383 results on '"Huang, Katherine"'
Search Results
2. Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets
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Cao, Siyan, Nguyen, Khai, Ma, Kaiming, Du, Xiaotang, Liu, Xiuli, Ulezko Antonova, Alina, Rood, Richard P., Gremida, Anas, Chen, Chien-Huan, Gutierrez, Alexandra, Rubin, Deborah C., Gregory, Martin H., Gergely, Mate, Oliva Escudero, Guadalupe, Huang, Katherine, Jaeger, Natalia, Cella, Marina, Newberry, Rodney D., Davidson, Nicholas O., Ciorba, Matthew A., Deepak, Parakkal, and Colonna, Marco
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- 2024
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3. Evaluating the Change in 18F-Fluorodeoxyglucose Uptake in Perianal Fistulas on PET/CT over Time: A Serial Retrospective Analysis
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Garuba, Favour, Ganapathy, Aravinda, Huang, Katherine, Bishop, Grace, Zhang, Hanjing, Lovato, Addie, Itani, Malak, Viswanath, Satish E., Fraum, Tyler J., Deepak, Parakkal, and Ballard, David H.
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- 2024
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4. Effect of Immunosuppression on the Immunogenicity of mRNA Vaccines to SARS-CoV-2
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Deepak, Parakkal, Kim, Wooseob, Paley, Michael A, Yang, Monica, Carvidi, Alexander B, Demissie, Emanuel G, El-Qunni, Alia A, Haile, Alem, Huang, Katherine, Kinnett, Baylee, Liebeskind, Mariel J, Liu, Zhuoming, McMorrow, Lily E, Paez, Diana, Pawar, Niti, Perantie, Dana C, Schriefer, Rebecca E, Sides, Shannon E, Thapa, Mahima, Gergely, Maté, Abushamma, Suha, Akuse, Sewuese, Klebert, Michael, Mitchell, Lynne, Nix, Darren, Graf, Jonathan, Taylor, Kimberly E, Chahin, Salim, Ciorba, Matthew A, Katz, Patricia, Matloubian, Mehrdad, O'Halloran, Jane A, Presti, Rachel M, Wu, Gregory F, Whelan, Sean PJ, Buchser, William J, Gensler, Lianne S, Nakamura, Mary C, Ellebedy, Ali H, and Kim, Alfred HJ
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Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Research ,Prevention ,Rare Diseases ,Emerging Infectious Diseases ,Immunization ,Vaccine Related ,3.4 Vaccines ,Prevention of disease and conditions ,and promotion of well-being ,Good Health and Well Being ,Public Health and Health Services - Abstract
BackgroundPatients with chronic inflammatory disease (CID) treated with immunosuppressive medications have increased risk for severe COVID-19. Although mRNA-based SARS-CoV-2 vaccination provides protection in immunocompetent persons, immunogenicity in immunosuppressed patients with CID is unclear.ObjectiveTo determine the immunogenicity of mRNA-based SARS-CoV-2 vaccines in patients with CID.DesignProspective observational cohort study.SettingTwo U.S. CID referral centers.ParticipantsVolunteer sample of adults with confirmed CID eligible for early COVID-19 vaccination, including hospital employees of any age and patients older than 65 years. Immunocompetent participants were recruited separately from hospital employees. All participants received 2 doses of mRNA vaccine against SARS-CoV-2 between 10 December 2020 and 20 March 2021. Participants were assessed within 2 weeks before vaccination and 20 days after final vaccination.MeasurementsAnti-SARS-CoV-2 spike (S) IgG+ binding in all participants, and neutralizing antibody titers and circulating S-specific plasmablasts in a subset to assess humoral response after vaccination.ResultsMost of the 133 participants with CID (88.7%) and all 53 immunocompetent participants developed antibodies in response to mRNA-based SARS-CoV-2 vaccination, although some with CID developed numerically lower titers of anti-S IgG. Anti-S IgG antibody titers after vaccination were lower in participants with CID receiving glucocorticoids (n = 17) than in those not receiving them; the geometric mean of anti-S IgG antibodies was 357 (95% CI, 96 to 1324) for participants receiving prednisone versus 2190 (CI, 1598 to 3002) for those not receiving it. Anti-S IgG antibody titers were also lower in those receiving B-cell depletion therapy (BCDT) (n = 10). Measures of immunogenicity differed numerically between those who were and those who were not receiving antimetabolites (n = 48), tumor necrosis factor inhibitors (n = 39), and Janus kinase inhibitors (n = 11); however, 95% CIs were wide and overlapped. Neutralization titers seemed generally consistent with anti-S IgG results. Results were not adjusted for differences in baseline clinical factors, including other immunosuppressant therapies.LimitationsSmall sample that lacked demographic diversity, and residual confounding.ConclusionCompared with nonusers, patients with CID treated with glucocorticoids and BCDT seem to have lower SARS-CoV-2 vaccine-induced antibody responses. These preliminary findings require confirmation in a larger study.Primary funding sourceThe Leona M. and Harry B. Helmsley Charitable Trust, Marcus Program in Precision Medicine Innovation, National Center for Advancing Translational Sciences, and National Institute of Arthritis and Musculoskeletal and Skin Diseases.
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- 2021
5. Bugs and Brains, the Gut and Mental Health Study: a mixed-methods study investigating microbiota composition and function in anxiety, depression and irritable bowel syndrome.
