Stability of steepest descent with momentum for quadratic functions. - Manabu Torii; Martin T. Hagan (IEEE Trans. Neural Networks, 2002)

An Investigation of Various Information Sources for Classifying Biological names. - Manabu Torii; Sachin Kamboj; K. Vijay-Shanker (BioNLP@ACL, 2003)

Using name-internal and contextual features to classify biological terms. - Manabu Torii; Sachin Kamboj; K. Vijay-Shanker (J. Biomed. Informatics, 2004)

Rapid Adaptation of POS Tagging for Domain Specific Uses. - John E. Miller; Michael Bloodgood; Manabu Torii; K. Vijay-Shanker (BioNLP@NAACL-HLT, 2006)

Headwords and Suffixes in Biomedical Names. - Manabu Torii; Hongfang Liu (KDLL, 2006)

An online literature mining tool for protein phosphorylation. - X. Yuan; Zhang-Zhi Hu; H. T. Wu; Manabu Torii; Meenakshi Narayanaswamy; K. E. Ravikumar; K. Vijay-Shanker; Cathy H. Wu (Bioinform., 2006)

Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. - Hongfang Liu; Zhang-Zhi Hu; Manabu Torii; Cathy H. Wu; Carol Friedman (J. Am. Medical Informatics Assoc., 2006)

Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information. - Manabu Torii; Hongfang Liu (AMIA, 2007)

Adaptation of POS Tagging for Multiple BioMedical Domains. - John E. Miller; Manabu Torii; K. Vijay-Shanker (BioNLP@ACL, 2007)

Building Domain-Specific Taggers without Annotated (Domain) Data. - John E. Miller; Manabu Torii; K. Vijay-Shanker (EMNLP-CoNLL, 2007)

Mapping Gene/Protein Names in Free Text to Biomedical Databases. - Hongfang Liu; Manabu Torii; Zhang-Zhi Hu; Cathy H. Wu (ICDM Workshops, 2007)

Classifier Ensemble for Biomedical Document Retrieval. - Manabu Torii; Hongfang Liu (LBM (Short Papers), 2007)

A comparison study on algorithms of detecting long forms for short forms in biomedical text. - Manabu Torii; Zhang-Zhi Hu; Min Song 001; Cathy H. Wu; Hongfang Liu (BMC Bioinform., 2007)

Sortal Anaphora Resolution in Medline Abstracts. - Manabu Torii; K. Vijay-Shanker (Comput. Intell., 2007)

Document Classification for Mining Host Pathogen Protein-Protein Interactions. - Guixian Xu; Lanlan Yin; Manabu Torii; Zhendong Niu; Cathy H. Wu; Zhang-Zhi Hu; Hongfang Liu (BIBM, 2008)

Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature. - Hongfang Liu; Manabu Torii; Guixian Xu; Zhang-Zhi Hu; Johannes Goll (BioLINK@ISMB/ECCB, 2008)

Support Vector Machine-Based Mucin-Type O-linked Glycosylation Site Prediction Using Enhanced Sequence Feature Encoding. - Manabu Torii; Hongfang Liu; Zhang-Zhi Hu (AMIA, 2009)

Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System. - Manabu Torii; Zhang-Zhi Hu; Cathy H. Wu; Hongfang Liu (J. Am. Medical Informatics Assoc., 2009)

An exploratory study of news article clustering for web-based bio-surveillance. - Manabu Torii; Burt-Ujin Bayarsaikhan; Hongfang Liu; Thang Nguyen; Kevin Jones; Noele P. Nelson; David M. Hartley (IHI, 2010)

Evaluating gene/protein name tagging and mapping for article retrieval. - Chong Min Lee; Manabu Torii; Zhang-Zhi Hu; Yi-Ting Tsai; Jinesh Shah; Hongfang Liu (Semantic Mining in Biomedicine, 2010)

Document classification for mining host pathogen protein-protein interactions. - Lanlan Yin; Guixian Xu; Manabu Torii; Zhendong Niu; José M. Maisog; Cathy H. Wu; Zhang-Zhi Hu; Hongfang Liu (Artif. Intell. Medicine, 2010)

Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval. - Hongfang Liu; Manabu Torii; Guixian Xu; Johannes Goll (Int. J. Comput. Model. Algorithms Medicine, 2010)

Human gene/protein synonym dictionary from WikiLinks. - Kavishwar B. Wagholikar; Manabu Torii; Hongfang Liu (BCB, 2011)

Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. - Yang Chen 033; Manabu Torii; Chang-Tien Lu; Hongfang Liu (BIBM Workshops, 2011)

