Article
Biochemistry & Molecular Biology
Hye Lim Choi, Ha Rim Yang, Ha Gyeong Shin, Kyusang Hwang, Ji Woong Kim, Ji Hyun Lee, Taehoon Ryu, Yushin Jung, Sukmook Lee
Summary: Antibody phage display is a crucial technology for discovering and developing target-specific monoclonal antibodies. This study constructed a large human combinatorial single-chain variable fragment library with high diversity, which can be used for the rapid development of recombinant human monoclonal antibodies for therapeutic and diagnostic applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Public, Environmental & Occupational Health
Jillian N. N. Socea, Victoria N. N. Stone, Xiaorong Qian, Paula L. L. Gibbs, Kara J. J. Levinson
Summary: The importance of next-generation sequencing (NGS) for diagnostic testing and surveillance-based screening has become more evident due to COVID-19. However, many laboratories face barriers such as limited staff, lack of expertise in sequencing, difficulties in assay standardization, and inability to handle samples within expected turnaround times. Workflow automation provides an opportunity to overcome these challenges.
FRONTIERS IN PUBLIC HEALTH
(2023)
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sanjay Joshi, Hadia Awan, Priyanka Paul, Ran Tian, Sharyn E. Perry
Summary: AGL15, a member of the MADS-domain transcription factor family, primarily accumulates in plant embryos and promotes plant regeneration. Through the use of different technological platforms, researchers have identified an interaction between AGL15 and the brassinosteroid hormone signaling pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Juan Wang, Yuwei Sheng, Ying Yang, Xiaoxia Dai, Changjun You
Summary: This study found that the N-6-methyldeoxyadenosine (6mdA) modification has minimal impact on the efficiency and accuracy of DNA replication in human cells. Depletion of specific DNA polymerases also did not significantly alter the biological consequences of 6mdA during replication. These results support the potential role of 6mdA in epigenetic gene expression.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Medical Laboratory Technology
Bennett Oh Vic Shum, Carel Jacobus Pretorius, Letitia Min Fen Sng, Ilya Henner, Paulette Barahona, Emre Basar, Jim McGill, Urs Wilgen, Anna Zournazi, Lilian Downie, Natalie Taylor, Liam Cheney, Sylvania Wu, Natalie Angela Twine, Denis Carolin Bauer, Gerald Francis Watts, Akash Navilebasappa, Kishore Rajagopal Kumar, Jacobus Petrus Johannes Ungerer, Glenn Bennett
Summary: The study found that newborn screening can be expanded using targeted gene sequencing (TGS), which is a feasible and cost-effective method. The TGS assay had a high sensitivity (>99%) and specificity (100%) with a turnaround time of 7 to 10 days and a maximum batch size of 1536 samples. This approach can increase the number of conditions screened and improve the effectiveness of newborn screening programs.
CLINICAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Raphael Rodriguez, Yamuna Krishnan
Summary: This article reviews the historical development of next-generation sequencing chemistry, highlighting the significant impact of the underlying chemical principles on biology.
NATURE BIOTECHNOLOGY
(2023)
Review
Genetics & Heredity
Ziga I. Remec, Katarina Trebusak Podkrajsek, Barbka Repic Lampret, Jernej Kovac, Urh Groselj, Tine Tesovnik, Tadej Battelino, Marusa Debeljak
Summary: Newborn screening was introduced in the 1960s, and has expanded over time with the advancement of technology, particularly high-throughput sequencing. Genomic sequencing is now widely used in clinical applications, including newborn screening, but has also raised various concerns and challenges.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Melanie A. Mallory, Weston C. Hymas, Keith E. Simmon, Michael T. Pyne, Jeffery B. Stevenson, Adam P. Barker, David R. Hillyard, Kimberly E. Hanson
Summary: This study developed and validated an amplicon-based Ion Torrent NGS method for simultaneous analysis of CMV resistance mutations in multiple genes. Compared to standard Sanger sequencing, the NGS assay had a low error rate and high accuracy, and generated high-quality sequence from low viral load specimens. The assay showed excellent agreement with Sanger and detected resistance mutations missed by Sanger in low-frequency variants.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Oncology
Bassel Nazha, Tony Z. Zhuang, Hiba Dada, Leylah M. Drusbosky, Jacqueline T. Brown, Deepak Ravindranathan, Bradley C. Carthon, Omer Kucuk, Jamie Goldman, Viraj A. Master, Mehmet Asim Bilen
Summary: This study evaluated the genomic landscape of adrenocortical carcinoma (ACC) using blood-based DNA testing. The findings suggest that a significant proportion of ACC patients have actionable mutations, which could inform personalized treatment options or clinical trials for this aggressive malignancy.
