE on Fluctuations and Noise, Austin,
TX, May 2005.
Invited Talks and Poster Presentations

“Using Random Matrix Theory to uncover epistatic interactions in RNA
viruses”, invited talk, DARPA, Washington DC, February 2014.

“Using Random Matrix Theory to uncover epistatic interactions in RNA
viruses”, invited talk, NIH meeting, San Francisco, May 2014.

“Understanding cellular architecture in cancer cells”, invited
colloquium, University of California Irvine, October 31, 2012.

“Predicting Disease Extinction”, invited talk, SIAM 2011 Dynamical
Systems conference, Snowbird UT, May 23 2011.

“Diseases with multistrain interactions: cross immunity and antibodydependent enhancement”, invited talk, Center for Quantitative Bioscience,
University of California, San Francisco, March, 12 2010.

"Diseases with multistrain interactions: cross immunity and antibodydependent enhancement", invited plenary talk, First Workshop on Dynamical
Systems Applied to Biology and Natural Science, Lisbon, Portugal, February
1-3, 2010.

“Epidemics with multistrain interactions: cross immunity and antibodydependent enhancement”, Department of Mathematics, George Mason
University, invited talk, October 16, 2009.

“Asymmetry-Induced Stabilization in Multistrain Disease Spread on
Migration-Coupled Patches”, 2009 SIAM conference on Dynamical Systems,
Snowbird, UT, invited talk, May 17-21, 2009.

“Chaos in spreading of epidemics: Cross immunity and antibody-dependent
enhancement”, Department of Physics, University of North Texas, invited
talk, October 7, 2008.

“Unexpected Volatility and Intraday Serial Correlation”, Conference on
Volatility and High-Frequency Data, Stevanovich Center for Financial
Mathematics, Chicago, invited poster presentation, April 21-22, 2007.

“Complexity as Aging non-Poisson Renewal processes”, Dept. of
Biostatistics and Computational Biology, Dana-Farber Cancer Institute,
Harvard Medical School, invited talk, April 4, 2007.

“Complexity as Aging non-Poisson Renewal processes”, Center for Complex
Network Research, Dept. of Physics, University of Notre Dame, invited
talk, February 2, 2007.
Publications

B. Jones, J. Lessler, S. Bianco, and J. Kaufman, “Statistical Mechanics
and Thermodynamics of Viral Evolution”, submitted to PloS One

S. Bianco, Y. Xiao, I. Rouzine, and R. Andino, “Recombination and
Mutation shape the fitness landscape of RNA viruses”, in preparation.

K. Hu, S. Bianco, S. Edlund, and J. Kaufman, “Sensitivity of Ebola to
Interventions: A numerical analysis of burial and hospitalization rates”,
submitted to PLOS Currents Outbreaks.

K. Hu, S. Bianco, S. Edlund, and J. Kaufman, “The impact of human
behavioral changes in the 2014 West Africa Ebola outbreak”, Social
Computing, Behavioral-Cultural Modeling and Prediction - Lecture Notes in
Computer Science. 75-81 (2015).
A. Stern, S. Bianco, M. T. Yeh, C. Wright, K. Butcher, C. Tang, R.
Nielsen, and R. Andino, “Costs and benefits of mutational robustness”,
Cell Reports, 8(4), 1026-1036 (2014). This paper has been featured in the

news. http://news.cell.com/cellreports/cell-reports/mutational-robustnessjust-another-trade-off

S. Bianco, M. Chan, S. Rafelski, M. Truitt, W. Marshall, D. Ruggero, and
C. Tang, “Understanding cellular architecture in cancer cells”, in
preparation, 2013. A talk based on this research has been mentioned in the
2011 APS news.
http://www.aps.org/publications/apsnews/201105/cancerbacteria.cfm

Z. Li, S. Bianco, and C. Tang, “Generic properties of random gene
regulatory networks”, Quantitative Biology (2014). This paper has been
chosen to be featured on the cover of an upcoming 2014 issue of the
journal.

K. Hu, C. Thoens, S. Bianco, S. Edlund, M. Davis, J. Douglas, and J.
Kaufman, “Modeling the Dynamics of Dengue Fever”, Social Computing,
Behavioral-Cultural Modeling and Prediction - Lecture Notes in Computer
Science. 486-494 (2013).

K. Hu, C. Thoens, S. Bianco, S. Edlund, M. Davis, J. Douglas and J.H.
Kaufman, “The effect of antibody-dependent enhancement, cross immunity,
and vector population on the dynamics of dengue fever”, J. Theoretical
Biology, 319:62-74 (2013).

I. B. Schwartz, E. Forgoston, S. Bianco, and L. B. Shaw, “Converging
towards the optimal path to extinction”, with J. Royal Soc. Interface
8:65, 1699-1707 (2011).

E. Forgoston, S. Bianco, L. B. Shaw, and I. B. Schwartz, “Maximal
sensitive dependence and the optimal path to disease extinction”, Bull.
Math. Biol., 73:3, 495-514 (2011). 2012 BMB Editor's Choice article.

S. Bianco and L. B. Shaw, “Asymmetry in the presence of migration
stabilizes multistrain disease outbreaks”, Bull. Math. Biol., 73:1 248260 (2011).