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Simpson, Carra A, Schwartz, Orli S, Eliby, Djamila, Butler, Catherine A, Huang, Katherine, O'Brien-Simpson, Neil, Callaghan, Bridget L, Dashper, Stuart G, Gooley, Paul R, Whittle, Sarah, Haslam, Nick, and Simmons, Julian G
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Humans ,Irritable Bowel Syndrome ,RNA ,Ribosomal ,16S ,Depression ,Anxiety ,Mental Health ,Anxiety Disorders ,Adolescent ,Adult ,Female ,Young Adult ,Microbiota ,Gastrointestinal Microbiome ,anxiety disorders ,depression & mood disorders ,functional bowel disorders ,microbiology ,psychiatry ,depression & ,mood disorders ,Prevention ,Brain Disorders ,Digestive Diseases ,Behavioral and Social Science ,Nutrition ,Pain Research ,Clinical Research ,Chronic Pain ,2.3 Psychological ,social and economic factors ,Oral and gastrointestinal ,Mental health ,Clinical Sciences ,Public Health and Health Services ,Other Medical and Health Sciences - Abstract
IntroductionResearch has highlighted relationships between the micro-organisms that inhabit our gastrointestinal tract (oral and gut microbiota) with host mood and gastrointestinal functioning. Mental health disorders and functional gastrointestinal disorders co-occur at high rates, although the mechanisms underlying these associations remain unclear. The Bugs and Brains Study aims to investigate complex relationships between anxiety/depression and irritable bowel syndrome (IBS) in two ways. First, its primary component will compare the gut and oral microbiota in females with anxiety/depression and/or IBS relative to controls, and investigate underlying physiological, endocrine and immune factors, as well as associations with diet and psychosocial factors. In an ancillary component, the study will also investigate gastrointestinal and mental health symptoms in a larger sample, and explore relationships with diet, exercise, oral health, substance use, medical history, early life adversity and psychosocial factors.Methods and analysisThe Bugs and Brains Study aims to recruit 160 females to the primary component: (1) 40 controls; (2) 40 participants with a depressive/anxiety disorder, but no IBS; (3) 40 participants with IBS, but no depressive/anxiety disorder and (4) 40 participants with both depressive/anxiety disorder and IBS. Participation is completed within 1 month, and involves comprehensive questionnaires, anthropometrics, a diagnostic clinical interview, collection of two saliva samples, and stool, urine and hair samples. This study aims to use a systems biology approach to characterise oral and gut microbial composition and function using 16S rRNA gene sequencing and nuclear MR spectroscopy. As part of the ancillary component, it will collect questionnaire data from 1000 participants aged 18-40 years, capturing mental health, gastrointestinal health, oral health, diet and psychosocial factors.Ethics and disseminationApproval was granted by the University of Melbourne Human Research Ethics Committee (#1749221). All participants voluntarily provided informed consent. Results will be published in peer-reviewed journals and presented at scientific conferences.
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- 2021
6. Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
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Misek, Sean A., Fultineer, Aaron, Kalfon, Jeremie, Noorbakhsh, Javad, Boyle, Isabella, Roy, Priyanka, Dempster, Joshua, Petronio, Lia, Huang, Katherine, Saadat, Alham, Green, Thomas, Brown, Adam, Doench, John G., Root, David E., McFarland, James M., Beroukhim, Rameen, and Boehm, Jesse S.
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- 2024
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7. Canada’s Geothermal Energy Update in 2023
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Huang, Katherine, primary, Dehghani-Sanij, Alireza, additional, Hickson, Catherine, additional, Grasby, Stephen E., additional, Smejkal, Emily, additional, Miranda, Mafalda M., additional, Raymond, Jasmin, additional, Fraser, Derek, additional, Harbottle, Kass, additional, Torres, Daniel Alonso, additional, Ebell, John, additional, Dixon, Julie, additional, Olsen, Emily, additional, Vany, Jeanine, additional, Marcia, Kirsten, additional, Colpron, Maurice, additional, Wigston, Andrew, additional, Brasnett, Gordon, additional, Unsworth, Martyn, additional, and Harms, Phil, additional
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- 2024
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8. Copy number variations and young duplicate genes have high methylation levels in sticklebacks
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Huang, Katherine M. and Chain, Frédéric J. J.
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- 2021
9. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
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Yang, Fan, Wang, Jiebiao, Consortium, The GTEx, Pierce, Brandon L, Chen, Lin S, Aguet, François, Ardlie, Kristin G, Cummings, Beryl B, Gelfand, Ellen T, Getz, Gad, Hadley, Kane, Handsaker, Robert E, Huang, Katherine H, Kashin, Seva, Karczewski, Konrad J, Lek, Monkol, Li, Xiao, MacArthur, Daniel G, Nedzel, Jared L, Nguyen, Duyen T, Noble, Michael S, Segrè, Ayellet V, Trowbridge, Casandra A, Tukiainen, Taru, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Engelhardt, Barbara E, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, McDowell, Ian C, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, Nobel, Andrew B, Oliva, Meritxell, Ongen, Halit, Palowitch, John J, Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J, Peterson, Christine B, Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, Sul, Jae Hoon, Tsang, Emily K, Urbut, Sarah, van de Bunt, Martijn, and Wang, Gao
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,2.1 Biological and endogenous factors ,Underpinning research ,Aetiology ,1.1 Normal biological development and functioning ,Generic health relevance ,Good Health and Well Being ,Databases ,Genetic ,Gene Expression Profiling ,Gene Expression Regulation ,Gene Regulatory Networks ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Genomics ,Humans ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,Selection ,Genetic ,Tissue Distribution ,GTEx Consortium ,Medical and Health Sciences ,Bioinformatics - Abstract
The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is "mediation" by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are "cis-mediators" of trans-eQTLs, including those "cis-hubs" involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types.
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- 2017
10. Co-expression networks reveal the tissue-specific regulation of transcription and splicing
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Saha, Ashis, Kim, Yungil, Gewirtz, Ariel DH, Jo, Brian, Gao, Chuan, McDowell, Ian C, Consortium, The GTEx, Engelhardt, Barbara E, Battle, Alexis, Aguet, François, Ardlie, Kristin G, Cummings, Beryl B, Gelfand, Ellen T, Getz, Gad, Hadley, Kane, Handsaker, Robert E, Huang, Katherine H, Kashin, Seva, Karczewski, Konrad J, Lek, Monkol, Li, Xiao, MacArthur, Daniel G, Nedzel, Jared L, Nguyen, Duyen T, Noble, Michael S, Segrè, Ayellet V, Trowbridge, Casandra A, Tukiainen, Taru, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chen, Lin S, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Kang, Eun Yong, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, Nobel, Andrew B, Oliva, Meritxell, Ongen, Halit, Palowitch, John J, Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J, Peterson, Christine B, Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, and Sul, Jae Hoon
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Bayes Theorem ,Databases ,Genetic ,Gene Expression Profiling ,Gene Expression Regulation ,Gene Regulatory Networks ,Genotyping Techniques ,Humans ,Organ Specificity ,Polymorphism ,Single Nucleotide ,RNA Splicing ,Sequence Analysis ,RNA ,GTEx Consortium ,Medical and Health Sciences ,Bioinformatics - Abstract
Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues. We used the Genotype-Tissue Expression (GTEx) project v6 RNA sequencing data across 50 tissues and 449 individuals. First, we developed a framework called Transcriptome-Wide Networks (TWNs) for combining total expression and relative isoform levels into a single sparse network, capturing the interplay between the regulation of splicing and transcription. We built TWNs for 16 tissues and found that hubs in these networks were strongly enriched for splicing and RNA binding genes, demonstrating their utility in unraveling regulation of splicing in the human transcriptome. Next, we used a Bayesian biclustering model that identifies network edges unique to a single tissue to reconstruct Tissue-Specific Networks (TSNs) for 26 distinct tissues and 10 groups of related tissues. Finally, we found genetic variants associated with pairs of adjacent nodes in our networks, supporting the estimated network structures and identifying 20 genetic variants with distant regulatory impact on transcription and splicing. Our networks provide an improved understanding of the complex relationships of the human transcriptome across tissues.
