Surgery, Thoracic Surgery Division

Research Output 1967 2019

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Conference contribution
2016

HapIso: An accurate method for the haplotype-specific isoforms reconstruction from long single-molecule reads

Mangul, S., Taegyun Yang, H., Hormozdiari, F., Tseng, E., Zelikovsky, A. & Eskin, E., Jan 1 2016, Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Proceedings. Bourgeois, A., Skums, P., Wan, X. & Zelikovsky, A. (eds.). Springer Verlag, p. 80-92 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9683).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Haplotype
Molecules
Error Rate
Sequencing
RNA
1 Citation (Scopus)

Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants

Artyomenko, A., Wu, N. C., Mangul, S., Eskin, E., Sun, R. & Zelikovsky, A., Jan 1 2016, Research in Computational Molecular Biology - 20th Annual Conference, RECOMB 2016, Proceedings. Singh, M. (ed.). Springer Verlag, p. 164-175 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9649).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Influenza
Viruses
Mutant
Virus
Resolve
3 Citations (Scopus)

Reference-free comparison of microbial communities via de Bruijn graphs

Mangul, S. & Koslicki, D., Oct 2 2016, ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 68-77 10 p. (ACM-BCB 2016 - 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA
Earth (planet)
Throughput
Health
Tissue
2015

2SNV: Quasispecies reconstruction from PacBio reads

Artyomenko, A., Wu, N. C., Mangul, S., Eskin, E., Sun, R. & Zelikovsky, A., Dec 2 2015, 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015. Institute of Electrical and Electronics Engineers Inc., 7344730. (2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Quasispecies
Frequency estimation
Viruses
Maximum likelihood
Frequency Estimation
2014

Deterministic regression algorithm for transcriptome frequency estimation

Caciula, A., Glebova, O., Artyomenko, A., Mangul, S., Lindsay, J., Məndoiu, I. I. & Zelikovsky, A., Jul 24 2014, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014. Institute of Electrical and Electronics Engineers Inc., 6863946. (2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Frequency estimation
RNA
Transcriptome
Experiments
Datasets
1 Citation (Scopus)

Reconstruction of influenza a virus variants from PacBio reads

Artyomenko, A., Mangul, S., Wu, N. C., Eskin, E., Sun, R. & Zelikovsky, A., Jul 24 2014, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014. Institute of Electrical and Electronics Engineers Inc., 6863935. (2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hamming distance
Random errors
Orthomyxoviridae
Viruses
Influenza A virus
4 Citations (Scopus)

VGA: A method for viral quasispecies assembly from ultra-deep sequencing data

Mangul, S., Wu, N. C., Mancuso, N., Zelikovsky, A., Sun, R. & Eskin, E., Jul 24 2014, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014. Institute of Electrical and Electronics Engineers Inc., 6863932. (2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Virus Assembly
High-Throughput Nucleotide Sequencing
Viral Genome
Genes
HIV
2013

Flexible approach for novel transcript reconstruction from RNA-seq data using maximum likelihood integer programming

Mangul, S., Caciula, A., Seesi, S. A., Brinza, D., Banday, A. R., Kanadia, R., Mandoiu, I. & Zelikovsky, A., Sep 13 2013, 5th International Conference on Bioinformatics and Computational Biology 2013, BICoB 2013. p. 25-33 9 p. (5th International Conference on Bioinformatics and Computational Biology 2013, BICoB 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Integer programming
RNA
Maximum likelihood
Transcriptome
Gears

Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data

Caciula, A., Zelikovsky, A., Mangul, S., Lindsay, J. & Mandoiu, I., Dec 9 2013, 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013. 6629228. (2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Frequency estimation
RNA
2012
10 Citations (Scopus)

An Integer Programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

Mangul, S., Caciula, A., Al Seesi, S., Brinza, D., Banday, A. R. & Kanadia, R., Nov 26 2012, 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012. p. 369-376 8 p. (2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Integer programming
RNA
Transcriptome
Technology
Information Dissemination
3 Citations (Scopus)

Granger causality analysis of functional connectivity of spiking neurons in orofacial motor cortex during chewing and swallowing

Takahashi, K., Pesce, L. L., Iriarte-Díaz, J., Kim, S., Coleman, T. P., Hatsopoulos, N. G. & Ross, C. F., Dec 14 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2012. p. 4587-4590 4 p. 6346988. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mastication
Motor Cortex
Deglutition
Causality
Neurons
2 Citations (Scopus)

