Brice Horton Ii Paul

Professor

  • 5250 Citations
  • 20 h-Index
1992 …2019
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Research Output 1992 2019

2019

Estimating genome-wide off-target effects for pyrrole-imidazole polyamide binding by a pathway-based expression profiling approach

Lin, J., Krishnamurthy, S., Yoda, H., Shinozaki, Y., Watanabe, T., Koshikawa, N., Takatori, A., Paul, B. H. I. & Nagase, H., 2019 Apr 1, In : PloS one. 14, 4, e0215247.

Research output: Contribution to journalArticle

Open Access
pyrroles
Pyrroles
imidazoles
Nylons
Genes
1 Citation (Scopus)

Novel lineage-specific transmembrane β-barrel proteins in the endoplasmic reticulum of Entamoeba histolytica

Santos, H. J., Imai, K., Makiuchi, T., Tomii, K., Paul, B. H. I., Nozawa, A., Okada, K., Tozawa, Y. & Nozaki, T., 2019 Sep 1, In : FEBS Journal. 286, 17, p. 3416-3432 17 p.

Research output: Contribution to journalArticle

Endoplasmic Reticulum
Entamoeba
Membrane Proteins
Membranes
Proteins
2018

A bioinformatics potpourri

Schönbach, C., Li, J., Ma, L., Horton, P., Sjaugi, M. F. & Ranganathan, S., 2018 Jan 19, In : BMC genomics. 19, 920.

Research output: Contribution to journalEditorial

Computational Biology
Genomics
Metagenomics
Posters
Precision Medicine
1 Citation (Scopus)

EAGLE: Explicit Alternative Genome Likelihood Evaluator

Kuo, T., Frith, M. C., Sese, J. & Horton, P., 2018 Apr 20, In : BMC Medical Genomics. 11, 28.

Research output: Contribution to journalArticle

Genome
Benchmarking
Uncertainty
Exome
Eagles

Sequence homology in eukaryotes (SHOE): Interactive visual tool for promoter analysis 06 Biological Sciences 0604 Genetics

Polouliakh, N., Horton, P., Shibanai, K., Takata, K., Ludwig, V., Ghosh, S. & Kitano, H., 2018 Sep 27, In : BMC genomics. 19, 1, 715.

Research output: Contribution to journalArticle

Biological Science Disciplines
Sequence Homology
Eukaryota
Transcription Factors
Gene Expression
2017
18 Citations (Scopus)

Extensive cargo identification reveals distinct biological roles of the 12 importin pathways

Kimura, M., Morinaka, Y., Imai, K., Kose, S., Paul, B. H. I. & Imamoto, N., 2017 Jan 24, In : eLife. 6, e21184.

Research output: Contribution to journalArticle

Karyopherins
Proteins
Isotope Labeling
Biological Phenomena
Cell Nucleus Active Transport
2 Citations (Scopus)

Ten simple rules for forming a scientific professional society

Gaëta, B. A., De Las Rivas, J., Horton, P., Meysman, P., Mulder, N., Romano, P. & Welch, L., 2017 Mar, In : PLoS Computational Biology. 13, 3, e1005226.

Research output: Contribution to journalEditorial

2016

A commentary on evaluation of the evenness score in next-generation sequencing

Paul, B. H. I., 2016 Jul 1, In : Journal of Human Genetics. 61, 7, 1 p.

Research output: Contribution to journalComment/debate

High-Throughput Nucleotide Sequencing
Genomics
DNA Sequence Analysis
3 Citations (Scopus)

Identification of binding targets of a pyrrole-imidazole polyamide KR12 in the LS180 colorectal cancer genome

Lin, J., Hiraoka, K., Watanabe, T., Kuo, T., Shinozaki, Y., Takatori, A., Koshikawa, N., Chandran, A., Otsuki, J., Sugiyama, H., Horton, P. & Nagase, H., 2016 Oct, In : PloS one. 11, 10, e0165581.

