Article
Biochemical Research Methods
Athira Kanathezath, Vrinda Chembra, Sunil Kumar Padingare Variyath, Gopakumar Gopalakrishnan Nair
Summary: This study identified functionally significant modules from gene co-expression network of cancerous tissues and extracted prognostic genes related to multiple stages of breast cancer. Modularity optimization method was used to identify functional modules, which enriched many Gene Ontology terms associated with cancer. Additionally, stage-specific genes and lncRNAs were identified for potential therapeutic targeting in breast cancer therapy.
CURRENT BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Areti Strati, Michail Nikolaou, Vassilis Georgoulias, Evi S. Lianidou
Summary: This study evaluated the prognostic significance of gene expression in CTCs of 46 MBC patients, showing that combined gene expression analysis can provide prognostic information for MBC.
Article
Genetics & Heredity
Congzhi Yan, Conghui Liu, Zhixuan Wu, Yinwei Dai, Erjie Xia, Wenjing Hu, Xuanxuan Dai
Summary: This study successfully predicted the prognosis of breast cancer patients by establishing a signature comprising necroptosis-related genes, and identified potential treatment targets. This novel approach holds significance for cancer research.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Cuicui Li, Lei Kang, Kevin Fan, Carolina A. Ferreira, Kaelyn Becker, Nan Huo, Hanxiao Liu, Yunan Yang, Jonathan W. Engle, Rongfu Wang, Xiaojie Xu, Dawei Jiang, Weibo Cai
Summary: The study investigated the use of Cu-64-NOTA-YY146 for imaging CD146 expressions in breast cancer, demonstrating its potential for diagnosis, prognosis prediction, and monitoring therapeutic response in orthotopic and metastatic tumor models.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Li Wang, Lei Yu, Jian Shi, Feng Li, Caiyu Zhang, Haotian Xu, Xiangzhe Yin, Lixia Wang, Shihua Lin, Anastasiia Litvinova, Yanyan Ping, Shangwei Ning, Hongying Zhao
Summary: This study systematically investigated the functional regulations between genetic alteration-driven genes and drug target genes in breast cancer. Several gene pairs were identified as potential prognostic biomarkers and therapeutic targets for breast cancer.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Huamei Li, Yiting Huang, Amit Sharma, Wenglong Ming, Kun Luo, Zhongze Gu, Xiao Sun, Hongde Liu
Summary: This study utilized single-cell transcriptome data to construct a cell type-specific reference gene expression profile for breast cancer, accurately predicting cellular infiltration and developing a functional gene set-based prognostic model that effectively differentiates the overall survival and therapeutic response of tumor patients.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Rui Wu, Hao Zhuang, Yu-Kun Mei, Jin-Yu Sun, Tao Dong, Li-Li Zhao, Zhi-Ning Fan, Li Liu
Summary: By combining DEGs and WGCNA, CCNB1 was identified as the hub gene in esophageal cancer, upregulated in tumor tissues, and associated with poor prognosis in esophageal cancer patients with higher expression.