Granger causality analysis of state dependent functional connectivity of neurons in orofacial motor cortex during chewing and swallowing

Takahashi, K., Pesce, L. L., Iriarte-Diaz, J., Best, M., Kim, S., Coleman, T. P., Hatsopoulos, N. G. & Ross, C. F., Dec 1 2012, 6th International Conference on Soft Computing and Intelligent Systems, and 13th International Symposium on Advanced Intelligence Systems, SCIS/ISIS 2012. p. 1067-1071 5 p. 6505189. (6th International Conference on Soft Computing and Intelligent Systems, and 13th International Symposium on Advanced Intelligence Systems, SCIS/ISIS 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mastication
Neurons
Kinematics

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

Mangul, S., Caciula, A., Mandoiu, I. & Zelikovsky, A., May 8 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 6182673. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA
Sequencing
Fragment
DNA Sequencing
Quantification
2011
2 Citations (Scopus)

Maximum likelihood estimation of incomplete genomic spectrum from HTS data

Mangul, S., Astrovskaya, I., Nicolae, M., Tork, B., Mandoiu, I. & Zelikovsky, A., Sep 26 2011, Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Proceedings. p. 213-224 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6833 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Maximum likelihood estimation
Quasispecies
Maximum Likelihood Estimation
Genomics
Expectation Maximization
4 Citations (Scopus)

RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes

Mangul, S., Caciula, A., Mandoiu, I. & Zelikovsky, A., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 118-123 6 p. 6112363. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA
Transcriptome
Genes
Genome
2010
20 Citations (Scopus)

Estimation of alternative splicing isoform frequencies from RNA-seq data

Nicolae, M., Mangul, S., Mǎndoiu, I. & Zelikovsky, A., Nov 10 2010, Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings. p. 202-214 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6293 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Alternative Splicing
RNA
Sequencing
Expectation-maximization Algorithm
Pairing

Repeatability and classifier bias in computer-aided diagnosis for breast ultrasound

Drukker, K., Pesce, L. L. & Giger, M. L., Jan 1 2010, Medical Imaging 2010: Computer-Aided Diagnosis. Summers, R. M. & Karssemeijer, N. (eds.). SPIE, 76242B. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 7624).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Computer aided diagnosis
Discriminant Analysis
classifiers
breast
neural nets

Stratified sampling for case selection criteria for evaluating CAD

Nishikawa, R. M. & Pesce, L. L., Jul 21 2010, Digital Mammography - 10th International Workshop, IWDM 2010, Proceedings. p. 534-539 6 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6136 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Stratified Sampling
Computer aided design
Sampling
Cancer
Performance Assessment
2009
15 Citations (Scopus)

A study of the effect of noise injection on the training of artificial neural networks

Jiang, Y., Zur, R. M., Pesce, L. L. & Drukker, K., Nov 18 2009, 2009 International Joint Conference on Neural Networks, IJCNN 2009. p. 1428-1432 5 p. 5178981. (Proceedings of the International Joint Conference on Neural Networks).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Neural networks
Computer aided diagnosis
1 Citation (Scopus)

Comparison of ROC methods for partially-paired data

Gallas, B. D. & Pesce, L. L., Jun 22 2009, Medical Imaging 2009: Image Perception, Observer Performance, and Technology Assessment. 72630V. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 7263).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Statistics
curves
ROC Curve
Area Under Curve
statistics
2007

A Bayesian interpretation of the "proper" binormal ROC model using a uniform prior distribution for the area under the curve

Zur, R. M., Pesce, L. L., Jiang, Y. & Metz, C. E., Oct 15 2007, Medical Imaging 2007: Image Perception, Observer Performance, and Technology Assessment. 651511. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 6515).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

ROC Curve
Area Under Curve
receivers
Markov processes
Maximum likelihood
1 Citation (Scopus)

Imputation methods for temporal radiographic texture analysis in the detection of periprosthetic osteolysis

Wilkie, J. R., Giger, M. L., Pesce, L. L., Engh, C. A., Hopper, R. H. & Martell, J. M., Oct 18 2007, Medical Imaging 2007: Computer-Aided Diagnosis. PART 1 ed. 65141L. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 6514, no. PART 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Osteolysis
textures
Textures
bones
iteration