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- 2017
11. Dynamic landscape and regulation of RNA editing in mammals
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Aguet, François, Ardlie, Kristin G, Cummings, Beryl B, Gelfand, Ellen T, Getz, Gad, Hadley, Kane, Handsaker, Robert E, Huang, Katherine H, Kashin, Seva, Karczewski, Konrad J, Lek, Monkol, Li, Xiao, MacArthur, Daniel G, Nedzel, Jared L, Nguyen, Duyen T, Noble, Michael S, Segrè, Ayellet V, Trowbridge, Casandra A, Tukiainen, Taru, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chen, Lin S, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Engelhardt, Barbara E, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, McDowell, Ian C, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, Nobel, Andrew B, Oliva, Meritxell, Ongen, Halit, Palowitch, John J, Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J, Peterson, Christine B, Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, Sul, Jae Hoon, Tsang, Emily K, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A, Xi, Hualin S, Yeger-Lotem, Esti, and Zappala, Zachary
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Adenosine Deaminase ,Animals ,Female ,Genotype ,HEK293 Cells ,Humans ,Male ,Mice ,Muscles ,Nuclear Proteins ,Organ Specificity ,Primates ,Proteolysis ,RNA Editing ,RNA-Binding Proteins ,Spatio-Temporal Analysis ,Species Specificity ,Transcriptome ,GTEx Consortium ,Laboratory ,Data Analysis &Coordinating Center (LDACC)—Analysis Working Group ,Statistical Methods groups—Analysis Working Group ,Enhancing GTEx (eGTEx) groups ,NIH Common Fund ,NIH/NCI ,NIH/NHGRI ,NIH/NIMH ,NIH/NIDA ,Biospecimen Collection Source Site—NDRI ,Biospecimen Collection Source Site—RPCI ,Biospecimen Core Resource—VARI ,Brain Bank Repository—University of Miami Brain Endowment Bank ,Leidos Biomedical—Project Management ,ELSI Study ,Genome Browser Data Integration &Visualization—EBI ,Genome Browser Data Integration &Visualization—UCSC Genomics Institute ,University of California Santa Cruz ,General Science & Technology - Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.
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- 2017
12. Landscape of X chromosome inactivation across human tissues
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Aguet, François, Ardlie, Kristin G, Cummings, Beryl B, Gelfand, Ellen T, Getz, Gad, Hadley, Kane, Handsaker, Robert E, Huang, Katherine H, Kashin, Seva, Karczewski, Konrad J, Lek, Monkol, Li, Xiao, MacArthur, Daniel G, Nedzel, Jared L, Nguyen, Duyen T, Noble, Michael S, Segrè, Ayellet V, Trowbridge, Casandra A, Tukiainen, Taru, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chen, Lin S, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Engelhardt, Barbara E, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, McDowell, Ian C, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, Nobel, Andrew B, Oliva, Meritxell, Ongen, Halit, Palowitch, John J, Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J, Peterson, Christine B, Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, Sul, Jae Hoon, Tsang, Emily K, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A, Xi, Hualin S, Yeger-Lotem, Esti, and Zappala, Zachary
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Genetics ,Clinical Research ,Human Genome ,Generic health relevance ,Good Health and Well Being ,Chromosomes ,Human ,X ,Female ,Genes ,X-Linked ,Genome ,Human ,Genomics ,Humans ,Male ,Organ Specificity ,Phenotype ,Sequence Analysis ,RNA ,Single-Cell Analysis ,Transcriptome ,X Chromosome Inactivation ,GTEx Consortium ,Laboratory ,Data Analysis &Coordinating Center (LDACC)—Analysis Working Group ,Statistical Methods groups—Analysis Working Group ,Enhancing GTEx (eGTEx) groups ,NIH Common Fund ,NIH/NCI ,NIH/NHGRI ,NIH/NIMH ,NIH/NIDA ,Biospecimen Collection Source Site—NDRI ,Biospecimen Collection Source Site—RPCI ,Biospecimen Core Resource—VARI ,Brain Bank Repository—University of Miami Brain Endowment Bank ,Leidos Biomedical—Project Management ,ELSI Study ,Genome Browser Data Integration &Visualization—EBI ,Genome Browser Data Integration &Visualization—UCSC Genomics Institute ,University of California Santa Cruz ,General Science & Technology - Abstract
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.
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- 2017
13. The impact of rare variation on gene expression across tissues
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Aguet, François, Ardlie, Kristin G, Cummings, Beryl B, Gelfand, Ellen T, Getz, Gad, Hadley, Kane, Handsaker, Robert E, Huang, Katherine H, Kashin, Seva, Karczewski, Konrad J, Lek, Monkol, Li, Xiao, MacArthur, Daniel G, Nedzel, Jared L, Nguyen, Duyen T, Noble, Michael S, Segrè, Ayellet V, Trowbridge, Casandra A, Tukiainen, Taru, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chen, Lin S, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Engelhardt, Barbara E, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, McDowell, Ian C, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, Nobel, Andrew B, Oliva, Meritxell, Ongen, Halit, Palowitch, John J, Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J, Peterson, Christine B, Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, Sul, Jae Hoon, Tsang, Emily K, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A, Xi, Hualin S, Yeger-Lotem, Esti, and Zappala, Zachary
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Bayes Theorem ,Female ,Gene Expression Profiling ,Genetic Variation ,Genome ,Human ,Genomics ,Genotype ,Humans ,Male ,Models ,Genetic ,Organ Specificity ,Sequence Analysis ,RNA ,GTEx Consortium ,Laboratory ,Data Analysis &Coordinating Center (LDACC)—Analysis Working Group ,Statistical Methods groups—Analysis Working Group ,Enhancing GTEx (eGTEx) groups ,NIH Common Fund ,NIH/NCI ,NIH/NHGRI ,NIH/NIMH ,NIH/NIDA ,Biospecimen Collection Source Site—NDRI ,Biospecimen Collection Source Site—RPCI ,Biospecimen Core Resource—VARI ,Brain Bank Repository—University of Miami Brain Endowment Bank ,Leidos Biomedical—Project Management ,ELSI Study ,Genome Browser Data Integration &Visualization—EBI ,Genome Browser Data Integration &Visualization—UCSC Genomics Institute ,University of California Santa Cruz ,General Science & Technology - Abstract
Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.
