Filippo Utro  Filippo Utro photo         

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Research Scientist: Computational Biology
Thomas J. Watson Research Center, Yorktown Heights, NY USA.


Professional Associations

Professional Associations:  ACM  |  BITS  |  International Society for Computational Biology

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Impact of Clinical and Genomic Factors on COVID-19 Disease Severity
S. Dey, A. Bose, S. SahaP. Chakraborty, M. Ghalwash, 1 A. Guzm?n-S?ens, F. Utro, K. Ng, J. Hu, L. Parida, D. Sow
AMIA, pp. 278--387, 2021

Convergence of resistance patterns in breast cancer after multiple lines of treatment through analysis of rapid autopsy samples
Ignaty Leshchiner, Elizabeth E. Martin, Christopher T. Chen, Elizaveta Leshchiner, Thomas Zhang, Christopher Pinto, Filippo Utro, Kahn Rhrissorrakrai, Chaya Levovitz, Brian P. Danysh, Kara Slowik, Raquel A. Jacobs, Laxmi Parida, Gad Getz, Dejan Juric
Cancer Research 81(13 Supplement), 37--37, American Association for Cancer Research, 2021

Mechanisms of primary and acquired resistance to venetoclax in chronic lymphocytic leukemia (CLL)
I. Murali, J. Cha, I. Leshchiner, Y. Kuang, K. Vasquez, J. Khalsa, S.M. Fernandes, F. Utro, K. Rhrissorrakrai, C. Levovitz, B.P. Danysh, K. Slowik, R.A. Jacobs, C.P. Paweletz, L. Parida, G. Getz, J.R. Brown
Cancer Research 81(13 Supplement), 1097--1097, American Association for Cancer Research, 2021

Parallel genomic alterations of antigen and payload targets mediate polyclonal acquired clinical resistance to sacituzumab govitecan in triple-negative breast cancer
J.T. Coates, S. Sun, I. Leshchiner, N. Thimmiah, E.E. Martin, D. McLoughlin, B.P. Danysh, K. Slowik, R.A. Jacobs, K. Rhrissorrakrai, F. Utro, C. Levovitz, E. Denault, C.S. Walmsley, A. Kambadakone, J.R. Stone, S.J. Isakoff, L. Parida, D. Juric, G. Getz, A. Bardia and L.W. Ellisen
Cancer Discovery, 2021

Functional profiling of COVID-19 respiratory tract microbiomes
N. Haiminen, F. Utro, E. Seabolt, L. Parida
Scientific Reports11, 2021

Re-purposing software for functional characterization of the microbiome
L.-J. Gardiner, N. Haiminen, F. Utro, L. Parida, E. Seabolt, R. Krishna and J.H. Kaufman
Microbiome, 2021

K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses
Z. Chen, F. Utro, D. Platt, R. DeSalle, L. Parida, P.K.S. Chan, R.D. Burk
International Journal of Molecular Sciences 22(17), 2021


Estimation of lesion-specific mutation shedding in cfDNA from rapid autopsy study
F. Utro, K. Rhrissorrakrai, C. Levovitz, I. Leshchiner, L. Martin, C. Chen, C. Pinto, B. Danysh, K. Slowik, L. Goyal, R. Allen, M.W. Broudo, D. Juric, G. Getz, L. Parida
Cancer Research, AACR, 80, 1509-1509, 2020

Genetic Determinants and Evolutionary History of Richters Syndrome
E.M. Parry, R. Guieze, I. Leshchiner, D. Rosebrock, B. Persaud, C.K. Lemvigh, E. Tausch, M.S. Davids, J. Bloehdorn, C. Schneider, L. Elagina, A.Z. Martinez, A. Taylor-Weiner, N. Jain, W.G. Wierda, L.Z. Rassenti, T.J. Kipps, J. Broseus, F. Cymbalista, N.E. Kay, K.J. Livak, S. Li, T. Huang, N. Purroy, A.J. Anandappa, S.M. Fernandes, F. Utro, K. Rhrissorrakrai, C. Levovitz, B Danish, K. Slowik, S.A. Parikh, J.R. Brown, L. Parida, D.S. Neuberg, S. Stilgenbauer, G. Getz, C.J. Wu
Blood, ASH, 136, 47-48, 2020

Hierarchically labeled database indexing allows scalable characterization of microbiomes
F. Utro, N. Haiminen, E. Siragusa, L.-J. Gardiner, E. Seabolt, R. Krishna, J.H. Kaufman, L. Parida
iScience, 2020

Simultaneous Phasing of Multiple Polyploids
L. Parida and F. Utro
CIBB 2018: Computational Intelligence Methods for Bioinformatics and Biostatistics, pp. 50-68, 2020


Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA
L. Parida, C. Haferlach, K. Rhrissorrakrai, F. Utro, C. Levovitz, W. Kern, N. Nadarajah, S. Twardziok, S. Hutter, M. Meggendorfer, W. Walter, C. Baer, T. Haferlach
PLoS Comput Biology 15(8), 2019

Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata
M. Klaas, N. Haiminen, J. Grant, P. Cormican, J. Finnan, S.K. Arojju, F. Utro, T. Vellani, L. Parida, S. Barth
Annals of botany, 2019

Sequencing and curation strategies for identifying candidate glioblastoma treatments
M.O. Frank, T. Koyama, K. Rhrissorrakrai, N. Robine, F. Utro, and others
BMC Medical Genomics 12(56), 2019

A Quantitative and Qualitative Characterization of k-mer Based Alignment-Free Phylogeny Construction
F. Utro, D.E. Platt, L. Parida
Computational Intelligence Methods for Bioinformatics and Biostatistics , pp. 19-31, Springer, 2019

Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
A.R. Parikh, I. Leshchiner, L. Elagina, L. Goyal, C. Levovitz, G. Siravegna, D. Livitz, K. Rhrissorrakrai, E.E. Martin, E.E. Van Seventer, M. Hanna, K. Slowik, F. Utro, et al
Nature Medicine25, 1415-1421, 2019


Essential Simplices in Persistent Homology and Subtle Admixture Detection
S. Basu, F. Utro, L. Parida
18th International Workshop on Algorithms in Bioinformatics (WABI 2018), pp. 14:1-14:10

DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
R. Giancarlo, S.E. Rombo, F. Utro
Theoretical Computer Science, 2018

Broad/IBM Project: Discovery of treatment resistance mechanisms through use of liquid biopsy genomics services
G. Getz, C. Cibulskis, I. Leshchiner, M. Hanna, D. Livitz, K. Slowik, C. Levovitz, F. Utro, K. Rhrissorrakrai, D. Rotem, and others
Cancer Research, AACR, 2018

In vitro vs in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
R. Giancarlo, S.E. Rombo, F. Utro
Bioinformatics, 2018


Computation Cluster Validation in the Big Data Era
R. Giancarlo, F. Utro
Reference Module in Life Sciences, 2017

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing
M.M. Patel, V.V. Michelini, J.M. Snell, S. Balu, A.P. Hoyle, J.S. Parker, M.C. Hayward, D.A. Eberhard, A.H. Salazar, P. McNeillie, and others
The Oncologist, AlphaMed Press, 2017

Linear time algorithms to construct populations fitting multiple constraint distributions at genomic scales
E. Siragusa, N. Haiminen, F. Utro, L. Parida
IEEE/ACM Transactions on Computational Biology and Bioinformatics PP(99), 2017

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma
K.O. Wrzeszczynski, M.O. Frank, T. Koyama, K. Rhrissorrakrai, N. Robine, F. Utro, A.-K. Emde, B.-J. Chen, K. Arora, M. Shah, and others
Neurology Genetics 3(4), e164, AAN Enterprises, 2017


Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins
Z. Waks, O. Weissbrod, B. Carmeli, R. Norel, F. Utro, Y. Goldschmidt
Scientific Reports 6, 38988, Nature Publishing Group, 2016


Implementation of Watson Genomic Analytics processing to improve the efficiency of interpreting whole genome sequencing data on patients with advanced cancers
T. Koyama, S. Jones, F. Utro, Y. Ma, K. Rhrissorrakrai, Y. Shen, B. Carmeli, M.Jones, Z. Waks, E. Pleasance, R. Norel, R. Moore, E. Bilal, A.J. Mungall, K. Beaty, J. Schein, V.V. Michelini, M. Marra, A. Royyuru, J.J. Laskin
Journal of Clinical Oncology33, 2015
Abstract   whole genome sequencing, transcriptome sequencing, transcriptome, rationalization, pathology, genome, data integrity, computational biology, cancer, biology, bioinformatics, analytics

Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning
R. Giancarlo, S.E. Rombo, F. Utro
Bioinformatics 31(18), 2939-2946, Oxford Univ Press, 2015

Topological Signatures for Population Admixture
L. Parida, F. Utro, D. Yorukoglu, A.P. Carrieri, D. Kuhn, S. Basu
RECOMB 2015: Research in Computational Molecular Biology, pp. 261-275, Springer

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis
R. Giancarlo, D. Scaturro, F. Utro
Computer Methods and Programs in Biomedicine, Elsevier, 2015


Comparative exomics of Phalaris cultivars under salt stress
N. Haiminen, M. Klaas, Z. Zhou, F. Utro, P. Cormican, T. Didion, C. Sig Jensen, C.E. Mason, S. Barth, L. Parida
BMC Genomics 15(Suppl 6), S18, BioMed Central Ltd, 2014

