Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Medicine, Research & Experimental
Qihang Zhong, Minzhen Lu, Wanqiong Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao, Jing Hang
Summary: This study identified three molecular subtypes of cervical cancer through multi-omics integration analysis, incorporating 617 differentially expressed lncRNAs and 1395 differentially expressed PCGs. The functional enrichment analysis revealed that the identified lncRNAs were mainly involved in tumor metabolism, immunity, and pathways related to cervical cancer development. A prognostic risk model based on lncRNAs was established and validated to be effective in prognosis management of cervical cancer patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Sharon L. Freshour, Susanna Kiwala, Kelsy C. Cotto, Adam C. Coffman, Joshua F. McMichael, Jonathan J. Song, Malachi Griffith, Obi L. Griffith, Alex H. Wagner
Summary: The Drug-Gene Interaction Database (DGIdb) is a web resource that provides information on drug-gene interactions and druggable genes. DGIdb 4.0 is the latest major version release, featuring integration with crowdsourced efforts, addition of new sources, and updates to the data.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Biochemical Research Methods
Ajay Anand Kumar, Bart Loeys, Gerarda van de Beek, Nils Peeters, Wim Wuyts, Lut Van Laer, Geert Vandeweyer, Maaike Alaerts
Summary: This study introduces a novel tool called varAmpliCNV for detecting CNVs in amplicon-based targeted resequencing data. VarAmpliCNV outperforms existing methods, achieving higher sensitivity and specificity.
Article
Biochemical Research Methods
Bin Liu, Jin Wang, Kaiwei Sun, Grigorios Tsoumakas
Summary: The discovery of drug-target interactions (DTIs) is crucial in pharmaceutical development. Computational methods are promising in predicting novel DTIs. This study presents a Fine-Grained Selective similarity integration approach (FGS) that captures and exploits the importance of similarities at a finer granularity.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yi-An Chen, Rodolfo S. Allendes Osorio, Kenji Mizuguchi
Summary: This paper introduces the latest version of TargetMine, which adds new visualization options, integrates previously disaggregated functionality, and migrates the front-end to the newly available Bluegenes service.
Article
Cell Biology
Huihui Hu, Hangdi Xu, Fen Lu, Jisong Zhang, Li Xu, Shan Xu, Hanliang Jiang, Qingxin Zeng, Enguo Chen, Zhengfu He
Summary: This study focused on analyzing the CNV, lncRNA, mRNA, and microRNA of lung cancer, identifying nine lncRNAs that could affect the CNV-associated ceRNA network constructed, with two showing promise in determining tumor response to drug treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Clinical Neurology
Aurelien Perrin, Raul Juntas Morales, Francoise Chapon, Corinne Theze, Delphine Lacourt, Henri Pegeot, Emmanuelle Uro-Coste, Diane Giovannini, Nicolas Leboucq, Martial Mallaret, Emmeline Lagrange, Valerie Rigau, Karen Gaudon, Pascale Richard, Michel Koenig, Corinne Metay, Mireille Cossee
Summary: This study analyzed patients from two distinct families with a novel distal titinopathy phenotype associated with the same CNV in the TTN gene. The CNV reported in this study is the most proximal out-of-frame TTN variant and leads to aberrant splicing transcripts, resulting in frameshift and possibly dominant effects. This data represents a novel phenotype-genotype association and provides hypotheses for its dominant effects.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: The study developed a tool called Montage to enhance the accuracy of detecting mosaic copy number variants, identified numerous mosaic CNVs associated with phenotypes, and presented a novel algorithm for efficient detection of mosaic CNVs.
Review
Biochemical Research Methods
Maryam Bagherian, Elyas Sabeti, Kai Wang, Maureen A. Sartor, Zaneta Nikolovska-Coleska, Kayvan Najarian
Summary: Predicting interactions between drugs and targets is crucial in drug discovery, necessitating the development of efficient prediction approaches to avoid costly and uncertain experimental determinations. These approaches should timely identify potential drug-target interactions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Construction & Building Technology
Gokhan Demirdogen, Zeynep Isik, Yusuf Arayici
Summary: Facility management is the most costly stage in the building lifecycle of healthcare buildings. Building Information Modeling (BIM) has the potential to address the information management needs of healthcare facility management. However, its static nature hinders its use in facility management, which requires dynamic information handling. This paper aims to develop a healthcare facility management system using Big Data Analytics (BDA), BIM, and NoSQL database to enable information query and Key Performance Indicator (KPI) visualization. The findings show that the proposed system effectively enables practitioners in healthcare facility management to retrieve and analyze facility management data.
