Filippo Utro  Filippo Utro photo         

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


2019

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
Abstract

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
Abstract

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
Abstract


2018

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
Abstract

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
Abstract

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
Abstract

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


2017

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
Abstract

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
Abstract

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
Abstract


2016



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
Abstract


2015

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
Abstract

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


2014

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
Abstract

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

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


2013

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
Abstract

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
Abstract

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
Abstract

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
Abstract

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


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


2012

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
Abstract

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


2011

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
10.1007/978-3-642-21946-7_2

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

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


2010

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


2009

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


2008

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



2007

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