CANCER CELL INTERNATIONAL
(2021)
Article
Genetics & Heredity
Min Fu, Qiang Wang, Hanbo Wang, Yun Dai, Jin Wang, Weiting Kang, Zilian Cui, Xunbo Jin
Summary: In this study, a robust immune-related prognostic gene signature for prostate cancer was explored using methods such as WGCNA. Analysis of 259 IRGs identified nine functional modules correlated with biochemical recurrence of prostate cancer and 35 IRGs associated with prognosis, improving the scientific and accurate treatment decisions for clinicians.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Aleix Prat, Fara Braso-Maristany, Olga Martinez-Saez, Esther Sanfeliu, Youli Xia, Meritxell Bellet, Patricia Galvan, Debora Martinez, Tomas Pascual, Mercedes Marin-Aguilera, Anna Rodriguez, Nuria Chic, Barbara Adamo, Laia Pare, Maria Vidal, Mireia Margeli, Ester Ballana, Marina Gomez-Rey, Mafalda Oliveira, Eudald Felip, Judit Matito, Rodrigo Sanchez-Bayona, Anna Sunol, Cristina Saura, Eva Ciruelos, Pablo Tolosa, Montserrat Munoz, Blanca Gonzalez-Farre, Patricia Villagrasa, Joel S. Parker, Charles M. Perou, Ana Vivancos
Summary: This study uses shallow WGS to create machine learning signatures to identify tumor phenotypes and predict therapy response in metastatic breast cancer patients. Machine learning multi-gene signatures obtained from ctDNA can identify complex biological features similar to those obtained from direct tumor tissue DNA or RNA profiling.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Rajdeep Das, Martin Sjostrom, Raunak Shrestha, Christopher Yogodzinski, Emily A. Egusa, Lisa N. Chesner, William S. Chen, Jonathan Chou, Donna K. Dang, Jason T. Swinderman, Alex Ge, Junjie T. Hua, Shaheen Kabir, David A. Quigley, Eric J. Small, Alan Ashworth, Felix Y. Feng, Luke A. Gilbert
Summary: The study integrates clinical and functional genomics data, identifying potential driver genes KIF4A and WDR62 for metastatic prostate cancer. These genes are shown to drive aggressive prostate cancer phenotypes in multiple models, regardless of AR status, and are associated with poor patient outcomes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Xingyi Li, Ju Xiang, Jianxin Wang, Jinyan Li, Fang-Xiang Wu, Min Li
Summary: This study proposed a method to identify prognostic and heterogeneous breast cancer biomarkers by considering patient sample heterogeneity and biological information from multiple sources. By clustering samples, weighting genes, and ranking them via a label propagation model on a fusion network, the identified biomarkers were biologically interpretable and had strong discriminative power in differentiating patients with different prognostic outcomes.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Murtada K. K. Elbashir, Mohanad Mohammed, Henry Mwambi, Bernard Omolo
Summary: Breast cancer is the most common cancer type among women and the second leading cause of death. Early detection and prediction of breast cancer are crucial for prognosis and targeted therapy. Developing computational techniques to determine informative genes and aid in early diagnosis is important.
APPLIED SCIENCES-BASEL
(2023)
Article
Oncology
Yujie Weng, Wei Liang, Yucheng Ji, Zhongxian Li, Rong Jia, Ying Liang, Pengfei Ning, Yingqi Xu
Summary: In this study, bioinformatics methods were used to identify key genes in HER2+ breast cancer, which are associated with important processes such as cell cycle. These key genes provide potential new approaches for the diagnosis and treatment of HER2+ breast cancer.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2021)
Article
Oncology
Meng-jie Shan, Ling-bing Meng, Peng Guo, Yuan-meng Zhang, Dexian Kong, Ya-bin Liu
Summary: This study identified CDH3, LEF1, and MMP7 as potential biomarkers for gastric cancer through gene expression analysis, and established a neural network model for early diagnosis.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Brian G. Hunt, James C. Davis, Levi H. Fox, Sara Vicente-Munoz, Carissa Lester, Susanne I. Wells, Susan E. Waltz
Summary: The RON receptor plays a crucial role in the recurrence and metastasis of breast cancer, and inhibiting RON can prevent the progression and recurrence of tumors.