JOURNAL OF BUILDING ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Sunghwan Kim, Tiejun Cheng, Siqian He, Paul A. Thiessen, Qingliang Li, Asta Gindulyte, Evan E. Bolton
Summary: PubChem is a public chemical database that serves as a vital resource for biomedical research communities. It provides information on chemicals related to biological targets, helping users analyze and interpret the biological activity data of molecules. The database contains data from hundreds of contributors and is organized into various collections based on different record types.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Oncology
Z. Yao, L. Deng, Z. Y. Xu-Monette, G. C. Manyam, P. Jain, A. Tzankov, C. Visco, G. Bhagat, J. Wang, K. Dybkaer, W. Tam, E. D. Hsi, J. H. van Krieken, M. Ponzoni, A. J. M. Ferreri, M. B. Moller, J. N. Winter, M. A. Piris, L. Fayad, Y. Liu, Y. Song, R. Z. Orlowski, H. Kantarjian, L. J. Medeiros, Y. Li, J. Cortes, K. H. Young
Article
Pathology
Qingqing Ding, Yan Wang, Zhuang Zuo, Yun Gong, Savitri Krishnamurthy, Chia-Wei Li, Yun-Ju Lai, Wei Wei, Jing Wang, Ganiraju C. Manyam, Lixia Diao, Xinna Zhang, Feng Lin, William F. Symmans, Li Sun, Chang-Gong Liu, Xiuping Liu, Bisrat G. Debeb, Naoto T. Ueno, Kenichi Harano, Ricardo H. Alvarez, Yun Wu, Massimo Cristofanilli, Lei Huo
Article
Oncology
Xiaoxiao Wang, Xin Cao, Ruifang Sun, Charlene Tang, Alexandar Tzankov, Jun Zhang, Ganiraju C. Manyam, Min Xiao, Yi Miao, Kausar Jabbar, Xiaohong Tan, Yuyang Pang, Carlo Visco, Yan Xie, Karen Dybkaer, April Chiu, Attilio Orazi, Youli Zu, Govind Bhagat, Kristy L. Richards, Eric D. Hsi, William W. L. Choi, J. Han van Krieken, Jooryung Huh, Maurilio Ponzoni, Andres J. M. Ferreri, Michael B. Moller, Ben M. Parsons, Jane N. Winter, Miguel A. Piris, Shaoying Li, Roberto N. Miranda, L. Jeffrey Medeiros, Yong Li, Zijun Y. Xu-Monette, Ken H. Young
Article
Multidisciplinary Sciences
Suprateek Kundu, Yichen Cheng, Minsuk Shin, Ganiraju Manyam, Bani K. Mallick, Veerabhadran Baladandayuthapani
Article
Multidisciplinary Sciences
Goodwin G. Jinesh, Ganiraju C. Manyam, Chinedu O. Mmeje, Keith A. Baggerly, Ashish M. Kamat
SCIENTIFIC REPORTS
(2017)
Article
Biochemistry & Molecular Biology
Anil Korkut, Sobia Zaidi, Rupa S. Kanchi, Shuyun Rao, Nancy R. Gough, Andre Schultz, Xubin Li, Philip L. Lorenzi, Ashton C. Berger, Gordon Robertson, Lawrence N. Kwong, Mike Datto, Jason Roszik, Shiyun Ling, Visweswaran Ravikumar, Ganiraju Manyam, Arvind Rao, Simon Shelley, Yuexin Liu, Zhenlin Ju, Donna Hansel, Guillermo de Velasco, Arjun Pennathur, Jesper B. Andersen, Colm J. O'Rourke, Kazufumi Ohshiro, Wilma Jogunoori, Bao-Ngoc Nguyen, Shulin Li, Hatice U. Osmanbeyoglu, Jaffer A. Ajani, Sendurai A. Mani, Andres Houseman, Maciej Wiznerowicz, Jian Chen, Shoujun Gu, Wencai Ma, Jiexin Zhang, Pan Tong, Andrew D. Cherniack, Chuxia Deng, Linda Resar, John N. Weinstein, Lopa Mishra, Rehan Akbani
Article
Biotechnology & Applied Microbiology
Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo, Kevin R. Coombes
Article
Oncology
Liana Adam, F. Anthony San Lucas, Richard Fowler, Yao Yu, Wenhui Wu, Yulun Liu, Huamin Wang, David Menter, Michael T. Tetzlaff, Joe Ensor, Ganiraju Manyam, Stefan T. Arold, Chad Huff, Scott Kopetz, Paul Scheet, Michael J. Overman
CLINICAL CANCER RESEARCH
(2019)
Article
Oncology
Zachary B. Abrams, Suli Li, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Nyla A. Heerema, Lynne Abruzzo, Kevin R. Coombes
Article
Biochemical Research Methods
Zachary B. Abrams, Dwayne G. Tally, Lynne Abruzzo, Kevin R. Coombes
Summary: Cytogenetics data, stored as karyotypes, are now being analyzed on a large scale thanks to tools like CytoGPS. The development of RCytoGPS further facilitates the analysis and visualization of karyotype data, advancing the field of computational cytogenetic pathology.
Article
Biochemistry & Molecular Biology
Caitlin E. Coombes, Kevin R. Coombes, Naleef Fareed
Summary: We present a novel model of time-series analysis for learning from electronic health record (EHR) data in the context of infection occurrence in the intensive care unit (ICU). By applying methods from proteomics and Bayesian statistics, we analyzed a large dataset of ICU patients and identified physician actions that were individually associated with increased risk of infection. Our approach also demonstrated the ability to predict the administration of antibiotics with reasonably high accuracy.
CHEMISTRY & BIODIVERSITY
(2022)
Meeting Abstract
Oncology
Ganesh Rao, Khatri Latha, Jun Yan, Yuhui Yang, Ganiraju Manyam, Ravesanker Ezhilarasan, Erik Sulman, Arvind Rao, Amy Heimberger, Shulin Li
Meeting Abstract
Hematology
Irene Ganan-Gomez, Ana Alfonso, Hui Yang, Andrea Santoni, Valentina Marchica, Elena Fiorini, Guillermo Montalban-Bravo, Yamini Ogoti, Ganiraju Manyam, Shan Jiang, Naran Bao, Christopher Jackson, Ashley Rose, Rashmi Kanagal-Shamanna, Carlos E. Bueso-Ramos, Benedetta Cambo, Nicola Giuliani, Monica Crugnola, Marina Y. Konopleva, Karen Clise-Dwyer, Guillermo Garcia-Manero, Simona Colla
Meeting Abstract
Oncology
Amir Mehrvarz Sarshekeh, Jonathan M. Loree, Ganiraju C. Manyam, Allan Andresson Lima Pereira, Kanwal Pratap Singh Raghav, Michael Lam, Jennifer S. Davis, A. Dasari, Van Karlyle Morris, David Menter, Cathy Eng, Russell Broaddus, Mark Routbort, Rajyalakshmi Luthra, Dipen M. Maru, Michael J. Overman, Funda Meric-Bernstam, Scott Kopetz
JOURNAL OF CLINICAL ONCOLOGY
(2018)
Meeting Abstract
Hematology
Zijun Yidan Xu-Monette, Li Yu, Thai Tran, Lisa Adams, Nathan Roscoe, Ganiraju Manyam, Carlo Visco, Alexandar Tzankov, Karen Dybkaer, Govind Bhagat, April Chiu, Wayne Tam, Youli Zu, Eric D. Hsi, Joannes H. J. M. Van Krieken, Jooryung Huh, Maurilio Ponzoni, Andres Ferreri, Michael Boe Moller, Miguel Angel Piris, Jane N. Winter, L. Jeffrey Medeiros, George Rassidakis, Christine Angela Vaupel, Yong Li, Naveen Dakappagari, Ken H. Young