Search Results - "Raja, Kalpana"

Machine learning workflow to enhance predictions of Adverse Drug Reactions (ADRs) through drug-gene interactions: application to drugs for cutaneous diseases by Raja, Kalpana, Patrick, Matthew, Elder, James T., Tsoi, Lam C.

“…Adverse drug reactions (ADRs) pose critical public health issues, affecting over 6% of hospitalized patients. While knowledge of potential drug-drug…”
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Drug Repurposing Prediction for Immune-Mediated Cutaneous Diseases using a Word-Embedding–Based Machine Learning Approach by Patrick, Matthew T., Raja, Kalpana, Miller, Keylonnie, Sotzen, Jason, Gudjonsson, Johann E., Elder, James T., Tsoi, Lam C.

“…Immune-mediated diseases affect more than 20% of the population, and many autoimmune diseases affect the skin. Drug repurposing (or repositioning) is a…”
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Integrated Approaches to Identify miRNA Biomarkers Associated with Cognitive Dysfunction in Multiple Sclerosis Using Text Mining, Gene Expression, Pathways, and GWAS by Prabahar, Archana, Raja, Kalpana

“…Multiple sclerosis (MS), a chronic autoimmune disorder, affects the central nervous system of many young adults. More than half of MS patients develop…”
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Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models by Millikin, Robert J, Raja, Kalpana, Steill, John, Lock, Cannon, Tu, Xuancheng, Ross, Ian, Tsoi, Lam C, Kuusisto, Finn, Ni, Zijian, Livny, Miron, Bockelman, Brian, Thomson, James, Stewart, Ron

“…The PubMed archive contains more than 34 million articles; consequently, it is becoming increasingly difficult for a biomedical researcher to keep up-to-date…”
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Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors challenge by Cormack, James, Nath, Chinmoy, Milward, David, Raja, Kalpana, Jonnalagadda, Siddhartha R.

“…[Display omitted] •We used a data-driven methodology for rule-based information extraction.•This was applied to the i2b2 cardiac risk factors challenge.•It…”
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ProNormz – An integrated approach for human proteins and protein kinases normalization by Subramani, Suresh, Raja, Kalpana, Natarajan, Jeyakumar

“…[Display omitted] •We present ‘ProNormz’ as a freely available web-based tool for human protein normalization.•Besides normalization ProNormz distinguishes…”
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Large Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression by Bhasuran, Balu, Manoharan, Sharanya, Iyyappan, Oviya Ramalakshmi, Murugesan, Gurusamy, Prabahar, Archana, Raja, Kalpana

“…microRNA (miRNA)-messenger RNA (mRNA or gene) interactions are pivotal in various biological processes, including the regulation of gene expression, cellular…”
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A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes by Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie A, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam M, Swanson, Scott A, Jiang, Peng, Clegg, Dennis O, Jarvis, Erich D, Thomson, James A, Stewart, Ron, Chaisson, Mark J. P, Bukhman, Yury V

“…Abstract Background The Nile rat ( Avicanthis niloticus ) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a…”
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A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries by Yang, Yuyang, Madu, Desmond, Gao, Yilin, Patrick, Matthew, Raja, Kalpana, Tsoi, Lam C.

“…In the past decade, the volume of “omics” data generated by the different high-throughput technologies has expanded exponentially. The managing, storing, and…”
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Integrative Approach to Reveal Cell Type Specificity and Gene Candidates for Psoriatic Arthritis Outside the MHC by Patrick, Matthew T, Stuart, Philip E, Raja, Kalpana, Chi, Sunyi, He, Zhi, Voorhees, John J, Tejasvi, Trilokraj, Gudjonsson, Johann E, Kahlenberg, J Michelle, Chandran, Vinod, Rahman, Proton, Gladman, Dafna D, Nair, Rajan P, Elder, James T, Tsoi, Lam C