Bayesian versus data driven model selection for microarray data
R. Giancarlo, G. Lo Bosco, F. Utro
Natural Computing, 1-10, Springer Netherlands, 2014

Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome
D.E Platt, F. Utro, L. Parida
Computational Biology and Chemistry, Elsevier, 2014


The Three Steps of Clustering In The Post-Genomic Era
R. Giancarlo, G. Lo Bosco, L. Pinello, F. Utro
Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data, pp. 519--556, Wiley Online Library, 2013

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies
R. Giancarlo, S.E. Rombo, F. Utro
Briefings in bioinformatics, bbt088, Oxford Univ Press, 2013

Genetic History of Populations: Limits to Inference
D.E Platt, F. Utro, M. Pybus, L. Parida
Models and Algorithms for Genome Evolution, pp. 309--323, Springer, 2013

Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes
N. Haiminen, F. Utro, C. Lebreton, P. Flament, Z. Karaman, L. Parida
Algorithms 6(3), 430--441, 2013

iXora: Exact haplotype inferencing and trait association
F. Utro, N. Haiminen, D. Livingstone, O.E. Cornejo, S. Royaert, R. Schnell, J.C. Motamayor, D.N. Kuhn, L. Parida
BMC Genetics 14(1), 48, BioMed Central Ltd, 2013

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
J.C. Motamayor*, K. Mockaitis*, J. Schmutz*, N. Haiminen*, D. Livingstone, O.E. Cornejo, S. Findley, P. Zheng, F. Utro, S. Royaert, C. Saski, J. Jenkins, R. Podicheti, M. Zhao, B. Scheffler, others
Genome Biology 14(6), R53, BioMed Central Ltd, 2013
Abstract   IBM 100 Icons of Progress:

Sum of parts is greater than the whole: inference of common genetic history of populations
F. Utro, M. Pybus, L. Parida
BMC Genomics 14(Suppl 1), S10, BioMed Central Ltd, 2013


ARG-based genome-wide analysis of cacao cultivars
F. Utro, O.E. Cornejo, D. Livingstone, J.C. Motamayor, L. Parida
BMC Bioinformatics 13(Suppl 19), S17, BioMed Central Ltd, 2012

GenomicTools: an open source platform for developing high-throughput analytics in genomics
A. Tsirigos, N. Haiminen, E. Bilal, F. Utro
Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond, Woodhead Publishing Series in Biomedicine No. 16, 2012

Stability-Based Model Selection for High Throughput Genomic Data: An Algorithmic Paradigm
R. Giancarlo, F. Utro
Artificial Immune Systems, pp. 260--270, Springer, 2012

GenomicTools: a computational platform for developing high-throughput analytics in genomics
A. Tsirigos, N. Haiminen, E. Bilal, F. Utro
Bioinformatics 28(2), 282--283, Oxford University Press, 2012

Textual data compression in computational biology: Algorithmic techniques
R Giancarlo, D Scaturro, F Utro
Computer Science Review, Elsevier, 2012

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia
P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M. Sol Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, J. Siegle, others
Nature medicine 18(2), 298--303, Nature Publishing Group, 2012


The Three Steps of Clustering in the Post-Genomic Era: A Synopsis
R Giancarlo, G Lo Bosco, L Pinello, F Utro
Computational Intelligence Methods for Bioinformatics and Biostatistics, pp. 13-30, Springer Berlin / Heidelberg, 2011

IRiS: Construction of ARG networks at genomic scales
A Javed, M Pybus, M Melè, F Utro, J Bertranpetit, F Calafell, L Parida
Bioinformatics, 2011

Speeding up the Consensus Clustering methodology for microarray data analysis
R Giancarlo, F Utro
Algorithms for Molecular Biology 6(1), 1, BioMed Central Ltd, 2011


Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures (Extended Abstract)
D Corona, V Di Benedetto, A Gabriele, R Giancarlo, F Utro
Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010


Basic Statistical Indices for SeqAn
SE Rombo, F Utro, R Giancarlo
Biological Sequence Analysis Using the SeqAn C++ Library, Taylor and Francis-CRC, 2009

Statistical Indices for Computational and Data Driven Class Discovery in Microarray Data
R Giancarlo, D Scaturro, F Utro
Biological Data Mining, pp. 295, Chapman & Hall, 2009

Textual data compression in computational biology: a synopsis
R Giancarlo, D Scaturro, F Utro
Bioinformatics 25(13), 1575, Oxford Univ Press, 2009


A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data
R Giancarlo, D Scaturro, F Utro
Mathematics in Computer Science 1(4), 655--672, Springer, 2008


A basic analysis toolkit for biological sequences
R Giancarlo, A Siragusa, E Siragusa, F Utro
Algorithms for Molecular Biology 2(1), 10, 2007