Research output: Contribution to journalArticle

pyrroles
Pyrroles
imidazoles
Nylons
colorectal neoplasms
2015
9 Citations (Scopus)

A novel mitosomal β-barrel outer membrane protein in Entamoeba

Santos, H. J., Imai, K., Makiuchi, T., Tomii, K., Paul, B. H. I., Nozawa, A., Ibrahim, M., Tozawa, Y. & Nozaki, T., 2015 Jan 1, In : Scientific reports. 5, 8545.

Research output: Contribution to journalArticle

Entamoeba
Membrane Proteins
Endopeptidase K
Entamoeba histolytica
Membranes

GIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history

Schönbach, C., Horton, P., Yiu, S. M., Tan, T. W. & Ranganathan, S., 2015 Jan 1, In : BMC genomics. 16, p. I1

Research output: Contribution to journalArticle

Computational Biology
History
Joints
Research
Posters

GIW and InCoB are advancing bioinformatics in the Asia-Pacific

Schönbach, C., Horton, P., Yiu, S. M., Tan, T. W. & Ranganathan, S., 2015 Dec 18, In : BMC Bioinformatics. 16, 18, I1.

Research output: Contribution to journalArticle

Informatics
Bioinformatics
Computational Biology
Genome
Genes

Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014)

Shibuya, T., Tang, C. Y., Paul, B. H. I. & Asai, K., 2015 Jul 1, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 4, p. 761-762 2 p., 7180484.

Research output: Contribution to journalEditorial

Informatics
Tokyo
Genomics
Genome
Genes

Introduction to selected papers from GIW/InCoB 2015

Paul, B. H. I., Schönbach, C., Ranganathan, S. & Yiu, S. M., 2015 Oct 1, In : Journal of Bioinformatics and Computational Biology. 13, 5, 1502003.

Research output: Contribution to journalEditorial

Genomics
Computational Biology
109 Citations (Scopus)

MitoFates: Improved prediction of mitochondrial targeting sequences and their cleavage sites

Fukasawa, Y., Tsuji, J., Fu, S. C., Tomii, K., Horton, P. & Imai, K., 2015 Apr 1, In : Molecular and Cellular Proteomics. 14, 4, p. 1113-1126 14 p.

Research output: Contribution to journalArticle

Mitochondria
Mitochondrial Proteins
Genes
Protein Isoforms
Position-Specific Scoring Matrices
69 Citations (Scopus)

Molecular architecture of the active mitochondrial protein gate

Shiota, T., Imai, K., Qiu, J., Hewitt, V. L., Tan, K., Shen, H. H., Sakiyama, N., Fukasawa, Y., Hayat, S., Kamiya, M., Elofsson, A., Tomii, K., Paul, B. H. I., Wiedemann, N., Pfanner, N., Lithgow, T. & Endo, T., 2015 Sep 25, In : Science. 349, 6255, p. 1544-1548 5 p.

Research output: Contribution to journalArticle

Mitochondrial Proteins
Cytosol
Mitochondria
Protein Isoforms
Proteins
2014
16 Citations (Scopus)

A bioinformatician's guide to the forefront of suffix array construction algorithms

Shrestha, A. M. S., Frith, M. C. & Paul, B. H. I., 2014 Jan 1, In : Briefings in Bioinformatics. 15, 2, p. 138-154 17 p., bbt081.

Research output: Contribution to journalArticle

Seed
Bioinformatics
Data structures
Seeds
Computational Biology

Editorial-The 25th international conference on genome informatics (GIW/ISCB-ASIA 2014)

Shibuya, T., Tang, C. Y., Paul, B. H. I. & Asai, K., 2014 Dec 29, In : Journal of Bioinformatics and Computational Biology. 12, 6, 1402002.

Research output: Contribution to journalEditorial

Medical Informatics
Informatics
Genomics
Computational Biology
Genes
1 Citation (Scopus)

Next-generation bioinformatics: Connecting bases to genes, networks and disease

Paul, B. H. I., 2014 Jan 1, In : Briefings in Bioinformatics. 15, 2, 1 p., bbt090.