- Published
- 2017
14. Genetic effects on gene expression across human tissues
- Author
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Aguet, François, Brown, Andrew A, Castel, Stephane E, Davis, Joe R, He, Yuan, Jo, Brian, Mohammadi, Pejman, Park, YoSon, Parsana, Princy, Segrè, Ayellet V, Strober, Benjamin J, Zappala, Zachary, Cummings, Beryl B, Gelfand, Ellen T, Hadley, Kane, Huang, Katherine H, Lek, Monkol, Li, Xiao, Nedzel, Jared L, Nguyen, Duyen Y, Noble, Michael S, Sullivan, Timothy J, Tukiainen, Taru, MacArthur, Daniel G, Getz, Gad, Addington, Anjene, Guan, Ping, Koester, Susan, Little, A Roger, Lockhart, Nicole C, Moore, Helen M, Rao, Abhi, Struewing, Jeffery P, Volpi, Simona, Brigham, Lori E, Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F, Lonsdale, John T, McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Bryan, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A, Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A, Gillard, Bryan M, Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T, Jewell, Scott D, Montroy, Robert G, Rohrer, Daniel C, Valley, Dana, Mash, Deborah C, Davis, David A, Sobin, Leslie, Barcus, Mary E, Branton, Philip A, Abell, Nathan S, Balliu, Brunilda, Delaneau, Olivier, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Han, Buhm, He, Amy Z, Hormozdiari, Farhad, Li, Xin, Liu, Boxiang, Kang, Eun Yong, McDowell, Ian C, Ongen, Halit, Palowitch, John J, Peterson, Christine B, Quon, Gerald, Ripke, Stephan, Saha, Ashis, Shabalin, Andrey A, Shimko, Tyler C, Sul, Jae Hoon, Teran, Nicole A, Tsang, Emily K, Zhang, Hailei, Zhou, Yi-Hui, Bustamante, Carlos D, Cox, Nancy J, and Guigó, Roderic
- Subjects
Human Genome ,Genetics ,Biotechnology ,1.1 Normal biological development and functioning ,2.1 Biological and endogenous factors ,Aetiology ,Underpinning research ,Generic health relevance ,Alleles ,Chromosomes ,Human ,Disease ,Female ,Gene Expression Profiling ,Gene Expression Regulation ,Genetic Variation ,Genome ,Human ,Genotype ,Humans ,Male ,Organ Specificity ,Quantitative Trait Loci ,GTEx Consortium ,Laboratory ,Data Analysis &Coordinating Center (LDACC)—Analysis Working Group ,Statistical Methods groups—Analysis Working Group ,Enhancing GTEx (eGTEx) groups ,NIH Common Fund ,NIH/NCI ,NIH/NHGRI ,NIH/NIMH ,NIH/NIDA ,Biospecimen Collection Source Site—NDRI ,Biospecimen Collection Source Site—RPCI ,Biospecimen Core Resource—VARI ,Brain Bank Repository—University of Miami Brain Endowment Bank ,Leidos Biomedical—Project Management ,ELSI Study ,Genome Browser Data Integration &Visualization—EBI ,Genome Browser Data Integration &Visualization—UCSC Genomics Institute ,University of California Santa Cruz ,Lead analysts: ,Laboratory ,Data Analysis &Coordinating Center (LDACC): ,NIH program management: ,Biospecimen collection: ,Pathology: ,eQTL manuscript working group: ,General Science & Technology - Abstract
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
- Published
- 2017
15. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020
- Author
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Wu, Fuqing, Xiao, Amy, Zhang, Jianbo, Moniz, Katya, Endo, Noriko, Armas, Federica, Bushman, Mary, Chai, Peter R., Duvallet, Claire, Erickson, Timothy B., Foppe, Katelyn, Ghaeli, Newsha, Gu, Xiaoqiong, Hanage, William P., Huang, Katherine H., Lee, Wei Lin, McElroy, Kyle A., Rhode, Steven F., Matus, Mariana, Wuertz, Stefan, Thompson, Janelle, and Alm, Eric J.
- Published
- 2021
- Full Text
- View/download PDF
16. Design and user experience testing of a polygenic score report: a qualitative study of prospective users
- Author
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Brockman, Deanna G., Petronio, Lia, Dron, Jacqueline S., Kwon, Bum Chul, Vosburg, Trish, Nip, Lisa, Tang, Andrew, O’Reilly, Mary, Lennon, Niall, Wong, Bang, Ng, Kenney, Huang, Katherine H., Fahed, Akl C., and Khera, Amit V.
- Published
- 2021
- Full Text
- View/download PDF
17. Quantifying 18F-Fluorodeoxyglucose Uptake in Perianal Fistulas on PET/CT: A Retrospective Analysis
- Author
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Huang, Katherine, primary, Garuba, Favour, additional, Ganapathy, Aravinda Krishna, additional, Bishop, Grace, additional, Zhang, Hanjing, additional, Lovato, Adriene, additional, Itani, Malak, additional, Viswanath, Satish E, additional, Fraum, Tyler J, additional, Deepak, Parakkal, additional, and Ballard, David, additional
- Published
- 2023
- Full Text
- View/download PDF
18. Functional genomics identifies new synergistic therapies for retinoblastoma
- Author
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Aubry, Arthur, Pearson, Joel D., Huang, Katherine, Livne-bar, Izhar, Ahmad, Mohammad, Jagadeesan, Madhavan, Khetan, Vikas, Ketela, Troy, Brown, Kevin R., Yu, Tao, Lu, Suying, Wrana, Jeffrey L., Moffat, Jason, and Bremner, Rod
- Published
- 2020
- Full Text
- View/download PDF
19. Loss of Integrin αvβ8 in Murine Hepatocytes Accelerates Liver Regeneration
- Author
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Greenhalgh, Stephen N., Matchett, Kylie P., Taylor, Richard S., Huang, Katherine, Li, John T., Saeteurn, Koy, Donnelly, Mhairi C., Simpson, Eilidh E.M., Pollack, Joshua L., Atakilit, Amha, Simpson, Kenneth J., Maher, Jacquelyn J., Iredale, John P., Sheppard, Dean, and Henderson, Neil C.
