Filippo Utro
contact information
Research Scientist: Computational BiologyThomas J. Watson Research Center, Yorktown Heights, NY USA. +1
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Professional Associations
Professional Associations: ACM | BITS | International Society for Computational Biologymore information
More information: Twitter2021
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
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
A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
F. Utro, C. Levovitz, K. Rhrissorrakrai, L. Parida
BMC Genomics22, 581, 2021
F. Utro, C. Levovitz, K. Rhrissorrakrai, L. Parida
BMC Genomics22, 581, 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
Abstract
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
Abstract
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
Abstract
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
Abstract
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
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
Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination
A. Bose, F. Utro, D.E. Platt, L. Parida
Algorithms14, 2021
A. Bose, F. Utro, D.E. Platt, L. Parida
Algorithms14, 2021
Functional profiling of COVID-19 respiratory tract microbiomes
N. Haiminen, F. Utro, E. Seabolt, L. Parida
Scientific Reports11, 2021
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
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
Abstract
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
Abstract
2020
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
Abstract
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
Abstract
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Sampling ARG of multiple populations under complex configurations of subdivision and admixture
A.P. Carrieri, F. Utro, L. Parida
Bioinformatics 32(7), 1048-1056, Oxford Univ Press, 2016
A.P. Carrieri, F. Utro, L. Parida
Bioinformatics 32(7), 1048-1056, Oxford Univ Press, 2016
The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes
F. Utro, V. Di Benedetto and F.F.V. Corona, R. Giancarlo
Bioinformatics 32(6), 835-842, Oxford Univ Press, 2016
F. Utro, V. Di Benedetto and F.F.V. Corona, R. Giancarlo
Bioinformatics 32(6), 835-842, Oxford Univ Press, 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
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
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
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
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
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
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
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
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
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
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
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
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
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 IBM 100 Icons of Progress: https://www.ibm.com/ibm/history/ibm100/us/en/icons/cocoagene/
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: https://www.ibm.com/ibm/history/ibm100/us/en/icons/cocoagene/
A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis
R. Giancarlo, G. Lo Bosco, L. Pinello, F. Utro
BMC Bioinformatics 14(Suppl 1), S6, BioMed Central Ltd, 2013
R. Giancarlo, G. Lo Bosco, L. Pinello, F. Utro
BMC Bioinformatics 14(Suppl 1), S6, BioMed Central Ltd, 2013
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
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
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
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
R. Giancarlo, F. Utro
Artificial Immune Systems, pp. 260--270, Springer, 2012
Algorithmic paradigms for stability-based cluster validity and model selection statistical methods, with applications to microarray data analysis
R. Giancarlo, F. Utro
Theoretical Computer Science, Elsevier, 2012
R. Giancarlo, F. Utro
Theoretical Computer Science, Elsevier, 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
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
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
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
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
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
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
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
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
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
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
R Giancarlo, D Scaturro, F Utro
Mathematics in Computer Science 1(4), 655--672, Springer, 2008
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer
R Giancarlo, D Scaturro, F Utro
BMC bioinformatics 9(1), 462, BioMed Central Ltd, 2008
R Giancarlo, D Scaturro, F Utro
BMC bioinformatics 9(1), 462, BioMed Central Ltd, 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
R Giancarlo, A Siragusa, E Siragusa, F Utro
Algorithms for Molecular Biology 2(1), 10, 2007
Projects and Groups
- Cancer Genomic Medicine
- Comparative Genomics
- Computational Genomics
- GenomicTools
- Human Population Genomics
- iXora: Exact Haplotype Inferencing
and Trait Association - Meta-omics
- Pattern discovery
- Plant Genomics
- RoDEO: Robust Differential Gene Expression
- SimBA: Simulation using Best-fit Algorithms
- Topological Data Analysis