Research output: Contribution to journalComment/debate

Protein Interaction Maps
High-Throughput Nucleotide Sequencing
Gene Regulatory Networks
Bioinformatics
Computational Biology
8 Citations (Scopus)

Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals

Fukasawa, Y., Leung, R. K. K., Tsui, S. K. W. & Paul, B. H. I., 2014 Jan 20, In : BMC genomics. 15, 1, 46.

Research output: Contribution to journalArticle

Amino Acid Sequence
Proteins
Cell Biology
Mammals
Transcription Factors
2013
3 Citations (Scopus)

Finding Protein-Coding Genes through Human Polymorphisms

Wijaya, E., Frith, M. C., Horton, P. & Asai, K., 2013 Jan 29, In : PloS one. 8, 1, e54210.

Research output: Contribution to journalArticle

Polymorphism
Open Reading Frames
Genes
genetic polymorphism
open reading frames
24 Citations (Scopus)

Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics

Kimura, M., Kose, S., Okumura, N., Imai, K., Furuta, M., Sakiyama, N., Tomii, K., Horton, P., Takao, T. & Imamoto, N., 2013 Jan 1, In : Molecular and Cellular Proteomics. 12, 1, p. 145-157 13 p.

Research output: Contribution to journalArticle

Nucleocytoplasmic Transport Proteins
Karyopherins
Isotope Labeling
Carrier transport
Cell culture
1 Citation (Scopus)

Localization prediction and structure-based in silico analysis of bacterial proteins: With emphasis on outer membrane proteins

Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A. & Paul, B. H. I., 2013 Jan 8, Data Mining for Systems Biology: Methods and Protocols. Mamitsuka, H., Kanehisa, M. & DeLisi, C. (eds.). p. 115-140 26 p. (Methods in Molecular Biology; vol. 939).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacterial Proteins
Computer Simulation
Membrane Proteins
Proteins
Escherichia coli

Summary of talks and papers at ISCB-Asia/SCCG 2012

Tretyakov, K., Goldberg, T., Jin, V. X. & Paul, B. H. I., 2013 Apr 29, In : BMC genomics. 14, SUPPL. 2, I1.

Research output: Contribution to journalEditorial

Genomics
Precision Medicine
China
Software
Messenger RNA
42 Citations (Scopus)

ValidNESs: A database of validated leucine-rich nuclear export signals

Fu, S. C., Huang, H. C., Paul, B. H. I. & Juan, H. F., 2013 Jan 1, In : Nucleic acids research. 41, D1

Research output: Contribution to journalArticle

Nuclear Export Signals
Leucine
Databases
Maintenance
Proteins
2012
42 Citations (Scopus)

Mammalian NUMT insertion is non-random

Tsuji, J., Frith, M. C., Tomii, K. & Paul, B. H. I., 2012 Oct 1, In : Nucleic acids research. 40, 18, p. 9073-9088 16 p.

Research output: Contribution to journalArticle

Retroelements
Insertional Mutagenesis
Mitochondrial Genome
Genome
Computational Biology
2 Citations (Scopus)

Paving the future: Finding suitable ismb venues

Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., Morrison Mckay, B. J., Schneider, R., Paul, B. H. I. & Kelso, J., 2012 Oct 1, In : Bioinformatics. 28, 19, p. 2556-2559 4 p., bts420.

Research output: Contribution to journalArticle

Molecular biology
Molecular Biology
Computational Biology
Intelligent systems
Bioinformatics

RecountDB: A database of mapped and count corrected transcribed sequences

Wijaya, E., Frith, M. C., Asai, K. & Horton, P., 2012 Jan 1, In : Nucleic acids research. 40, D1, p. D1089-D1092

Research output: Contribution to journalArticle

RNA Caps
Databases
Aptitude
Transcription Initiation Site
Genome
2011
396 Citations (Scopus)

Adaptive seeds tame genomic sequence comparison

Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C., 2011 Mar 1, In : Genome Research. 21, 3, p. 487-493 7 p.

Research output: Contribution to journalArticle

Seeds
DNA
19 Citations (Scopus)

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

Imai, K., Fujita, N., Gromiha, M. M. & Paul, B. H. I., 2011 Jan 28, In : BMC genomics. 12, 79.