- Published
- 2019
- Full Text
- View/download PDF
20. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer
- Author
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Bullman, Susan, Pedamallu, Chandra S., Sicinska, Ewa, Clancy, Thomas E., Zhang, Xiaoyang, Cai, Diana, Neuberg, Donna, Huang, Katherine, Guevara, Fatima, Nelson, Timothy, Chipashvili, Otari, Hagan, Timothy, Walker, Mark, Ramachandran, Aruna, Diosdado, Begoña, Serna, Garazi, Mulet, Nuria, Landolfi, Stefania, Ramon y Cajal, Santiago, Fasani, Roberta, Aguirre, Andrew J., Ng, Kimmie, Élez, Elena, Ogino, Shuji, Tabernero, Josep, Fuchs, Charles S., Hahn, William C., Nuciforo, Paolo, and Meyerson, Matthew
- Published
- 2017
21. Mfge8 suppresses airway hyperresponsiveness in asthma by regulating smooth muscle contraction
- Author
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Kudo, Makoto, Soltani, SM Amin Khalifeh, Sakuma, Stephen A, McKleroy, William, Lee, Ting-Hein, Woodruff, Prescott G, Lee, Jae Woo, Huang, Katherine, Chen, Chun, Arjomandi, Mehrdad, Huang, Xiaozhu, and Atabai, Kamran
- Subjects
Biochemistry and Cell Biology ,Medical Physiology ,Biomedical and Clinical Sciences ,Biological Sciences ,Lung ,Clinical Research ,Asthma ,2.1 Biological and endogenous factors ,Aetiology ,Respiratory ,Analysis of Variance ,Animals ,Antigens ,Surface ,Blotting ,Western ,Bronchial Hyperreactivity ,Bronchoalveolar Lavage ,Calcium ,Flow Cytometry ,Fluorescent Antibody Technique ,Humans ,Interleukin-13 ,Mice ,Mice ,Knockout ,Milk Proteins ,Muscle Contraction ,Muscle ,Smooth ,NF-kappa B ,Point Mutation ,rho GTP-Binding Proteins ,rhoA GTP-Binding Protein ,calcium sensitivity ,lactadherin - Abstract
Airway obstruction is a hallmark of allergic asthma and is caused primarily by airway smooth muscle (ASM) hypercontractility. Airway inflammation leads to the release of cytokines that enhance ASM contraction by increasing ras homolog gene family, member A (RhoA) activity. The protective mechanisms that prevent or attenuate the increase in RhoA activity have not been well studied. Here, we report that mice lacking the gene that encodes the protein Milk Fat Globule-EGF factor 8 (Mfge8(-/-)) develop exaggerated airway hyperresponsiveness in experimental models of asthma. Mfge8(-/-) ASM had enhanced contraction after treatment with IL-13, IL-17A, or TNF-α. Recombinant Mfge8 reduced contraction in murine and human ASM treated with IL-13. Mfge8 inhibited IL-13-induced NF-κB activation and induction of RhoA. Mfge8 also inhibited rapid activation of RhoA, an effect that was eliminated by an inactivating point mutation in the RGD integrin-binding site in recombinant Mfge8. Human subjects with asthma had decreased Mfge8 expression in airway biopsies compared with healthy controls. These data indicate that Mfge8 binding to integrin receptors on ASM opposes the effect of allergic inflammation on RhoA activity and identify a pathway for specific inhibition of ASM hypercontractility in asthma.
- Published
- 2013
22. Transmission of human-associated microbiota along family and social networks
- Author
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Brito, Ilana L., Gurry, Thomas, Zhao, Shijie, Huang, Katherine, Young, Sarah K., Shea, Terrence P., Naisilisili, Waisea, Jenkins, Aaron P., Jupiter, Stacy D., Gevers, Dirk, and Alm, Eric J.
- Published
- 2019
- Full Text
- View/download PDF
23. IL-17A produced by αβ T cells drives airway hyper-responsiveness in mice and enhances mouse and human airway smooth muscle contraction
- Author
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Kudo, Makoto, Melton, Andrew C, Chen, Chun, Engler, Mary B, Huang, Katherine E, Ren, Xin, Wang, Yanli, Bernstein, Xin, Li, John T, Atabai, Kamran, Huang, Xiaozhu, and Sheppard, Dean
- Subjects
Medical Physiology ,Biomedical and Clinical Sciences ,Asthma ,Lung ,Aetiology ,2.1 Biological and endogenous factors ,Respiratory ,Analysis of Variance ,Animals ,CD11c Antigen ,CD4 Antigens ,Dendritic Cells ,Disease Models ,Animal ,Dose-Response Relationship ,Drug ,Enzyme Inhibitors ,Flow Cytometry ,Humans ,In Vitro Techniques ,Integrin alphaV ,Interleukin-17 ,Male ,Methacholine Chloride ,Mice ,Mice ,Inbred C57BL ,Mice ,Knockout ,Muscarinic Agonists ,Muscle Contraction ,Muscle ,Smooth ,Ovalbumin ,Potassium Chloride ,Respiratory System ,Signal Transduction ,Th17 Cells ,rho-Associated Kinases ,rhoA GTP-Binding Protein ,Medical and Health Sciences ,Immunology ,Biomedical and clinical sciences ,Health sciences - Abstract
Emerging evidence suggests that the T helper 17 (T(H)17) subset of αβ T cells contributes to the development of allergic asthma. In this study, we found that mice lacking the αvβ8 integrin on dendritic cells did not generate T(H)17 cells in the lung and were protected from airway hyper-responsiveness in response to house dust mite and ovalbumin sensitization and challenge. Because loss of T(H)17 cells inhibited airway narrowing without any obvious effects on airway inflammation or epithelial morphology, we examined the direct effects of T(H)17 cytokines on mouse and human airway smooth muscle function. Interleukin-17A (IL-17A), but not IL-17F or IL-22, enhanced contractile force generation of airway smooth muscle through an IL-17 receptor A (IL-17RA)-IL-17RC, nuclear factor κ light-chain enhancer of activated B cells (NF-κB)-ras homolog gene family, member A (RhoA)-Rho-associated coiled-coil containing protein kinase 2 (ROCK2) signaling cascade. Mice lacking integrin αvβ8 on dendritic cells showed impaired activation of this pathway after ovalbumin sensitization and challenge, and the diminished contraction of the tracheal rings in these mice was reversed by IL-17A. These data indicate that the IL-17A produced by T(H)17 cells contributes to allergen-induced airway hyper-responsiveness through direct effects on airway smooth muscle.
- Published
- 2012
24. The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
- Author
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Gevers, Dirk, Knight, Rob, Petrosino, Joseph F, Huang, Katherine, McGuire, Amy L, Birren, Bruce W, Nelson, Karen E, White, Owen, Methé, Barbara A, and Huttenhower, Curtis
- Subjects
Microbiology ,Biological Sciences ,Stem Cell Research - Nonembryonic - Human ,Clinical Research ,HIV/AIDS ,Genetics ,Stem Cell Research ,Cancer ,Human Genome ,Computational Biology ,Ecosystem ,Genes ,rRNA ,Genomics ,Health ,High-Throughput Nucleotide Sequencing ,Humans ,Internet ,Metagenome ,Organizations ,Phylogeny ,RNA ,Ribosomal ,16S ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Developmental Biology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
This manuscript describes the NIH Human Microbiome Project, including a brief review of human microbiome research, a history of the project, and a comprehensive overview of the consortium's recent collection of publications analyzing the human microbiome.
