Citations 2
The Human Phenotype Ontology in 2024: phenotypes around the world
Gargano, Michael , Matentzoglu, Nicolas , Coleman, Ben , Addo-Lartey, Eunice B, Anagnostopoulos, Anna V. , Anderton, Joel , Avillach, Paul , Bagley, Anita , Bakštein, Eduard , Balhoff, James P. , Baynam, Gareth , Bertram, Holli , Bishop, Somer , Bodenstein, David F. , Botas, Pablo , Cady, J , Cameron, Rhiannon , Castellanos, F , Chan, Lauren , Cruz-Rojo, Jaime , Dahan‐Oliel, Noémi , Davids, Jon R. , Dieuleveult, Maud de , Souza, Vinícius de , Vries, Bert B.A. de , Diaz‐Byrd, Claudia , Duyzend, Michael , Elfeky, Reem , Essaid, Shahim , Fabrizzi, Carolina , Freudenberg‐Hua, Yun , Gabriel, Davera , Moses, Rachel Gore , Green, Ian, Gu, Weihong, Guthrie, Julia, Hamosh, Ada , Hanauer, Marc , Hanušová, Kateřina , He, Yongqun , Helbig, Ingo , Huang, Shangzhi, Joseph, Lisa , Keramatian, Kamyar , King, Bryan , Knoflach, Katrin , Koolen, David A. , Kraus, Megan L , Kroll, Carlo , Kusters, Maaike , Ladewig, Markus S. , Lagorce, David , Laraway, Bryan , Li, Xiarong, Lucano, Caterina , Marazita, Mary L. , Martínez‐Glez, Víctor , McHenry, Toby H, McInnis, Melvin G. , Mihulová, Michaela , Millett, Caitlin E. , Moslerová, Veronika , Narutomi, Kenji, Nevado, Julián , Nierenberg, Andrew A. , Čajbiková, Nikola Novák , Ogishima, Soichi , Olson, Daniel , Ortiz, Abigail, Nanclares, Guiomar Pérez de , Peters, Amy T. , Rapp, Christina , Rath, Ana , Rekerle, Lauren , Roberts, Angharad M. , Roy, Suzy, Sanders, Stephan , Schuetz, Catharina , Schwarz, Martin , Scott, Katie , Seelow, Dominik , Seitz, Berthold , Shen, Yiping , Similuk, Morgan , Simon, Eric S. , Singh, Balwinder , Smith, Cynthia L. , Smolinsky, Jake T , Stafford, Elizabeth , Stefancsik, Ray , Steinhaus, Robin , Strawbridge, Rebecca , Sundaramurthi, Jagadish Chandrabose , Talapova, Polina , Castano, Jair A Tenorio , Tesner, Pavel , Thomas, Rhys H. , Turnovec, Marek , Gijn, Mariëlle van , Vlčková, Markéta , Walden, Anita , Ware, James S. , Wiafe, Addo A, Wiafe, Samuel Agyei , Wiggins, Lisa D. , Williams, Andrew E. , Wu, Chen , 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Peters, Amy T , Putman, Tim , Rath, Ana , Reese, Justin , Rekerle, Lauren , Sanders, Stephan J , Schuetz, Catharina , Schulte, Eva , Schulze, Thomas , Schwarz, Martin , Scott, Katie , Seelow, Dominik , Seitz, Berthold , Similuk, Morgan N , Simon, Eric S , Singh, Balwinder , Smedley, Damian , Smith, Cynthia L , Smolinsky, Jake T , Sperry, Sarah , Stafford, Elizabeth , Stefancsik, Ray , Steinhaus, Robin , Strawbridge, Rebecca , Sundaramurthi, Jagadish Chandrabose , Talapova, Polina , Tenorio Castano, Jair A , Tesner, Pavel , Thomas, Rhys H , Thurm, Audrey , Turnovec, Marek , van Gijn, Marielle E , Vasilevsky, Nicole A , Vlčková, Markéta , Walden, Anita , Wang, Kai , Wapner, Ron , Ware, James S , Wiafe, Samuel A , Wiggins, Lisa D , Williams, Andrew , Wyrwoll, Margot J , Yalin, Nefize , Yamamoto, Yasunori , Yatham, Lakshmi N , Yocum, Anastasia K , Young, Allan H , Yüksel, Zafer , Zandi, Peter P , Zankl, Andreas , Zarante, Ignacio , Zvolský, Miroslav , Toro, Sabrina , Carmody, Leigh C , Harris, Nomi L , Munoz-Torres, Monica C , Danis, Daniel , Mungall, Christopher J , Köhler, Sebastian , Haendel, Melissa , Robinson, Peter N , Berk, Michael , Chute, Christopher G. , Fico, Giovanna , Fullerton, Janice M. , Giordano, Jessica L. , Jiang, Xiaofeng , Lai, Meng‐Chuan , Schulte, Eva C. , Smedley, Damian , Sperry, Sarah H. , Xiong, Hui
Nucleic Acids Research | October 19, 2023 | Volume: 52 | Issue: D1 | Pages: D1333-D1346
Abstract The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.