Research output: Contribution to journalArticle

Eukaryota
Sequence Analysis
Membrane Proteins
Yeasts
Arabidopsis
1 Citation (Scopus)

Evolutionary sequence divergence predicts protein sub-cellular localization signals

Fukasawa, Y., Leung, R. K. K., Tsui, S. K. W. & Paul, B. H. I., 2011 Jan 1, 2011 IEEE International Conference on Systems Biology, ISB 2011. IEEE Computer Society, p. 307-312 6 p. (2011 IEEE International Conference on Systems Biology, ISB 2011).

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

Amino Acid Sequence
Conservation
Cytology
Amino Acids
Sorting
39 Citations (Scopus)

Prediction of leucine-rich nuclear export signal containing proteins with NESsential

Fu, S. C., Imai, K. & Horton, P., 2011 Sep 1, In : Nucleic acids research. 39, 16, p. e111

Research output: Contribution to journalArticle

Nuclear Export Signals
Leucine
Proteins
Consensus Sequence
Signal Transduction
2010

Improved prediction of transcription binding sites from chromatin modification data

Sato, K., Whitington, T., Bailey, T. L. & Horton, P., 2010 Aug 20, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010. p. 220-226 7 p. 5510323. (2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010).

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

Transcription factors
Binding sites
Transcription
Learning systems
Feature extraction
47 Citations (Scopus)

Incorporating sequence quality data into alignment improves DNA read mapping

Frith, M. C., Wan, R. & Paul, B. H. I., 2010 Jan 27, In : Nucleic acids research. 38, 7, gkq010.

Research output: Contribution to journalArticle

Genome
DNA
Drosophila melanogaster
DNA Sequence Analysis
Technology
1 Citation (Scopus)

In search of true reads: A classification approach to next generation sequencing data selection

Wijaya, E., Pessiot, J. F., Frith, M. C., Fujibuchi, W., Asai, K. & Paul, B. H. I., 2010 Dec 1, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010. p. 561-566 6 p. 5703862. (2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010).

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

Support vector machines
Classifiers
Software
Technology
Error probability
111 Citations (Scopus)

Parameters for accurate genome alignment

Frith, M. C., Hamada, M. & Paul, B. H. I., 2010 Feb 9, In : BMC Bioinformatics. 11, 80.

Research output: Contribution to journalArticle

Genome
Alignment
Genes
Fungal Genome
Plant Genome
2009

A tiling bound for pairwise global sequence alignment

Paul, B. H. I. & Frith, M., 2009 Dec 1, Advances in Software Engineering: International Conference, ASEA 2008, and Its Special Sessions, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. Kim, T., Fang, W. C., Lee, C. & Arnett, K. P. (eds.). p. 93-98 6 p. (Communications in Computer and Information Science; vol. 30).

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

Sequence Alignment
Tiling
Pairwise
Alignment
Accelerate

Characterizing genes by marginal expression distribution

Wijaya, E., Harada, H. & Horton, P., 2009 Dec 1, Advances in Computational Science and Engineering: Second International Conference, FGCN 2008, Workshops and Symposia, Sanya, Hainan Island, China, December 13-15, 2008. Revised Selected Papers. Kim, T., Yang, L. T., Park, J. H., Chang, A. C-C., Vasilakos, T., Zhang, Y., Sauveron, D., Wang, X. & Jeong, Y-S. (eds.). p. 164-175 12 p. (Communications in Computer and Information Science; vol. 28).

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

Genes
Marginal Distribution
Gene
Gene Networks
Expectation-maximization Algorithm

Database development and discrimination algorithms for membrane protein functions

Gromiha, M. M., Yabuki, Y., Imai, K., Paul, B. H. I. & Fukui, K., 2009 Jan 1, In : World Academy of Science, Engineering and Technology. 37, p. 358-362 5 p.

Research output: Contribution to journalArticle

Proteins
Membranes
Amino acids
Genes
Carrier Proteins
1 Citation (Scopus)

HAMSTER: Visualizing microarray experiments as a set of minimum spanning trees

Wan, R., Kiseleva, L., Harada, H., Mamitsuka, H. & Horton, P., 2009 Nov 20, In : Source Code for Biology and Medicine. 4, 8.

