Genomics & Informatics

BLAH7 | Application note

September 30, 2021

A biomedically oriented automatically annotated Twitter COVID-19 dataset

Luis Alberto Robles Hernandez, Tiffany J. Callahan, Juan M. Banda

Genomics Inform. 2021;19(3):e21.

The use of social media data, like Twitter, for biomedical research has been gradually increasing over the years. With the coronavirus disease 2019 (COVID-19) pandemic, researchers have turned to more...

BLAH7 | Application note

September 30, 2021

Improving classification of low-resource COVID-19 literature by using Named Entity Recognition

Oscar Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi

Genomics Inform. 2021;19(3):e22.

Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus...

BLAH7 | Application note

September 30, 2021

LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19

Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia

Genomics Inform. 2021;19(3):e23.

Currently, coronavirus disease 2019 (COVID-19) literature has been increasing dramatically, and the increased text amount make it possible to perform large scale text mining and knowledge discovery. Therefore, curation of...

BLAH7 | Application note

September 30, 2021

COVID-19 recommender system based on an annotated multilingual corpus

Márcia Barros, Pedro Ruas, Diana Sousa, Ali Haider Bangash, Francisco M. Couto

Genomics Inform. 2021;19(3):e24.

Tracking the most recent advances in Coronavirus disease 2019 (COVID-19)‒related research is essential, given the disease's novelty and its impact on society. However, with the publication pace speeding up, researchers...

BLAH7 | Application note

September 30, 2021

Constructing Japanese MeSH term dictionaries related to the COVID-19 literature

Atsuko Yamaguchi, Terue Takatsuki, Yuka Tateisi, Felipe Soares

Genomics Inform. 2021;19(3):e25.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this...

BLAH7 | Application note

September 30, 2021

O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information

Felipe Soares, Yuka Tateisi, Terue Takatsuki, Atsuko Yamaguchi

Genomics Inform. 2021;19(3):e26.

Previous approaches to create a controlled vocabulary for Japanese have resorted to existing bilingual dictionary and transformation rules to allow such mappings. However, given the possible new terms introduced due...

BLAH7 | Application note

September 30, 2021

OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition

Pierre Larmande, Yusha Liu, Xinzhi Yao, Jingbo Xia

Genomics Inform. 2021;19(3):e27.

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural...

BLAH7 | Opinion

September 30, 2021

Visualizing the phenotype diversity: a case study of Alexander disease

Eisuke Dohi, Ali Haider Bangash

Genomics Inform. 2021;19(3):e28.

Since only a small number of patients have a rare disease, it is difficult to identify all of the features of these diseases. This is especially true for patients presenting...

Original article

September 30, 2021

Molecular insights into the role of genetic determinants of congenital hypothyroidism

Yedukondalu Kollati, Radha Rama Devi Akella, Shaik Mohammad Naushad, Rajesh K. Patel, G. Bhanuprakash Reddy, Vijaya R. Dirisala

Genomics Inform. 2021;19(3):e29.

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we...

Original article

September 30, 2021

Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay

Jiyon Chu, Juyoun Shin, Shinseok Kang, Sun Shin, Yeun-Jun Chung

Genomics Inform. 2021;19(3):e30.

Salmonella species are among the major pathogens that cause foodborne illness outbreaks. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid and sensitive...

Original article

September 30, 2021

Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients

Songtham Anuntakarun, Vorthon Sawaswong, Rungrat Jitvaropas, Kesmanee Praianantathavorn, Witthaya Poomipak, Yupin Suputtamongkol, Chintana Chirathaworn, Sunchai Payungporn

Genomics Inform. 2021;19(3):e31.

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of...

Original article

September 30, 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail

Jeong-An Gim, Kyung-Wan Baek, Young-Sool Hah, Ho Jin Choo, Ji-Seok Kim, Jun-Il Yoo

Genomics Inform. 2021;19(3):e32.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other...

Original article

September 30, 2021

Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation

Maheswari Patturaj, Aiswarya Munusamy, Nithishkumar Kannan, Ulaganathan Kandasamy, Yasodha Ramasamy

Genomics Inform. 2021;19(3):e33.