The gene normalization task in BioCreative III. - Zhiyong Lu; Hung-Yu Kao; Chih-Hsuan Wei; Minlie Huang; Jingchen Liu; Cheng-Ju Kuo; Chun-Nan Hsu; Richard Tzong-Han Tsai; Hong-Jie Dai; Naoaki Okazaki; Han-Cheol Cho; Martin Gerner; et al. (BMC Bioinform., 2011)

dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. - Jinlian Wang; Manabu Torii; Hongfang Liu; Gerald W. Hart; Zhang-Zhi Hu (BMC Bioinform., 2011)

An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics. - Manabu Torii; Lanlan Yin; Thang Nguyen; Chand T. Mazumdar; Hongfang Liu; David M. Hartley; Noele P. Nelson (Int. J. Medical Informatics, 2011)

Using machine learning for concept extraction on clinical documents from multiple data sources. - Manabu Torii; Kavishwar B. Wagholikar; Hongfang Liu (J. Am. Medical Informatics Assoc., 2011)

Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. - Xia Bi; Hongzhan Huang; Sherri Matis-Mitchell; Peter B. McGarvey; Manabu Torii; Hagit Shatkay; Cathy H. Wu (BIBM, 2012)

iSimp: A sentence simplification system for biomedicail text. - Yifan Peng 002; Catalina O. Tudor; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (BIBM, 2012)

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. - Carl J. Schmidt; Liang Sun; Cecilia N. Arighi; Keith Decker; K. Vijay-Shanker; Manabu Torii; Catalina O. Tudor; Cathy H. Wu; Peter D'Eustachio (BIBM Workshops, 2012)

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. - Siddhartha Jonnalagadda; Dingcheng Li; Sunghwan Sohn; Stephen Tze-Inn Wu; Kavishwar B. Wagholikar; Manabu Torii; Hongfang Liu (J. Am. Medical Informatics Assoc., 2012)

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Manabu Torii; K. Vijay-Shanker; Hongzhan Huang; Cathy H. Wu (BCB, 2013)

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. - Manabu Torii; Cecilia N. Arighi; Qinghua Wang 003; Cathy H. Wu; K. Vijay-Shanker (BCB, 2013)

BioC: a minimalist approach to interoperability for biomedical text processing. - Donald C. Comeau; Rezarta Islamaj Dogan; Paolo Ciccarese; Kevin Bretonnel Cohen; Martin Krallinger; Florian Leitner; Zhiyong Lu; Yifan Peng 002; Fabio Rinaldi 001; Manabu Torii; Alfonso Valencia; Karin Verspoor; et al. (Database J. Biol. Databases Curation, 2013)

Pooling annotated corpora for clinical concept extraction. - Kavishwar B. Wagholikar; Manabu Torii; Siddhartha Jonnalagadda; Hongfang Liu (J. Biomed. Semant., 2013)

A framework for biomedical figure segmentation towards image-based document retrieval. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Catalina O. Tudor; Manabu Torii; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (BMC Syst. Biol., 2013)

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. - Yifan Peng 002; Catalina O. Tudor; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2014)

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. - Manabu Torii; Gang Li 021; Zhiwen Li; Rose Oughtred; Francesca Diella; Irem Çelen; Cecilia N. Arighi; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (Database J. Biol. Databases Curation, 2014)

Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time? - Manabu Torii; Kavishwar B. Wagholikar; Hongfang Liu (J. Biomed. Semant., 2014)

A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. - Yifan Peng 002; Manabu Torii; Cathy H. Wu; K. Vijay-Shanker (BMC Bioinform., 2014)

Finding Difficult-to-Disambiguate Words: Towards an Efficient Workflow to Implement Word Sense Disambiguation. - Manabu Torii; Jungwei Fan 001; Daniel S. Zisook (ICHI, 2015)

Risk factor detection for heart disease by applying text analytics in electronic medical records. - Manabu Torii; Jungwei Fan 001; Weili Yang; Theodore Lee; Matthew T. Wiley; Daniel S. Zisook; Yang Huang 008 (J. Biomed. Informatics, 2015)

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. - Manabu Torii; Cecilia N. Arighi; Gang Li 021; Qinghua Wang 003; Cathy H. Wu; K. Vijay-Shanker (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A Preliminary Study of Clinical Concept Detection Using Syntactic Relations. - Manabu Torii; Elly W. Yang; Son Doan (AMIA, 2018)

Using Natural Language Processing to Extract Health-Related Causality from Twitter Messages. - Son Doan; Elly W. Yang; Sameer Tilak; Manabu Torii (ICHI Workshops, 2018)

Extracting health-related causality from twitter messages using natural language processing. - Son Doan; Elly W. Yang; Sameer S. Tilak; Peter W. Li; Daniel S. Zisook; Manabu Torii (BMC Medical Informatics Decis. Mak., 2019)

Task formulation for Extracting Social Determinants of Health from Clinical Narratives. - Manabu Torii; Ian M. Finn; Son Doan; Paul Wang; Elly W. Yang; Daniel S. Zisook (CoRR, 2023)