Article
Computer Science, Artificial Intelligence
Feras Al-Obeidat, Alvaro Rocha, Maryam Akram, Saad Razzaq, Fahad Maqbool
Summary: Cancer, a genetic disease with high mortality, can be detected early to reduce death rates. Oncogenomics utilizes RNA sequencing and gene expression profiling to identify cancer-related genes. The CDRGI approach, based on a Discrete Filtering technique, shows promise in identifying relevant genes and detecting cancer.
NEURAL COMPUTING & APPLICATIONS
(2022)
Article
Cell Biology
You Zhou, Bin Xu, Yi Zhou, Jian Liu, Xiao Zheng, Yingting Liu, Haifeng Deng, Ming Liu, Xiubao Ren, Jianchuan Xia, Xiangyin Kong, Tao Huang, Jingting Jiang
Summary: This study identified dozens of new genes with potential diagnostic and therapeutic value in LUAD through differential correlation analysis, providing new insights into the gene regulatory mechanisms during the transition from normal to tumor.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Clinical Neurology
Peter McColgan, Sarah Gregory, Paul Zeun, Angeliki Zarkali, Eileanoir B. Johnson, Christopher Parker, Kate Fayer, Jessica Lowe, Akshay Nair, Carlos Estevez-Fraga, Marina Papoutsi, Hui Zhang, Rachael Scahill, Sarah J. Tabrizi, Geraint Rees
Summary: McColgan et al. found that premanifest Huntington's disease gene carriers around 20 years from disease onset exhibit increased functional connectivity, which is correlated with elevated CSF neurofilament light. These changes occur in brain regions associated with gene expression specific to neuronal GABAergic and glutamatergic cells.
Article
Cell Biology
Tingna Chen, Qiuming He, Zhenxian Xiang, Rongzhang Dou, Bin Xiong
Summary: The study utilized WGCNA to identify three gene modules significantly correlated with gastric cancer and analyzed differentially correlated gene pairs within these modules using DiffCorr. GEMIN5 and PFDN2 were identified as key genes in the regulatory network, with their differential expression validated in cell lines and patient tissues.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Neurosciences
Qian Zhang, Jian Li, Ling Weng
Summary: This study aimed to identify and verify potential aging-related genes associated with Alzheimer's disease using bioinformatics analysis. Five ARDEGs (GFAP, PDGFRB, PLOD1, MAP4K4, and NFKBIA) were obtained, with biological functions related to aging, cellular senescence, and Ras protein signal transduction regulation. The diagnostic ability of these genes in discriminating AD from control samples demonstrated a favorable diagnostic value, with elevated mRNA expression levels in AD patients.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Cardiac & Cardiovascular Systems
Pengyuan Zhu, Haitao Huang, Tian Xie, Huoqi Liang, Xing Li, Xingyi Li, Hao Dong, Xiaoqiang Yu, Chunqiu Xia, Chongjun Zhong, Zhibing Ming
Summary: In this study, we identified 5 hub genes associated with the development of coronary artery disease (CAD) and successfully established a diagnostic model with a sensitivity of 92.59%.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Elena Yu. Bragina, Densema E. Gomboeva, Olga V. Saik, Vladimir A. Ivanisenko, Maxim B. Freidin, Maria S. Nazarenko, Valery P. Puzyrev
Summary: Cancer and neurodegenerative disorders pose significant challenges in healthcare worldwide. A study suggests that genes associated with apoptosis and Huntington's disease (HD) might also play a role in carcinogenesis, leading to a decrease in cancer rates among patients with neurodegenerative disorders. By reconstructing gene networks and analyzing genomic data, several high-priority candidate genes, including APOE, PSEN1, and IL6, were identified for further investigation of the molecular relationship between cancer and HD. Functional analysis and expression profiling of these genes were performed using publicly available datasets, revealing their potential roles in disease-specific tissues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Ke Mao, Meixian Zhang, Jinshuai Cao, Xiaoyuan Zhao, Liwang Gao, Liwan Fu, Hong Cheng, Chun Yan, Xiaopeng Xu, Xiaofeng Shi, Zhuoyuan Jiang, Bingqing Wang, Yong-Biao Zhang, Jie Mi
Summary: This study identified two coding variants significantly associated with pediatric adiposity, and demonstrated that they were expression quantitative trait loci for obesity-related genes. This provides new insights into the pathophysiology of Chinese childhood obesity.