- Published
- 2012
25. Defining the landscape of cancer vulnerabilities that are engendered by germline genetic variation
- Author
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Misek, Sean, primary, Fultineer, Aaron, additional, Kalfon, Jeremie, additional, Noorbakhsh, Javad, additional, Boyle, Isabella, additional, Dempster, Joshua, additional, Petronio, Lia, additional, Huang, Katherine, additional, Green, Thomas, additional, Brown, Adam, additional, Doench, John, additional, Root, David, additional, McFarland, James, additional, Beroukhim, Rameen, additional, and Boehm, Jesse, additional
- Published
- 2023
- Full Text
- View/download PDF
26. High yield expression and purification of full-length Neurotensin with pyroglutamate modification
- Author
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Asadollahi, Kazem, primary, Huang, Katherine, additional, Yan, Fei, additional, de Zhang, Lazarus A., additional, Scott, Daniel J., additional, and Gooley, Paul R., additional
- Published
- 2023
- Full Text
- View/download PDF
27. Large Lineage-Specific Gene Expansions are Driven by Moble Genetic Elements
- Author
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Huang, Katherine H.
- Subjects
Basic biological sciences ,Lineage?specific expansion (LSE) ,prokaryotes ,phylogenetic trees ,mobile genetic elements (MGE) ,phage integration ,intergenomic - Abstract
Lineage-specific expansion (LSE) plays a vital role in how prokaryotes gain new genefunctions and adapt to their environments. To uncover the mechanisms behind LSE, we identify genes that arise from LSE by constructing phylogenetic trees of protein families across 400+ bacterial genomes. We found that LSE genes tend to cluster on the chromosomes and form hyper LSE regions. Such regions could not be explained solely by operon duplication. The locations of these hyper LSE regions are often remarkably conserved among closely related strains, even though the gene content may not be conserved. Furthermore, these hyper LSE regions frequently overlap with clusters of mobile genetic elements (MGE) and strain?specific genomic islands. We hypothesize that the majority of large strain-specific gene duplications are mediated by MGE and are concentrated in regions prone to site-specific MGE-driven recombinations. And for the same reasons, these regions are more susceptible to phage integration and to intergenomic information exchange.
- Published
- 2009
28. Large Lineage-Specific Expansions Are Driven By Mobile Genetic Elements
- Author
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Huang, Katherine
- Subjects
Basic biological sciences ,Environmental sciences ,microbiology ,comparative genomics ,functional genomics ,evolution ,bioremediation - Abstract
The MicrobesOnline database (http://microbesonline.org) currently contains 430 microbial genomes as of our March 2007 release and will soon be expanded to over 600 by Fall 2007. Together with a suite of visualization, analysis, and annotation tools, MicrobesOnline provides a comprehensive framework for studying important comparative and evolutionary genomic questions. MicrobesOnline offers many useful tools including a multi-species genome browser, operon and regulon prediction methods and results, gene ontology browser, capabilities for community annotation of genomes, and a user workbench, which allows users to store arbitrary sets of sequences for further analysis including the ability to generate multiple sequence alignments and custom gene trees. In our most recent software release, we've added a combined gene and species phylogeny browser (see Tree Browser), sequence motif detection and motif search tools in the user workbench, and tools for viewing and mining gene expression microarray, proteomic, and phenotype microarray data (see Expression Profile Searches).
- Published
- 2008
29. Global Transcriptional and Metabolite Analysis of Desulfovibrio vulgaris Hildenborough Responses to Long-Term Exposure to Elevated NaCl
- Author
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He, Zhili, Baidoo, Edward, Zhou, Aifen, He, Qiang, Benke, Peter, Phan, Richard, Joachimiak, Marcin, Fields, Matthew W., Mukhopadhyay, Aindrila, Alm, Eric J., Huang, Katherine, Wall, Judy, Hazen, Terry C., Keasling, Jay D., Arkin, Adam P., and Zhou, Jizhong
- Subjects
Evolutionary Biology ,Extremophiles ,Microarrays ,Stress Response ,Sulfate Reducers ,Transcriptomics - Abstract
The mechanisms of Desulfovibrio vulgaris Hildenborough responses to long-term NaCl exposure were studied by global transcriptional and metabolite analyses. The growth of D. vulgaris was inhibited by high salinity, and salt inhibition could be relieved by an addition of amino acids (e.g., glutamate, alanine) or yeast extract. Salt shock (sudden increase in salt concentration) and salt adaptation (inoculating cells in the medium containing high concentrations of salt) showed a significant difference in respective transcriptomes. Salt adaptation induced expression of genes involved in amino acid biosynthesis and transportation, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). Genes involved in energy metabolism, cell motility, and phage structures were repressed. Genes involved in Na+/H+ transport, K+ uptake and transportation, and proline biosynthesis and transportation were not significantly affected. Metabolite assays and external addition of amino acids into the growth medium of D. vulgaris suggest that amino acids, such as glutamate and alanine may accumulate as osmoprotectants in D. vulgaris. A conceptual model is proposed to link our observed results to currently available knowledge for further understanding the mechanisms of adaptation of D. vulgaris to sodium chloride.
- Published
- 2008
30. A large number of hypothetical proteins are differentially expressed during stress in desulfovibrio vulgaris
- Author
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Drury, Elliott C., Redding, Alyssa M., Mukhopadyay, Aindrila, Huang, Katherine H., Hazen, Terry C., Arkin, Adam P., Wall, Judy D., and Elias, Dwayne A.
- Subjects
Environmental Genomics ,Proteomics ,Sulfate Reducers - Published
- 2007
31. The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
- Author
-
Alm, Eric, Huang, Katherine, and Arkin, Adam
- Subjects
Comparative Genomics Environmental Genomics Evolutionary Biology Models Sequencing Signal Transduction - Abstract
Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche- specific signals, we analyzed the phylogenetic distribution of nearly 5000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage- specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. These results lead us to conclude that in the ongoing evolution of bacterial signal transduction machinery, some organisms serve as 'producers' generating novel genetic diversity, while others serve as 'consumers' capitalizing on the existing diversity of their peers.