Research output: Contribution to journalArticle

Microarrays
Cluster Analysis
Gene expression
Experiments
Data visualization
36 Citations (Scopus)

Recount: expectation maximization based error correction tool for next generation sequencing data.

Wijaya, E., Frith, M. C., Suzuki, Y. & Paul, B. H. I., 2009 Jan 1, In : Genome informatics. International Conference on Genome Informatics. 23, 1, p. 189-201 13 p.

Research output: Contribution to journalArticle

Technology
Genome
Gene Expression
Datasets
2008

Erratum: CellMontage: Similar expression profile search server (Bioinformatics (2007) vol. 23 (22) (3103-3104))

Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H. & Horton, P., 2008 May 1, In : Bioinformatics. 24, 9, 1 p.

Research output: Contribution to journalComment/debate

Bioinformatics
Server
Profile
11 Citations (Scopus)

Mitochondrial β-Barrel Proteins, an Exclusive Club?

Imai, K., Gromiha, M. M. & Paul, B. H. I., 2008 Dec 26, In : Cell. 135, 7, p. 1158-1159 2 p.

Research output: Contribution to journalLetter

Mitochondrial Membrane Transport Proteins
Mitochondria
Animals
Proteins
3 Citations (Scopus)

Modeling the marginal distribution of gene expression with mixture models

Wijaya, E., Harada, H. & Paul, B. H. I., 2008 Dec 1, Proceedings of the 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008 and BSBT 2008: 2008 International Conference on Bio-Science and Bio-Technology. p. 84-89 6 p. 4734285. (Proceedings of the 2008 2nd International Conference on Future Generation Communication and Networking, FGCN 2008 and BSBT 2008: 2008 International Conference on Bio-Science and Bio-Technology; vol. 3).

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

Gene expression
Genes
Gene Expression
Gene Regulatory Networks
Reference Values
55 Citations (Scopus)

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Genome Information Integration Project and H-Invitational 2 Consortium, 2008 Jan, In : Nucleic acids research. 36, SUPPL. 1, p. D793-D799

Research output: Contribution to journalArticle

Databases
Genes
Molecular Sequence Annotation
Proteins
Transcriptome
2007
2 Citations (Scopus)

An upper bound on the hardness of exact matrix based motif discovery

Paul, B. H. I. & Fujibuchi, W., 2007 Jan 1, In : Journal of Discrete Algorithms. 5, 4 SPEC. ISS., p. 706-713 8 p.

Research output: Contribution to journalArticle

Motif Discovery
Hardness
Upper bound
Transcription factors
Binding sites
34 Citations (Scopus)

CellMontage: Similar expression profile search server

Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H. & Horton, P., 2007 Nov 1, In : Bioinformatics. 23, 22, p. 3103-3104 2 p.

Research output: Contribution to journalArticle

Search Engine
Microarrays
Microarray
Servers
Server
31 Citations (Scopus)

Computational prediction of subcellular localization

Nakai, K. & Paul, B. H. I., 2007 May 21, Protein Targeting Protocols, Second Edition. p. 429-466 38 p. (Methods in Molecular Biology; vol. 390).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteomics
Amino Acid Sequence
Proteins
Amino Acids

Exhaustive search of maximal biclusters in gene expression data

Okada, Y., Fujibuchi, W. & Paul, B. H. I., 2007 Dec 1, IMECS 2007 - International MultiConference of Engineers and Computer Scientists 2007. p. 307-312 6 p. (Lecture Notes in Engineering and Computer Science).

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

Gene expression
Proteins
Genes
Experiments
1582 Citations (Scopus)

WoLF PSORT: Protein localization predictor

Paul, B. H. I., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J. & Nakai, K., 2007 Jul 1, In : Nucleic acids research. 35, SUPPL.2

Research output: Contribution to journalArticle

Proteins
Nucleotide Motifs
Gene Ontology
Sequence Alignment
Amino Acid Sequence