Article
Neurosciences
Ai Guo, Bin Gao, Mengting Zhang, Xiaoyu Shi, Weina Jin, Decai Tian
Summary: Using microarray data from a murine model of ischemic stroke, we identified hub genes and pathways associated with massive cerebral infarction (MCI) and also identified potential therapeutic agents for MCI treatment.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
Ekta Shah, Pradipta Maji
Summary: Gene expression data sets and protein-protein interaction networks are important heterogeneous data sources that capture co-expression patterns and topological connections among genes. A new disease gene identification algorithm, called DiGId, is proposed based on multi-view kernel learning. The algorithm aims to learn a consensus kernel that captures heterogeneous information and the underlying cluster structure. The effectiveness of the approach is demonstrated through extensive analysis on cancer-related data sets and PPI networks.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Cell Biology
Eli J. Mueller, Brandon R. Munn, Michelle J. Redinbaugh, Joseph Lizier, Michael Breakspear, Yuri B. Saalmann, James M. Shine
Summary: The interaction between the cerebral cortex and the diffusely projecting matrix thalamic nuclei plays a key role in arousal and anesthesia. Using a whole-brain corticothalamic neural mass model based on empirical data, we investigate these processes. The model captures key features of propofol anesthesia, including diminished network integration, lowered state diversity, impaired susceptibility to perturbation, and decreased corticocortical coherence. Selectively stimulating the matrix thalamus reproduces empirical results in macaque and induces wake-like information processing states, demonstrating the role of matrix thalamocortical projections in shaping complex cortical dynamics to support conscious awareness.
Article
Endocrinology & Metabolism
Zhuo Gao, S. Aishwarya, Xiao-mei Li, Xin-lun Li, Li-na Sui
Summary: This study identified potential key genes and pathways involved in the progression of DKD through integrated bioinformatics analysis. Several differentially expressed genes with roles in DKD progression were identified, along with two drugs that have a validated role in reversing the observed differential gene expression patterns.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Oncology
Pushpinder Kaur, Tania B. Porras, Anthony Colombo, Alexander Ring, Janice Lu, Irene Kang, Julie E. Lang
Summary: The study found that over 30% of tumors carried potentially actionable events targetable by existing drugs, identified genes with multiple targetable alterations as candidates for combination therapy, and drivers in primary breast tumors fall into five categories. Analysis showed that copy number alterations and mutations in genes were significantly associated with gene expression, validating copy number events as a dominant oncogenic mechanism in breast cancer.
BRITISH JOURNAL OF CANCER
(2021)
Article
Biochemical Research Methods
Mahdieh Ghasemi, Maseud Rahgozar, Kaveh Kavousi
Summary: This article proposes a new heterogeneous biological network embedding approach, NetEM, to identify disease-associated genes. The experiments and case studies using real data demonstrate the superior performance of NetEM in identifying disease genes compared to three other algorithms.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Critical Care Medicine
Xiting Yan, Jen-Hwa Chu, Jose Gomez, Maria Koenigs, Carole Holm, Xiaoxuan He, Mario F. Perez, Hongyu Zhao, Shrikant Mane, Fernando D. Martinez, Carole Ober, Dan L. Nicolae, Kathleen C. Barnes, Stephanie J. London, Frank Gilliland, Scott T. Weiss, Benjamin A. Raby, Lauren Cohn, Geoffrey L. Chupp
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2015)
Article
Biotechnology & Applied Microbiology
Justin L. Chen, Kelly L. Walton, Sara L. Al-Musawi, Emily K. Kelly, Hongwei Qian, Mylinh La, Louis Lu, George Lovrecz, Mark Ziemann, Ross Lazarus, Assam El-Osta, Paul Gregorevic, Craig A. Harrison
Article
Anesthesiology