S. Bianco, L. B. Shaw, and I. B. Schwartz, “Epidemics with Multistrain
Interactions: The Interplay Between Cross Immunity and Antibody-Dependent
Enhancement”, Chaos, 19, 043123 (2009). A talk based on this paper has
been mentioned in the March 2008 issue of APS News among the most
interesting of its APS Meeting session (“The Econophysics of Epidemics”,
APS News, pag. 7, March 2008). Included in the Virtual Journal of
Biological Physics Research, December 15, 2009, Vol. 18, Issue 12.
Proc.

S. Bianco, F. Corsi, and R. Reno', “Intraday LeBaron effects”,
Natl. Acad. Sci. USA, 106, pag. 11439-11443 (2009).

S. Bianco and R. Reno', “Unexpected Volatility and Intraday Serial
Correlation”, Quantitative Finance, 9, pag. 465-475 (2009).

M. Ignaccolo, C. De Michele, and S. Bianco, “The drop-like nature of rain
and its invariant statistical properties”, Journal of Hydrometeorology,
10, pag. 79-95 (2009).

S. Bianco, E. Geneston, P. Grigolini, and M. Ignaccolo, “Renewal aging as
emerging property of phase synchronization”, Physica A, 387, pag. 13871392 (2008).

S. Bianco, M. Ignaccolo, M.S. Rider, M. Ross, P. Winsor, and P. Grigolini,
“Brain, music and non-Poisson renewal processes”, Phys. Rev. E, 75,
061911 (2007). Highlighted in the APS Physics Tip Sheet #68, June 12,
2007, and in the Science News section of Science Daily, June 15, 2007.
Included in the Virtual Journal of Biological Physics Research, July 1,
2007, Vol. 14, Issue 1.

O. Akin, S. Bianco, P. Grigolini, and P. Paradisi, “Renewal aging in nonhomogenous Poisson processes with periodic rate modulation”, Int. J. of
Bifurcations and Chaos, 18, pag. 2681 (2008).

S. Bianco, P. Grigolini, and P. Paradisi, “A fluctuating environment as a
source of periodic modulation”, Chem. Phys. Lett., 438, pag. 336-340
(2007).

S. Bianco and P. Grigolini, “Aging in financial market”,
Solitons and Fractals, 34, pag. 31-40 (2007).

S. Bianco and R. Reno', “Dynamics of intraday serial correlation in the
Italian futures market”, J. of Futures Market, 26, pag. 61-84 (2006).
Chaos,

S. Bianco, P. Grigolini, and P. Paradisi, “Fluorescence intermittency in
blinking quantum dots: renewal or slow modulation?”, J. Chem. Phys, 123,
174704 (2005).

S. Bianco and R. Reno', “Volatility and Serial Correlation: Revisiting
the LeBaron Effect”, Proceedings of SPIE -- 6601, 66010Y (2007).

S. Bianco and R. Reno', “Serial correlation in the Italian futures
market”, Proceedings of SPIE -- Vol. 5848 Noise and Fluctuations in
Econophysics and Finance, Derek Abbott, Jean-Philippe Bouchaud, Xavier
Gabaix, Joseph L. McCauley, Editors, May 2005, pp. 318-329.

P. Paradisi, P. Allegrini, F. Barbi S. Bianco, and P. Grigolini.“Renewal,
Modulation and Blinking Quantum Dots”, AIP Conf. Proc. , 800, 92 (2005)
[4-th International Conference on Unsolved Problems of Noise and
Fluctuations in Physics, Biology and High Technology, Gallipoli, Italy,
June 6-10, 2005].
News articles about my work

“Music: Mirror of the mind” American Physical Society tip sheet #68
http://www.aps.org/about/tipsheets/tip68.cfm

“Music: Mirror of the mind” Science Daily, 06/15/2007
http://www.sciencedaily.com/releases/2007/06/070614084241.htm

“The econophysics of epidemics”, APS news, March 2008
http://www.aps.org/publications/apsnews/200803/marchmeeting.cfm

“Next stop: Oblivion” Ideation, 07/16/2011
http://www.wm.edu/research/ideation/issues/2011-fall/next-stopoblivion6482.php

“Physics sheds light on cancer and bacteria evolution”, APS News, May
2011
http://www.aps.org/publications/apsnews/201105/cancerbacteria.cfm

“IBM scientists develop tools to predict dengue and malaria outbreaks”,
Vaccine news daily, 10/02/2013
http://vaccinenewsdaily.com/medical_countermeasures/327579-ibm-scientistsdevelop-tools-to-predict-dengue-and-malaria-outbreaks/

“IBM updates open-source Big Data disease modeling platform”, Fierce
BiotechIT, 10/07/2013 http://www.fiercebiotechit.com/story/ibm-updatesopen-source-big-data-disease-modeling-platform/2013-10-07

“IBM uses big data to predict outbreaks of dengue fever and malaria”,
VentureBeat, 09/29/2013
http://venturebeat.com/2013/09/29/ibm-uses-big-data-to-predict-outbreaksof-dengue-fever-and-malaria/

“Predict and Control – open source disease modelling with IBM”,
Pharmaceutical Technology, 11/07/2013
http://www.pharmaceutical-technology.com/features/feature-predict-controlopen-source-disease-modelling-ibm/

“Mutational robustness: Just another trade-off”, Cell News, 08/07/2014
http://news.cell.com/cellreports/cell-reports/mutational-robustness-justanother-trade-off

“17 IBM Rock Star employees that show the company's new direction”,
Business Insider, 04/09/2015
http://www.businessinsider.com/ibm-rock-star-employees-2015-4