A systems‐level analysis highlights microglial activation as a modifying factor in common epilepsies
Altmann, André , Ryten, Mina , Nunzio, Martina Di , Ravizza, Teresa , Reynolds, Regina H. , Somani, Alyma, Bacigaluppi, Marco , Iori, Valentina , Sapia, Rossella Di , Cerovic, Milica , Palma, Eleonora , Ruffolo, Gabriele , Botía, Juan A. , Absil, Julie , Alhusaini, Saud , Alvim, Marina K. M. , Auvinen, Pia, Bartolini, Emanuele , Bender, Benjamin , Bergo, Felipe P. G. , Bernardes, Tauana, Bernasconi, Andrea , Bernasconi, Neda , Bernhardt, Boris C. , Blackmon, Karen , Braga, Bárbara , Caligiuri, Maria Eugenia , Calvo, Anna, Carr, Sarah J. A. , Cavalleri, Gianpiero L. , Chen, Jian , Chen, Shuai , Cherubini, Andrea , Concha, Luis , David, Philippe, Delanty, Norman, Depondt, Chantal, Doherty, Colin P. , Domín, Martin , Foley, Sonya , França, Wendy, Gambardella, Antonio , Guerrini, Renzo , Hamandi, Khalid , Hibar, Derrek P., Isaev, Dmitry , Jahanshad, Neda , Kälviäinen, Reetta , Keller, Simon S. , Kotikalapudi, Raviteja , Kwan, Patrick , Langner, Sönke , Lenge, Matteo , Martin, Pascal , Meletti, Stefano , Morita‐Sherman, Marcia , Pariente, José C. , Richardson, Mark P. , Rummel, Christian , Saavalainen, Taavi, Semmelroch, Mira , Striano, Pasquale, Thesen, Thomas , Thomas, Rhys H. , Tondelli, Manuela , Vaudano, Anna Elisabetta , Vivash, Lucy , Podewils, Felix von , Wagner, Jan , Weber, Bernd , Wiest, Roland , Yasuda, Clarissa Lin , Zhang, Junsong , Group, ENIGMA‐Epilepsy Working, Leu, Costin , Avberšek, Andreja , Whelan, Christopher D. , Thompson, Paul M. , McDonald, Carrie R. , Di Sapia, Rossella , Bender, Benjamin , Severino, Mariasavina , Thom, Maria , Yasuda, Clarissa L , Doherty, Colin P , Cavalleri, Gianpiero L , Weber, Bernd , Thompson, Paul M , Richardson, Mark P , Guerrini, Renzo , Thomas, Rhys H , Leu, Costin , Tolomeo, Daniele , Micotti, Edoardo , Bargalló, Núria , Carlson, Chad , Cendes, Fernando , Devinsky, Orrin , Focke, Niels K. , Jackson, Graeme D. , Kochunov, Peter V , Kowalczyk, Magdalena A. , Kuzniecky, Ruben , Labate, Angelo , Liu, Min , Mascalchi, Mario , Morita, Márcia Elisabete , O’Brien, Terence J. , Rodríguez‐Cruces, Raúl , Tortora, Domenico , Zhang, Guohao , Group, ENIGMA‐Epilepsy Working, Vezzani, Annamaria , Sisodiya, Sanjay
Neuropathology and Applied Neurobiology | August 13, 2021 | Volume: 48 | Issue: 1 | Pages: No page available
Abstract Aims The causes of distinct patterns of reduced cortical thickness in the common human epilepsies, detectable on neuroimaging and with important clinical consequences, are unknown. We investigated the underlying mechanisms of cortical thinning using a systems‐level analysis. Methods Imaging‐based cortical structural maps from a large‐scale epilepsy neuroimaging study were overlaid with highly spatially resolved human brain gene expression data from the Allen Human Brain Atlas. Cell‐type deconvolution, differential expression analysis and cell‐type enrichment analyses were used to identify differences in cell‐type distribution. These differences were followed up in post‐mortem brain tissue from humans with epilepsy using Iba1 immunolabelling. Furthermore, to investigate a causal effect in cortical thinning, cell‐type‐specific depletion was used in a murine model of acquired epilepsy. Results We identified elevated fractions of microglia and endothelial cells in regions of reduced cortical thickness. Differentially expressed genes showed enrichment for microglial markers and, in particular, activated microglial states. Analysis of post‐mortem brain tissue from humans with epilepsy confirmed excess activated microglia. In the murine model, transient depletion of activated microglia during the early phase of the disease development prevented cortical thinning and neuronal cell loss in the temporal cortex. Although the development of chronic seizures was unaffected, the epileptic mice with early depletion of activated microglia did not develop deficits in a non‐spatial memory test seen in epileptic mice not depleted of microglia. Conclusions These convergent data strongly implicate activated microglia in cortical thinning, representing a new dimension for concern and disease modification in the epilepsies, potentially distinct from seizure control.