Brice Horton Ii Paul

Professor

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

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Article
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
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
2016
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
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
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
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
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
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
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

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
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
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
2006
6 Citations (Scopus)

Comparative genomic analysis of transcription regulation elements involved in human map kinase g-protein coupling pathway

Polouliakh, N., Natsume, T., Harada, H., Fujibuchchi, W. & Paul, B. H. I., 2006 Apr 1, In : Journal of Bioinformatics and Computational Biology. 4, 2, p. 469-482 14 p.

Research output: Contribution to journalArticle

Nucleic Acid Regulatory Sequences
Transcription
Protein Kinases
Phosphotransferases
Genes
20 Citations (Scopus)

Inference of scale-free networks from gene expression time series

Daisuke, T. & Horton, P., 2006 Apr 1, In : Journal of Bioinformatics and Computational Biology. 4, 2, p. 503-514 12 p.

Research output: Contribution to journalArticle

Complex networks
Gene expression
Time series
Gene Expression
Biological Models
2 Citations (Scopus)

Network-based de-noising improves prediction from microarray data

Kato, T., Murata, Y., Miura, K., Asai, K., Paul, B. H. I., Tsuda, K. & Fujibuchi, W., 2006 Mar 20, In : BMC Bioinformatics. 7, SUPPL.1, S4.

Research output: Contribution to journalArticle

Microarrays
Denoising
Microarray Data
Noise
Drugs
14 Citations (Scopus)

RaPiDS: an algorithm for rapid expression profile database search.

Paul, B. H. I., Kiseleva, L. & Fujibuchi, W., 2006 Jan 1, In : Genome informatics. International Conference on Genome Informatics. 17, 2, p. 67-76 10 p.

Research output: Contribution to journalArticle

Databases
Gene Expression
2005
63 Citations (Scopus)

Discrimination of outer membrane proteins using support vector machines

Park, K. J., Gromiha, M. M., Horton, P. & Suwa, M., 2005 Dec 1, In : Bioinformatics. 21, 23, p. 4223-4229 7 p.

Research output: Contribution to journalArticle

Membrane Protein
Discrimination
Support vector machines
Support Vector Machine
Membrane Proteins
2001
10 Citations (Scopus)
Branch and Bound Algorithm
Protein Sequence
DNA Sequence
Alignment
DNA
1997
403 Citations (Scopus)
Yeasts
Escherichia coli
Decision Trees
Fungal Proteins
Statistical Models
1996
6 Citations (Scopus)
Heuristics
216 Citations (Scopus)
Expert Systems
Fungal Proteins
Escherichia coli Proteins
Amino Acid Sequence
Proteins
1992
59 Citations (Scopus)

An assessment of neural network and statistical approaches for prediction of E.coli promoter sites

Horton, P. B. & Kanehisa, M., 1992 Aug 25, In : Nucleic acids research. 20, 16, p. 4331-4338 8 p.

Research output: Contribution to journalArticle

Escherichia coli
Neural Networks (Computer)
Research Personnel