- Published
- 2007
32. Nitrate stress response in Desulfovibrio vulgaris Hildenborough: Whole-Genome Transcriptomics and proteomics analyses
- Author
-
He, Qiang, He, Zhili, Chen, Wenqiong, Yang, Zamin, Alm, Eric J., Huang, Katherine H., Yen, Huei-Che, Joyner, Dominque C., Keller, Martin, Arkin, Adam P., Hazen, Terry C., Wall, Judy D., and Zhou, Jizhong
- Abstract
Sulfate reducing bacteria (SRB) are of interest for bioremediation with their ability to reduce and immobilize heavy metals. Nitrate, a common co-contaminant in DOE sites, is suggested to inhibit SRB via nitrite. Previous results indicate that nittite is indeed inhibitory to the growth of Desulfovibrio vulgaris. However, growth inhibition by nitrate alone was also observed. In this study, growth and expression responses to various concentrations of nitrate were investigated using the Omnilog phenotype arrays and whole-genome DNA microarrays. Changes in the proteome were examined with 3D-LC followed by MS-MS analysis.Microarray analysis found 5, 50, 115, and 149 genes significantly up-regulated and 36, 113, 205, and 149 down-regulated at 30, 60, 120, and 240 min, respectively. Both transcriptomic and proteomic profiles shared little similarities with those of salt stress, indicating a specific inhibitory mechanism beyond osmotic stress. Many of the genes (-50% at certain time points) with altered expression level were of unknown functions; however, the increasing number of ribosomal protein genes down-regulated with tinle could provide a direct explanation to the growth inhibition effect of nitrate. Further, several lines of evidence suggested that the downregulationof genes coding the ribosomal proteins could be the result of the changes in the energy flow upon nitrate exposure: 1) The down-regulation of genes for the ATPase subunits indicated reduced level of energy generation; 2) the up-regulation of phage shock protein genes (pspA and pspC) might indicate a reduced proton motive force; although damages to the cell envelope could also contribute to this outcome; 3) the gene for the hybrid cluster protein, a redox protein with roles in nitrogen metabolism, was highly up-regulated 120 and 240 min following nitrate stress at both transcriptomic and proteomic level, suggesting that nitrate was being actively reduced, shifting reducing equivalents away from normal energy production; 4) genes in the methionine biosynthesis pathway were among the most highly up-regulated genes throughout the experiment, potentially providing a convenient rnechanism for the simultaneous disposal of excess sulfur (from sulfate reduction) and nitrogen (from nitrate reduction); 5) One gene cluster consistently among the most up-regulated genes consisted of genes encoding two TRAP dicarboxylate family transpollers, a folmate acetyltransferase, and a pyruvate formate-lyase activating enzyme, which might be regulated to provide an increased carbon flow to keep pace with demand from amino acids biosynthesis. These observations indicated that the growth inhibition effect of nitrate might be due to energy limitation. Similar to the observations made during salt stress, the glycine/betaine transporter gene was among genes highly up-regulated, suggesting that NaN03 also constituted osmotic stress which was relieved by the mechanism of osmoprotectant accumulation. Osmoprotectant accumulation as the major resistance mechanism was further validated by the partial relief of growth inhibition by glycine betaine. It is also noted that, similar to nitrite stress, the ferric iron transporter genes were up-regulated during nitrate stress, suggesting an increased demand for iron. Unlike nitrite stress, however, no other genes in the Fur regulon were co-regulated during nitrate stress, pointing to a yet-to-known regulatory signal.In conclusion, excess NaN03 resulted in both osmotic stress and nitrate stress. D. vulgaris shifted nitrogen metabolism and energy production in response to nitrate stress. Resistance to osmotic stress was achieved primarily by the transport of osmoprotectant.
- Published
- 2007
33. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
- Author
-
Kettler, Gregory C, Martiny, Adam C, Huang, Katherine, Zucker, Jeremy, Coleman, Maureen L, Rodrigue, Sebastien, Chen, Feng, Lapidus, Alla, Ferriera, Steven, Johnson, Justin, Steglich, Claudia, Church, George M, Richardson, Paul, and Chisholm, Sallie W
- Subjects
bacterial gene ,bacterium isolate ,cell function ,chromosomal localization ,cladistics ,controlled study ,ecotype ,gene loss ,genetic difference ,genomic island ,nonhuman ,nucleotide sequence ,parsimony analysis ,phylogenetic tree ,phylogeny ,Prochlorococcus ,bacterial chromosome ,bacterial gene ,bacterial genome ,classification ,comparative study ,ecosystem ,evolution ,genetics ,isolation and purification ,metabolism ,species difference ,Synechococcus - Abstract
Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations inProchlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history ofProchlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.
- Published
- 2007
34. The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
- Author
-
Alm, Eric, Huang, Katherine, and Arkin, Adam
- Subjects
histidine protein kinases signal transduction horizontal gene transfer - Abstract
Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage-specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. Finally, while these two modes of gene acquisition are widespread across bacterial taxa, there are clear species-specific preferences for which mode is used.
- Published
- 2006
35. Operon Formation is Driven by Co-Regulation and Not by Horizontal Gene Transfer
- Author
-
Price, Morgan N., Huang, Katherine H., Arkin, Adam P., and Alm, Eric J.
- Subjects
Basic biological sciences - Abstract
Although operons are often subject to horizontal gene transfer (HGT), non-HGT genes are particularly likely to be in operons. To resolve this apparent discrepancy and to determine whether HGT is involved in operon formation, we examined the evolutionary history of the genes and operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli (indicating HGTi) form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous geneswithout paralogs (genes believed to undergo HGT rarely) often form new operons. We conclude that HGT is not associated with operon formation, but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.
- Published
- 2005
36. Whole-Genome Transcriptional Response of Desulfovibrio vulgaris to Nitrite
- Author
-
He, Qiang, He, Zhili, Huang, Katherine H., Alm, Eric J., Arkin, Adam P., Wall, Judy D., Hazen, Terry C., Fields, Matthew W., and Zhou, Jizhong
- Published
- 2004
37. A Novel Method for Accurate Operon Predictions in All Sequenced Prokaryotes
- Author
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Price, Morgan N., Huang, Katherine H., Alm, Eric J., and Arkin, Adam P.
- Subjects
Basic biological sciences ,Operons Comparative Genomics - Abstract
We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83 percent accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacter pylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from six phylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.