“…We recently conducted a large association analysis to compare the genetic profiles between patients with psoriatic arthritis (PsA) and cutaneous-only psoriasis…”
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Ultrasonographic delineation of a foreign body in the calf by Gnanavel, Shanmugapriya, Krishnan, Nagarajan, Raja, Kalpana, Subbiah, Srinivasan

“…With magnetic resonance imaging (MRI), wooden foreign bodies show variable signal intensity that was equal to or less than that of skeletal muscle on both T1-…”
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Mining protein phosphorylation information from biomedical literature using NLP parsing and Support Vector Machines by Raja, Kalpana, Natarajan, Jeyakumar

“…•Protein phosphorylation information plays an essential role in numerous biological processes including cellular functions and signal transduction.•A text…”
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Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach by Hu, Yan, Keloth, Vipina K, Raja, Kalpana, Chen, Yong, Xu, Hua

“…Abstract Motivation Automated extraction of population, intervention, comparison/control, and outcome (PICO) from the randomized controlled trial (RCT)…”
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Atopic Dermatitis Is an IL-13–Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis by Tsoi, Lam C., Rodriguez, Elke, Degenhardt, Frauke, Baurecht, Hansjörg, Wehkamp, Ulrike, Volks, Natalie, Szymczak, Silke, Swindell, William R., Sarkar, Mrinal K., Raja, Kalpana, Shao, Shuai, Patrick, Matthew, Gao, Yilin, Uppala, Ranjitha, Perez White, Bethany E, Getsios, Spiro, Harms, Paul W., Maverakis, Emanual, Elder, James T., Franke, Andre, Gudjonsson, Johann E., Weidinger, Stephan

“…Atopic dermatitis (AD) affects up to 20% of children and adults worldwide. To gain a deeper understanding of the pathophysiology of AD, we conducted a…”
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PPInterFinder--a mining tool for extracting causal relations on human proteins from literature by Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar

“…One of the most common and challenging problem in biomedical text mining is to mine protein-protein interactions (PPIs) from MEDLINE abstracts and full-text…”
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Caenorhabditis elegans as a possible model to screen anti-Alzheimer's therapeutics by Paul, Deepraj, Chipurupalli, Sandhya, Justin, Antony, Raja, Kalpana, Mohankumar, Suresh K.

“…Alzheimer's disease (AD) is regarded as one of the significant health burdens, as the prevalence is raising worldwide and gradually reaching to epidemic…”
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Advancement in predicting interactions between drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources by Patrick, Matthew T, Bardhi, Redina, Raja, Kalpana, He, Kevin, Tsoi, Lam C

“…Abstract Objective Drug–drug interactions (DDIs) can result in adverse and potentially life-threatening health consequences; however, it is challenging to…”
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Advancing entity recognition in biomedicine via instruction tuning of large language models by Keloth, Vipina K, Hu, Yan, Xie, Qianqian, Peng, Xueqing, Wang, Yan, Zheng, Andrew, Selek, Melih, Raja, Kalpana, Wei, Chih Hsuan, Jin, Qiao, Lu, Zhiyong, Chen, Qingyu, Xu, Hua

“…Large Language Models (LLMs) have the potential to revolutionize the field of Natural Language Processing, excelling not only in text generation and reasoning…”
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Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol by Raja, Kalpana, Natarajan, Jeyakumar, Kuusisto, Finn, Steill, John, Ross, Ian, Thomson, James, Stewart, Ron

“…Proteins perform their functions by interacting with other proteins. Protein-protein interaction (PPI) is critical for understanding the functions of…”
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Comorbidity-Guided Text Mining and Omics Pipeline to Identify Candidate Genes and Drugs for Alzheimer's Disease by Oviya, Iyappan Ramalakshmi, Sankar, Divya, Manoharan, Sharanya, Prabahar, Archana, Raja, Kalpana

“…Alzheimer's disease (AD), a multifactorial neurodegenerative disorder, is prevalent among the elderly population. It is a complex trait with mutations in…”
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