Tyler J. Wellman, Nicolas de Prost, Mauro Tucci, Tilo Winkler, Rebecca M. Baron, Piotr Filipczak, Benjamin Raby, Jen-hwa Chu, R. Scott Harris, Guido Musch, Luiz F. dos Reis Falcao, Vera Capelozzi, Jose G. Venegas, Marcos F. Vidal Melo
Article
Environmental Sciences
Jen-hwa Chu, Jaime E. Hart, Divya Chhabra, Eric Garshick, Benjamin A. Raby, Francine Laden
ENVIRONMENTAL HEALTH
(2016)
Article
Respiratory System
Argyris Tzouvelekis, Jose D. Herazo-Maya, Martin Slade, Jen-Hwa Chu, Giuseppe Deiuliis, Changwan Ryu, Qin Li, Koji Sakamoto, Gabriel Ibarra, Hongyi Pan, Mridu Gulati, Danielle Antin-Ozerkis, Erica L. Herzog, Naftali Kaminski
Article
Genetics & Heredity
Supinda Bunyavanich, Eric E. Schadt, Blanca E. Himes, Jessica Lasky-Su, Weiliang Qiu, Ross Lazarus, John P. Ziniti, Ariella Cohain, Michael Linderman, Dara G. Torgerson, Celeste S. Eng, Maria Pino-Yanes, Badri Padhukasahasram, James J. Yang, Rasika A. Mathias, Terri H. Beaty, Xingnan Li, Penelope Graves, Isabelle Romieu, Blanca del Rio Navarro, M. Towhid Salam, Hita Vora, Dan L. Nicolae, Carole Ober, Fernando D. Martinez, Eugene R. Bleecker, Deborah A. Meyers, W. James Gauderman, Frank Gilliland, Esteban G. Burchard, Kathleen C. Barnes, L. Keoki Williams, Stephanie J. London, Bin Zhang, Benjamin A. Raby, Scott T. Weiss
BMC MEDICAL GENOMICS
(2014)
Article
Mathematical & Computational Biology
Jen-hwa Chu, Craig P. Hersh, Peter J. Castaldi, Michael H. Cho, Benjamin A. Raby, Nan Laird, Russell Bowler, Stephen Rennard, Joseph Loscalzo, John Quackenbush, Edwin K. Silverman
BMC SYSTEMS BIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Antony Kaspi, Mark Ziemann, Samuel T. Keating, Ishant Khurana, Timothy Connor, Briana Spolding, Adrian Cooper, Ross Lazarus, Ken Walder, Paul Zimmet, Assam El-Osta
Article
Physiology
Oliver Neubauer, Surendran Sabapathy, Kevin J. Ashton, Ben Desbrow, Jonathan M. Peake, Ross Lazarus, Barbara Wessner, David Cameron-Smith, Karl-Heinz Wagner, Luke J. Haseler, Andrew C. Bulmer
JOURNAL OF APPLIED PHYSIOLOGY
(2014)
Article
Nutrition & Dietetics
Celine Latouche, Sarah E. Heywood, Sarah L. Henry, Mark Ziemann, Ross Lazarus, Assam El-Osta, James A. Armitage, Bronwyn A. Kingwell
JOURNAL OF NUTRITION
(2014)
Article
Genetics & Heredity
Q. L. Duan, J. Lasky-Su, B. E. Himes, W. Qiu, A. A. Litonjua, A. Damask, R. Lazarus, B. Klanderman, C. G. Irvin, S. P. Peters, J. P. Hanrahan, J. J. Lima, F. D. Martinez, D. Mauger, V. M. Chinchilli, M. Soto-Quiros, L. Avila, J. C. Celedon, C. Lange, S. T. Weiss, K. G. Tantisira
PHARMACOGENOMICS JOURNAL
(2014)
Article
Public, Environmental & Occupational Health
W. Katherine Yih, Noelle M. Cocoros, Molly Crockett, Michael Klompas, Benjamin A. Kruskal, Martin Kulldorff, Ross Lazarus, Lawrence C. Madoff, Monica J. Morrison, Sandra Smole, Richard Platt
PUBLIC HEALTH REPORTS
(2014)
Article
Multidisciplinary Sciences
Jeffrey A. Haspel, Sukrutha Chettimada, Rahamthulla S. Shaik, Jen-Hwa Chu, Benjamin A. Raby, Manuela Cernadas, Vincent Carey, Vanessa Process, G. Matthew Hunninghake, Emeka Ifedigbo, James A. Lederer, Joshua Englert, Ashley Pelton, Anna Coronata, Laura E. Fredenburgh, Augustine M. K. Choi
NATURE COMMUNICATIONS
(2014)
Article
Biotechnology & Applied Microbiology
Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, Galaxy Team, James Taylor, Anton Nekrutenko
Article
Respiratory System
Jen-hwa Chu, Wenlan Zang, Milica Vukmirovic, Xiting Yan, Taylor Adams, Giuseppe DeIuliis, Buqu Hu, Antun Mihaljinec, Jonas C. Schupp, Michael J. Becich, Harry Hochheiser, Kevin F. Gibson, Edward S. Chen, Alison Morris, Joseph K. Leader, Stephen R. Wisniewski, Yingze Zhang, Frank C. Sciurba, Ronald G. Collman, Robert Sandhaus, Erica L. Herzog, Karen C. Patterson, Maor Sauler, Charlie Strange, Naftali Kaminski
Summary: This study investigated gene expression profiles of BAL and PBMC in AATD individuals and identified a gene module, ME31, that correlated with clinical variables and clustered AATD individuals based on disease severity. The findings suggest the presence of previously unrecognized disease endotypes in AATD associated with T-lymphocyte immunity.