- Published
- 2004
38. The impact of rare variation on gene expression across tissues
- Author
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Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun
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Disease susceptibility -- Genetic aspects ,Genetic variation -- Observations ,Gene expression -- Observations ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]
- Published
- 2017
- Full Text
- View/download PDF
39. Dynamic landscape and regulation of RNA editing in mammals
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Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko
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Genetic research ,Mammals -- Genetic aspects ,RNA processing -- Research ,Genetic regulation ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]
- Published
- 2017
- Full Text
- View/download PDF
40. Landscape of X chromosome inactivation across human tissues
- Author
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Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir
- Subjects
Chromosomes -- Physiological aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]
- Published
- 2017
- Full Text
- View/download PDF
41. Sleep Disturbance and SARS–CoV‐2 Vaccinations in Patients With Chronic Inflammatory Disease
- Author
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Pawar, Niti, primary, Taylor, Kimberly E., additional, Yang, Monica, additional, Deepak, Parakkal, additional, Kim, Wooseob, additional, Paley, Michael A., additional, Matloubian, Mehrdad, additional, Carvidi, Alex, additional, Ciorba, Matthew A., additional, Demissie, Emanuel, additional, El‐Qunni, Alia, additional, Huang, Katherine, additional, Kinnett, Baylee, additional, McMorrow, Lily E., additional, Paez, Diana, additional, Poole, Mackenzie, additional, Rose, Abigail, additional, Schriefer, Rebecca E., additional, Kim, Alfred H. J., additional, Nakamura, Mary, additional, Katz, Patricia, additional, and Gensler, Lianne S., additional
- Published
- 2023
- Full Text
- View/download PDF
42. Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
- Author
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Misek, Sean A., primary, Fultineer, Aaron, additional, Kalfon, Jeremie, additional, Noorbakhsh, Javad, additional, Boyle, Isabella, additional, Dempster, Joshua, additional, Petronio, Lia, additional, Huang, Katherine, additional, Saadat, Alham, additional, Green, Thomas, additional, Brown, Adam, additional, Doench, John G., additional, Root, David, additional, McFarland, James, additional, Beroukhim, Rameen, additional, and Boehm, Jesse S., additional
- Published
- 2022
- Full Text
- View/download PDF
43. Systematic Review of NMR-Based Metabolomics Practices in Human Disease Research
- Author
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Huang, Katherine, primary, Thomas, Natalie, additional, Gooley, Paul R., additional, and Armstrong, Christopher W., additional
- Published
- 2022
- Full Text
- View/download PDF
44. Identifying personal microbiomes using metagenomic codes
- Author
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Franzosa, Eric A., Huang, Katherine, Meadow, James F., Gevers, Dirk, Lemon, Katherine P., Bohannan, Brendan J. M., and Huttenhower, Curtis
- Published
- 2015
45. Reactogenicity of the Messenger RNA SARS–CoV‐2 Vaccines Associated With Immunogenicity in Patients With Autoimmune and Inflammatory Disease
- Author
-
Yang, Monica M., primary, Taylor, Kimberly E., additional, Paez, Diana, additional, Carividi, Alex, additional, Demissie, Emanuel, additional, Pawar, Niti, additional, El‐Qunni, Alia A., additional, McMorrow, Lily E., additional, Schriefer, Rebecca E., additional, Huang, Katherine, additional, Kinnett, Baylee, additional, Klebert, Michael, additional, Haile, Alem, additional, O'Halloran, Jane A., additional, Presti, Rachel M., additional, Kim, Wooseob, additional, Ellebedy, Ali H., additional, Ciorba, Matthew A., additional, Paley, Michael A., additional, Deepak, Parakkal, additional, Kim, Alfred H. J., additional, Katz, Patricia, additional, Matloubian, Mehrdad, additional, Nakamura, Mary, additional, and Gensler, Lianne S., additional
- Published
- 2022
- Full Text
- View/download PDF
46. The underlying sex differences in neuroendocrine adaptations relevant to Myalgic Encephalomyelitis Chronic Fatigue Syndrome
- Author
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Thomas, Natalie, primary, Gurvich, Caroline, additional, Huang, Katherine, additional, Gooley, Paul R., additional, and Armstrong, Christopher W., additional
- Published
- 2022
- Full Text
- View/download PDF
47. Abstract 2173: Ancestry bias in CRISPR guide design impedes discovery of genetic dependencies
- Author
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Misek, Sean Alexander, primary, Fultineer, Aaron, additional, Kalfon, Jeremie, additional, Noorbakhsh, Javad, additional, Boyle, Isabella, additional, Dempster, Joshua, additional, Petronio, Lia, additional, Huang, Katherine, additional, McFarland, James, additional, Beroukhim, Rameen, additional, and Boehm, Jesse, additional
- Published
- 2022
- Full Text
- View/download PDF
48. Tu1456: TAUROURSODEOXYCHOLIC ACID (TUDCA) REDUCES ER STRESS AND CLINICAL DISEASE ACTIVITY IN ULCERATIVE COLITIS: FINAL RESULTS OF A PHASE I TRIAL
- Author
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Lamm, Vladimir, primary, Deng, Ruishu, additional, Huang, Katherine, additional, Soleymanjahi, Saeed, additional, Liu, Ta-Chiang, additional, Xie, Yan, additional, Gremida, Anas K., additional, Deepak, Parakkal, additional, Chen, Chien-Huan, additional, Davidson, Nicholas O., additional, Wang, Miao, additional, Kaufman, Randal J., additional, and Ciorba, Matthew A., additional
- Published
- 2022
- Full Text
- View/download PDF
49. Su1481: IMPACT OF IMMUNOSUPPRESSIVE THERAPIES ON ANTIBODY DECAY FOLLOWING MRNA VACCINATION TO SARS-COV-2 IN A PROSPECTIVE COHORT OF PATIENTS WITH CHRONIC INFLAMMATORY DISEASES
- Author
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Deepak, Parakkal, primary, Kim, Wooseob, additional, Paley, Michael, additional, Yang, Monica, additional, Burdess, Samantha, additional, Carvidi, Alexander B., additional, Demissie, Emanuel, additional, El-Qunni, Alia A., additional, Haile, Alem, additional, Huang, Katherine, additional, Escudero, Guadalupe Oliva, additional, McMorrow, Lily E., additional, Paez, Diana, additional, Pawar, Niti, additional, Perantie, Dana C., additional, Schriefer, Rebecca E., additional, Sides, Shannon E., additional, Thapa, Mahima, additional, Gergely, Maté, additional, Akuse, Sewuese E., additional, Klebert, Michael, additional, Mitchell, Lynne, additional, Nix, Billy D., additional, Graf, Jonathan, additional, Taylor, Kimberly E., additional, Chahin, Salim, additional, Ciorba, Matthew A., additional, Katz, Patricia, additional, Matloubian, Mehrdad, additional, O'Halloran, Jane A., additional, Presti, Rachel M., additional, Wu, Gregory F., additional, Gensler, Lianne S., additional, Nakamura, Mary C., additional, Ellebedy, Ali H., additional, and Kim, Alfred H., additional
- Published
- 2022
- Full Text
- View/download PDF
50. Tu1889 REAL-WORLD EFFECTIVENESS AND SAFETY OF OZANIMOD IN ULCERATIVE COLITIS: A MULTICENTER STUDY
- Author
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Lieto, Stephen, Scalzo, Nicholas, Huang, Katherine, Khan, Abdul, Xu, Anthony, Pekow, Joel, Rajauria, Palak, Ayoub, Malek, Johnson, Amanda M., Yarur, Andres, Patel, Anish, Bishu, Shrinivas, Shukla, Richa, Osterman, Mark T., Paul, Damemarie, Sokol, Uyen, Tharmarajah, Soba, Lawlor, Garrett, Ahmad, Harris, Rubin, David T., Sands, Bruce E., Deepak, Parakkal, and Ungaro, Ryan C.
- Published
- 2024
- Full Text
- View/download PDF
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