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A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies [chapter]

Naftali Kaminski, Ziv Bar-Joseph
2006 Lecture Notes in Computer Science  
Our model represents patient expression data using two levels, a gene level which corresponds to a common response pattern and a patient level which accounts for the patient specific expression patterns  ...  Pharmacogenomics and clinical studies that measure the temporal expression levels of patients can identify important pathways and biomarkers that are activated during disease progression or in response  ...  Using a hierarchical generative model, we were able to provide a probabilistic algorithm that can solve the above problems. Our algorithm generates a consensus expression curve for each gene.  ... 
doi:10.1007/11732990_6 fatcat:neyllkjr5jbvbdbntkxtia4ezq

A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies

Naftali Kaminski, Ziv Bar-Joseph
2007 Journal of Computational Biology  
Our model represents patient expression data using two levels, a gene level which corresponds to a common response pattern and a patient level which accounts for the patient specific expression patterns  ...  Pharmacogenomics and clinical studies that measure the temporal expression levels of patients can identify important pathways and biomarkers that are activated during disease progression or in response  ...  Using a hierarchical generative model, we were able to provide a probabilistic algorithm that can solve the above problems. Our algorithm generates a consensus expression curve for each gene.  ... 
doi:10.1089/cmb.2007.0001 pmid:17563314 fatcat:422t2cjxfzfr5ic2tlaapt3xoi

Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent Giant Cell Arteritis [article]

Elisabeth De Smit, Samuel W Lukowski, Lisa Anderson, Anne Senabouth, Kaisar Dauyey, Sharon Song, Bruce Wyse, Lawrie Wheeler, Christine Y Chen, Khoa Cao, Amy Wong Ten Yuen, Neil Shuey (+8 others)
2018 biorxiv/medrxiv   pre-print
Over the 12-month study period, polynomial modelling analyses identified 179 and 4 statistically significant transcripts with altered expression profiles (FDR < 0.05) between cases and controls in CD4+  ...  RNA was extracted from all 195 collected samples for subsequent RNA sequencing. The expression profiles of patients were compared to those of 16 age-matched controls.  ...  For quantitative clinical variables we used a linear model, and for categorical variables we used a logistic regression model.  ... 
doi:10.1101/243493 fatcat:5kgnvbjozvghlainwyyblxmtzq

Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis

Elisabeth De Smit, Samuel W. Lukowski, Lisa Anderson, Anne Senabouth, Kaisar Dauyey, Sharon Song, Bruce Wyse, Lawrie Wheeler, Christine Y. Chen, Khoa Cao, Amy Wong Ten Yuen, Neil Shuey (+8 others)
2018 BMC Medical Genomics  
RNA was extracted from all 195 collected samples for subsequent RNA sequencing. The expression profiles of patients were compared to those of 16 age-matched controls.  ...  Results: Over the 12-month study period, polynomial modelling analyses identified 179 and 4 statistically significant transcripts with altered expression profiles (FDR < 0.05) between cases and controls  ...  For quantitative clinical variables we used a linear model, and for categorical variables we used a logistic regression model.  ... 
doi:10.1186/s12920-018-0376-4 pmid:30037347 pmcid:PMC6057030 fatcat:ms235q2norgcjk4vapq2wigcsq

EndoTime: Non-categorical timing estimates for luteal endometrium [article]

Julia Lipecki, Andrew Mitchell, Joanne Muter, Emma Lucas, Komal Makwana, Katherine Fishwick, Joshua Odendaal, Amelia Hawkes, Pavle Vrljicak, Jan J Brosens, Sascha Ott
2021 biorxiv/medrxiv   pre-print
EndoTime enables accurate temporal profiling of any gene in luteal endometrial samples for a wide range of research applications and, potentially, clinical use.  ...  STUDY DESIGN, SIZE, DURATION Gene expression was measured by RT-qPCR in 260 endometrial biopsies obtained 4 to 12 days after a self-reported positive home ovulation test.  ...  Acknowledgements We are grateful to all the women who participated in this research.  ... 
doi:10.1101/2021.08.02.21261452 fatcat:62vy4qlznng4foq57ppqu5xw3e

Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study

Jose D Herazo-Maya, Jiehuan Sun, Philip L Molyneaux, Qin Li, Julian A Villalba, Argyrios Tzouvelekis, Heather Lynn, Brenda M Juan-Guardela, Cristobal Risquez, Juan C Osorio, Xiting Yan, George Michel (+16 others)
2017 The Lancet Respiratory Medicine  
Interpretation: Our results validate the use of a peripheral blood 52-gene expression signature for outcome prediction in IPF  ...  Mortality and transplant-free survival were studied using Competing risk and Cox proportional-hazard models, respectively. Gene expression trends were analyzed using linear mixed-effect models.  ...  a blood test using the 52-gene signature should be further developed and studied in clinical practice for risk stratification and disease monitoring in IPF.  ... 
doi:10.1016/s2213-2600(17)30349-1 pmid:28942086 pmcid:PMC5677538 fatcat:ot2duhwfvndclpx52wxm4xazlu

Analysis of factorial time-course microarrays with application to a clinical study of burn injury

B. Zhou, W. Xu, D. Herndon, R. Tompkins, R. Davis, W. Xiao, W. H. Wong, M. Toner, H. S. Warren, D. A. Schoenfeld, L. Rahme, G. P. McDonald-Smith (+50 others)
2010 Proceedings of the National Academy of Sciences of the United States of America  
For example, in the clinical study that motivated this work, gene expression of blood samples from patients was measured at different times after burn injury.  ...  The method was used to analyze the impact of age on the temporal gene response to burn injury in a large-scale clinical study.  ...  In particular, we wish to acknowledge the efforts of many individuals at participating institutions of the Glue Grant Program that generated the clinical and genomic data reported here.  ... 
doi:10.1073/pnas.1002757107 pmid:20479259 pmcid:PMC2890487 fatcat:l733miz3gfew3dbfunu4p6kk7i

Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients

Christoph Thiel, Henrik Cordes, Isabel Conde, José Vicente Castell, Lars Mathias Blank, Lars Kuepfer
2016 Archives of Toxicology  
Simulated pharmacokinetic profiles were therefore related to in vivo drug response predicted for genes associated with observed clinical symptoms and to clinical biomarkers measured in vivo.  ...  acute liver failure after multiple dosing of azathioprine was investigated in a patient case study by use of own clinical data.  ...  We thank Jos Kleinjans for helpful discussions.  ... 
doi:10.1007/s00204-016-1723-x pmid:27161439 pmcid:PMC5306109 fatcat:7ogfgyywvje67dmcjuup2jegjm

Predictive data mining in clinical medicine: a focus on selected methods and applications

Riccardo Bellazzi, Fulvia Ferrazzi, Lucia Sacchi
2011 Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery  
Predictive data mining in clinical medicine deals with learning models to predict patients' health. The models can be devoted to support clinicians in diagnostic, therapeutic, or monitoring tasks.  ...  The current challenge is to exploit data mining to build models able to take into account the dynamic and temporal nature of clinical care and to exploit the variety of information available at the bedside  ...  Gene expression microarrays are a wellestablished high-throughput technique for the expression profiling of tissue/cell samples. 85 One of the earliest areas in which the potential of expression arrays  ... 
doi:10.1002/widm.23 fatcat:n6juaunarbcclkfur3ojwb6zpq

Stromal and epithelial networks: Temporal gene expression profiling during invasive neoplasia

Arianne M. Wilson, Jacqueline Banyard
2009 Cell Adhesion & Migration  
A recent study from the Khavari group profiled the expression changes during progression to invasion in a Ras-inducible model of human epithelial neoplasia and used network modeling to analyze the molecular  ...  A subset of these altered genes was compiled into a "core tumor progression signature" (CTPS), which was shown to have clinical relevance in several cancer types.  ...  neoplastic malignancy in a regenerated human skin model. 5 Using these gene expression profiles they developed a "core tumor progression signature" (CTPS).  ... 
doi:10.4161/cam.3.4.9912 pmid:19829083 pmcid:PMC2802737 fatcat:anl7met7krad5mpjmkojz6xxyq

Using systems biology to simplify complex disease: Immune cartography

Ashoka D. Polpitiya, Jonathan E. McDunn, Anton Burykin, Bijoy K. Ghosh, J Perren Cobb
2009 Critical Care Medicine  
expression, and 4) a similar strategy can be used in the critically ill to follow septic patients and quantitatively determine immune recovery.  ...  We review herein a validated, systems biology approach demonstrating that 1) abdominal and pulmonary sepsis diagnoses can be made in mouse models using microarray (RNA) data from circulating blood, 2)  ...  ACKNOWLEDGMENTS We thank our colleagues in the Washington University Center for Critical Illness and Health Engineering and the National Institute of General Medical Sciences Inflammation and Host Response  ... 
doi:10.1097/ccm.0b013e3181920cb0 pmid:19104218 pmcid:PMC4077162 fatcat:u4pyxsq7vzd77le3kcldqzvk54