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. ...

Application note

September 30, 2021

High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array

Haeun Lee, Cherl-Joon Lee, Dong Hee Kim, Chun-Sung Cho, Wonseok Shin, Kyudong Han

Genomics Inform. 2021;19(3):e34.

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the...

Editor’s introduction to the special section on the 7th Biomedical Linked Annotation Hackathon (BLAH7) Jin-Dong Kim, Kevin Bretonnel Cohen, Fabio Rinaldi, Zhiyong Lu, Hyun-Seok Park Genomics Inform. 2021;19(3):e20. Editorial September 30, 2021 Full text PubReader ePub PDF	A biomedically oriented automatically annotated Twitter COVID-19 dataset Luis Alberto Robles Hernandez, Tiffany J. Callahan, Juan M. Banda Genomics Inform. 2021;19(3):e21. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF
Improving classification of low-resource COVID-19 literature by using Named Entity Recognition Oscar Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi Genomics Inform. 2021;19(3):e22. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF	LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19 Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia Genomics Inform. 2021;19(3):e23. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF
COVID-19 recommender system based on an annotated multilingual corpus Márcia Barros, Pedro Ruas, Diana Sousa, Ali Haider Bangash, Francisco M. Couto Genomics Inform. 2021;19(3):e24. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF	Constructing Japanese MeSH term dictionaries related to the COVID-19 literature Atsuko Yamaguchi, Terue Takatsuki, Yuka Tateisi, Felipe Soares Genomics Inform. 2021;19(3):e25. BLAH7 \| Application note September 30, 2021 Full text PubReader PDF
O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information Felipe Soares, Yuka Tateisi, Terue Takatsuki, Atsuko Yamaguchi Genomics Inform. 2021;19(3):e26. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF	OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition Pierre Larmande, Yusha Liu, Xinzhi Yao, Jingbo Xia Genomics Inform. 2021;19(3):e27. BLAH7 \| Application note September 30, 2021 Full text PubReader ePub PDF
Visualizing the phenotype diversity: a case study of Alexander disease Eisuke Dohi, Ali Haider Bangash Genomics Inform. 2021;19(3):e28. BLAH7 \| Opinion September 30, 2021 Full text PubReader ePub PDF	Molecular insights into the role of genetic determinants of congenital hypothyroidism Yedukondalu Kollati, Radha Rama Devi Akella, Shaik Mohammad Naushad, Rajesh K. Patel, G. Bhanuprakash Reddy, Vijaya R. Dirisala Genomics Inform. 2021;19(3):e29. Original article September 30, 2021 Full text PubReader ePub PDF Supplementary Material
Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay Jiyon Chu, Juyoun Shin, Shinseok Kang, Sun Shin, Yeun-Jun Chung Genomics Inform. 2021;19(3):e30. Original article September 30, 2021 Full text PubReader ePub PDF	Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients Songtham Anuntakarun, Vorthon Sawaswong, Rungrat Jitvaropas, Kesmanee Praianantathavorn, Witthaya Poomipak, Yupin Suputtamongkol, Chintana Chirathaworn, Sunchai Payungporn Genomics Inform. 2021;19(3):e31. Original article September 30, 2021 Full text PubReader ePub PDF Supplementary Material
Draft genome of Semisulcospira libertina, a species of freshwater snail Jeong-An Gim, Kyung-Wan Baek, Young-Sool Hah, Ho Jin Choo, Ji-Seok Kim, Jun-Il Yoo Genomics Inform. 2021;19(3):e32. Original article September 30, 2021 Full text PubReader ePub PDF Supplementary Material	Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation Maheswari Patturaj, Aiswarya Munusamy, Nithishkumar Kannan, Ulaganathan Kandasamy, Yasodha Ramasamy Genomics Inform. 2021;19(3):e33. Original article September 30, 2021 Full text PubReader ePub PDF Supplementary Material
High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array Haeun Lee, Cherl-Joon Lee, Dong Hee Kim, Chun-Sung Cho, Wonseok Shin, Kyudong Han Genomics Inform. 2021;19(3):e34. Application note September 30, 2021 Full text PubReader ePub PDF

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