Article
Biochemistry & Molecular Biology
Sara-Sophie Poethe, Julia Holtel, Jan-Philip Biermann, Trine Riemer, Melanie Grabmueller, Burkhard Madea, Ralf Thiele, Richard Jaeger
Summary: Forensic DNA profiles are typically established using multiplex PCR amplification and capillary electrophoresis (CE) analysis, but high-throughput next generation sequencing (NGS) techniques have recently been used as an alternative. In this study, an alternative NGS assay called maSTR assay was developed that is cost-effective and performs well in samples with low DNA content, mixed DNA, or PCR inhibitors. The maSTR assay, in conjunction with the SNiPSTR bioinformatics pipeline, is a simple and robust NGS-based STR typing method for human identification in forensic and biomedical contexts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Brian C. Searle, Ariana E. Shannon, Damien Beau Wilburn
Summary: Scribe is a new library search engine that uses deep learning fragmentation prediction software to predict fragmentation and retention times for peptides in a FASTA database, outperforming traditional database searching tools in terms of sensitivity and quantitative precision.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Virology
Ane Beth Sloth, Babak Bakhshinejad, Malte Jensen, Camilla Stavnsbjerg, Mikkel Baldtzer Liisberg, Maria Rossing, Andreas Kjaer
Summary: This study used deep sequencing to characterize the widely used Ph.DTM-12 phage display peptide library and found the presence of stop codons and a high abundance of wild-type clones in the naive library. Analysis of nucleotide and amino acid composition revealed significant bias, and principal component analysis showed the existence of four distinct clusters in the naive library. These findings suggest that the naive library represents substantial departures from randomness at the nucleotide, amino acid, and peptide levels.
Article
Microbiology
Andrew N. Miller, Jason Karakehian, Daniel B. Raudabaugh
Summary: Fungaria is an important resource for genetic data, especially for type specimens. However, ancient specimens often have fragmented and contaminated DNA, making sequencing difficult. This study successfully extracted and sequenced DNA from recent and ancient specimens, generating correct sequences for five samples. The results contribute to ongoing systematic studies.
Article
Chemistry, Physical
Yuyang Zhu, Wentong Zhou, Ellen M. Petryna, Brock R. Rogers, Cynthia S. Day, Amanda C. Jones
Article
Biochemistry & Molecular Biology
Yuyang Zhu, Maomao Yan, Yi Lasanajak, David F. Smith, Xuezheng Song
CARBOHYDRATE RESEARCH
(2018)
Article
Chemistry, Multidisciplinary
Yuyang Zhu, Cynthia S. Day, Lin Zhang, Katarina J. Hauser, Amanda C. Jones
CHEMISTRY-A EUROPEAN JOURNAL
(2013)
Article
Chemistry, Inorganic & Nuclear
Yuyang Zhu, Cynthia S. Day, Amanda C. Jones
Correction
Chemistry, Inorganic & Nuclear
Yuyang Zhu, Cynthia S. Day, Amanda C. Jones
Article
Chemistry, Inorganic & Nuclear
Madhavi Sriram, Yuyang Zhu, Andrew M. Camp, Cynthia S. Day, Amanda C. Jones
Article
Biochemical Research Methods
Yuyang Zhu, Xueyun Liu, Ying Zhang, Zhongfu Wang, Yi Lasanajak, Xuezheng Song
BIOCONJUGATE CHEMISTRY
(2018)
Article
Chemistry, Analytical
Ying Zhang, Bo Wang, Wanjun Jin, Yanan Wen, Lijing Nan, Mingming Yang, Rendan Liu, Yuyang Zhu, Chengjian Wang, Linjuan Huang, Xuezheng Song, Zhongfu Wang
ANALYTICA CHIMICA ACTA
(2019)
Article
Biochemical Research Methods
Ying Zhang, Yuyang Zhu, Yi Lasanajak, David F. Smith, Xuezheng Song
Article
Biochemical Research Methods
Yuyang Zhu, Thomas J. Bowen, Xuezheng Song
ANALYTICAL BIOCHEMISTRY
(2020)
Article
Chemistry, Analytical
Zhonghua Li, Qing Zhang, David Ashline, Yuyang Zhu, Yi Lasanajak, Tatiana Chernova, Vernon Reinhold, Richard D. Cummings, Peng G. Wang, Tongzhong Ju, David F. Smith, Xuezheng Song
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Inorganic & Nuclear
Carolin Griebel, Dwaine D. Hodges, Brock R. Yager, Fred L. Liu, Wentong Zhou, Katarina J. Makaravage, Yuyang Zhu, Skylar G. Norman, Ruichen Lan, Cynthia S. Day, Amanda C. Jones
Meeting Abstract
Chemistry, Multidisciplinary
Amanda Jones, Brock Yager, Wentong Zhou, Yuyang Zhu, Yoonsun Jee
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Meeting Abstract
Chemistry, Multidisciplinary
Yuyang Zhu, Lin Zhang, Amanda C. Jones
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2013)