Article
Oncology
Farhoud Faraji, Eleni M. Rettig, Hua-Ling Tsai, Margueritta El Asmar, Nicholas Fung, David W. Eisele, Carole Fakhry
Article
Oncology
Melina J. Windon, Gypsyamber D'Souza, Farhoud Faraji, Tanya Troy, Wayne M. Koch, Christine G. Gourin, Ana P. Kiess, Karen T. Pitman, David W. Eisele, Carole Fakhry
Article
Otorhinolaryngology
Mejd Jumaily, Farhoud Faraji, Donald Zhang, Ronald J. Walker, Gregory M. Ward
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2019)
Article
Medicine, Research & Experimental
Farhoud Faraji, Nicholas Fung, Munfarid Zaidi, Christine C. Gourin, David W. Eisele, Lisa M. Rooper, Carole Fakhry
Article
Medicine, Research & Experimental
Farhoud Faraji, Nafi Aygun, Stephanie F. Coquia, Christine G. Gourin, Marietta Tan, Lisa M. Rooper, David W. Eisele, Carole Fakhry
Article
Oncology
Melina J. Windon, Carole Fakhry, Farhoud Faraji, Tanya Troy, Christine G. Gourin, Ana P. Kiess, Wayne Koch, David W. Eisele, Gypsyamber D'Souza
Article
Multidisciplinary Sciences
Kerrie L. Marie, Antonella Sassano, Howard H. Yang, Aleksandra M. Michalowski, Helen T. Michael, Theresa Guo, Yien Che Tsai, Allan M. Weissman, Maxwell P. Lee, Lisa M. Jenkins, M. Raza Zaidi, Eva Perez-Guijarro, Chi-Ping Day, Kris Ylaya, Stephen M. Hewitt, Nimit L. Patel, Heinz Arnheiter, Sean Davis, Paul S. Meltzer, Glenn Merlino, Pravin J. Mishra
NATURE COMMUNICATIONS
(2020)
Article
Otorhinolaryngology
Carol H. Yan, Farhoud Faraji, Divya P. Prajapati, Benjamin T. Ostrander, Adam S. DeConde
INTERNATIONAL FORUM OF ALLERGY & RHINOLOGY
(2020)
Letter
Otorhinolaryngology
Jacquelyn K. Devries, Farhoud Faraji, David Bracken, Philip A. Weissbrod
JAMA OTOLARYNGOLOGY-HEAD & NECK SURGERY
(2020)
Article
Otorhinolaryngology
Carol H. Yan, Farhoud Faraji, Divya P. Prajapati, Christine E. Boone, Adam S. DeConde
INTERNATIONAL FORUM OF ALLERGY & RHINOLOGY
(2020)
Article
Veterinary Sciences
H. T. Michael, T. Waterhouse, M. Estrada, M. A. Seguin
Summary: During the early stages of the 2020 SARS-CoV-2 pandemic, testing of respiratory pathogen samples from dogs and cats showed that the majority were infected with common veterinary pathogens, indicating rare occurrences of SARS-CoV-2 infections in these pets.
JOURNAL OF SMALL ANIMAL PRACTICE
(2021)
Article
Genetics & Heredity
Mai Xu, Lindsey Mehl, Tongwu Zhang, Rohit Thakur, Hayley Sowards, Timothy Myers, Lea Jessop, Alessandra Chesi, Matthew E. Johnson, Andrew D. Wells, Helen T. Michael, Patricia Bunda, Kristine Jones, Herbert Higson, Rebecca C. Hennessey, Ashley Jermusyk, Michael A. Kovacs, Maria Teresa Landi, Mark M. Iles, Alisa M. Goldstein, Jiyeon Choi, Stephen J. Chanock, Struan F. A. Grant, Raj Chari, Glenn Merlino, Matthew H. Law, Kevin M. Brown
Summary: A melanoma-associated locus on chromosome band 7p21.1 has been identified, with rs117132860 as the lead SNP and associated with tanning ability and cutaneous squamous cell carcinoma. Further studies revealed rs117132860 as a functional variant related to AHR gene, altering melanocyte growth phenotypes.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Veterinary Sciences
H. T. Michael, R. M. Mack, E. Hegarty, D. J. McCrann, G. F. Grauer
Summary: This study evaluates the behavior of creatinine and SDMA in cats and dogs, showing that after an increase in creatinine, the probability of persistently increased levels is approximately 58% for cats and 49% for dogs, compared to only 7% and 3% for those without an increase. For animals with persistently increased creatinine, the probability of increased SDMA concentration is around 70-75%, increasing to 94% for cats and 88% for dogs by 24 months.
VETERINARY JOURNAL
(2021)
Article
Veterinary Sciences
R. M. Mack, E. Hegarty, D. J. McCrann, H. T. Michael, G. F. Grauer
Summary: SDMA is a sensitive marker for assessing glomerular filtration rate, and mild increases in SDMA levels could potentially help identify cats and dogs with kidney disease earlier. Persistently elevated SDMA values are associated with a higher likelihood of increased creatinine levels in the future.
VETERINARY JOURNAL
(2021)
Article
Otorhinolaryngology
Farhoud Faraji, Jason H. Lee, Farshid Faraji, Bridget MacDonald, Parisa Oviedo, Emelia Stuart, Michael Baxter, Caresse L. Vuong, Samuel H. Lance, Amanda A. Gosman, Edward M. Castillo, David B. Hom
LARYNGOSCOPE INVESTIGATIVE OTOLARYNGOLOGY
(2020)