Utility of Gene Expression Profiling Score Variability to Predict Clinical Events in Heart Transplant Recipients

Mario C. Deng, Barbara Elashoff, Michael X. Pham, Jeffrey J. Teuteberg, Abdallah G. Kfoury, Randall C. Starling, Thomas P. Cappola, Andrew Kao, Allen S. Anderson, William G. Cotts, Gregory A. Ewald, David A. Baran (+5 others)
2014 Transplantation  
Patients from the IMAGE study with rejection surveillance gene expression profiling tests performed at 1- to 6-month intervals were selected for this cohort study.  ...  Gene expression profiling ordinal score (range, 0-39), threshold score (binary value=1 if ordinal score ≥ 34), and score variability were studied in multivariate Cox regression models to predict future  ...  Based on the multivariate model, patient A with this low variability of gene expression profiling scores had a relatively low probability (2.6 %) of a clinical event in the future 12 months from visit  ... 
doi:10.1097/01.tp.0000443897.29951.cf pmid:24637869 pmcid:PMC3983476 fatcat:cjuz5ogbtjcjblgrrh3kjgy72y

Identifying targets for preventing epilepsy using systems biology

Jeffrey A. Loeb
2011 Neuroscience Letters  
Identification and testing of potential antiepileptic drug targets first in animal models and then in humans is thus becoming an important next step in the battle against epilepsy.  ...  While deductive approaches to drug target identification use our current state of knowledge, based mostly on animal models of epileptogenesis, a growing reductionist approach often referred to as systems  ...  For example, to make biological sense of a given gene expression change in a patient with epilepsy, it is important to know where the brain tissue came from (such as frontal or temporal cortex) which cell  ... 
doi:10.1016/j.neulet.2011.02.041 pmid:21382442 pmcid:PMC3109107 fatcat:4ed36mqi25ajvbhe2747o6irem

Detectable Changes in The Blood Transcriptome Are Present after Two Weeks of Antituberculosis Therapy

Chloe I. Bloom, Christine M. Graham, Matthew P. R. Berry, Katalin A. Wilkinson, Tolu Oni, Fotini Rozakeas, Zhaohui Xu, Jose Rossello-Urgell, Damien Chaussabel, Jacques Banchereau, Virginia Pascual, Marc Lipman (+3 others)
2012 PLoS ONE  
Objectives: To determine if blood transcriptional signatures change in response to antituberculosis treatment and could act as early biomarkers of a successful response.  ...  We thank Raylene Titus (University of Cape Town, South Africa), Yekiwe Hlombe, Relebohile Tsekela, Bekekile Kwaza and Rene Goliath for patient recruitment and retention in South Africa.  ...  Acknowledgments We thank the patients and volunteer participants.  ... 
doi:10.1371/journal.pone.0046191 pmid:23056259 pmcid:PMC3462772 fatcat:2l6xijsl7ndxfdixnvxcoayzke

Drug repositioning in epilepsy reveals novel antiseizure candidates

Leo Brueggeman, Morgan L. Sturgeon, Russell M. Martin, Andrew J. Grossbach, Yasunori Nagahama, Angela Zhang, Mathew A. Howard, Hiroto Kawasaki, Shu Wu, Robert A. Cornell, Jacob J. Michaelson, Alexander G. Bassuk
2018 Annals of Clinical and Translational Neurology  
We tested a low-cost, drug-repositioning strategy to identify candidate epilepsy drugs that are already FDA-approved and might be immediately tested in epilepsy patients who require new therapies.  ...  Epilepsy treatment falls short in ~30% of cases. A better understanding of epilepsy pathophysiology can guide rational drug development in this difficult to treat condition.  ...  Conflict of Interest The authors all have a patent pending related to the use of the drugs described in this manuscript for epilepsy.  ... 
doi:10.1002/acn3.703 pmid:30847362 pmcid:PMC6389756 fatcat:z3lkue3uv5dypflqxiakzugkgi
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