Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Jonas Reeb"'
Autor:
Bridget Riley-Gillis, Shirng-Wern Tsaih, Emily King, Sabrina Wollenhaupt, Jonas Reeb, Amy R. Peck, Kelsey Wackman, Angela Lemke, Hallgeir Rui, Zoltan Dezso, Michael J. Flister
Publikováno v:
iScience, Vol 26, Iss 9, Pp 107576- (2023)
Summary: Heritability in the immune tumor microenvironment (iTME) has been widely observed yet remains largely uncharacterized. Here, we developed a machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWA
Externí odkaz:
https://doaj.org/article/c7ce89221a684130966eeb85e931f3cc
Autor:
Ammar J. Alsheikh, Sabrina Wollenhaupt, Emily A. King, Jonas Reeb, Sujana Ghosh, Lindsay R. Stolzenburg, Saleh Tamim, Jozef Lazar, J. Wade Davis, Howard J. Jacob
Publikováno v:
BMC Medical Genomics, Vol 15, Iss 1, Pp 1-21 (2022)
Abstract Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field i
Externí odkaz:
https://doaj.org/article/d0874d4b110e421f9c22bf448f29db52
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-12 (2020)
Abstract Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, o
Externí odkaz:
https://doaj.org/article/e858d1c25c13471d9826ad7d7b40a1e7
Autor:
Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third C
Externí odkaz:
https://doaj.org/article/4c2b017b155b41ceab8d6d078186cafa
Autor:
Yannick Mahlich, Jonas Reeb, Maximilian Hecht, Maria Schelling, Tjaart Andries Petrus De Beer, Yana Bromberg, Burkhard Rost
Publikováno v:
Scientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
Abstract Any two unrelated individuals differ by about 10,000 single amino acid variants (SAVs). Do these impact molecular function? Experimental answers cannot answer comprehensively, while state-of-the-art prediction methods can. We predicted the f
Externí odkaz:
https://doaj.org/article/66cc665838b94fa7aa47fd0e62cc4786
Publikováno v:
PLoS Computational Biology, Vol 12, Iss 8, p e1005047 (2016)
Developments in experimental and computational biology are advancing our understanding of how protein sequence variation impacts molecular protein function. However, the leap from the micro level of molecular function to the macro level of the whole
Externí odkaz:
https://doaj.org/article/a8a411431af84254afaeb06639d38704
Autor:
Bridget Riley-Gillis, Shirng-Wern Tsaih, Emily King, Sabrina Wollenhaupt, Jonas Reeb, Amy R. Peck, Kelsey Wackman, Angela Lemke, Hallgeir Rui, Zoltan Dezso, Michael J. Flister
Heritability in the immune tumor microenvironment (iTME) has been widely observed, yet remains largely uncharacterized and systematic approaches to discover germline genetic modifiers of the iTME still being established. Here, we developed the first
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d7c5b9d1dd4eca3be6cbba5e84ce976a
https://doi.org/10.1101/2022.12.13.520300
https://doi.org/10.1101/2022.12.13.520300
Autor:
Ammar J. Alsheikh, Sabrina Wollenhaupt, Emily A. King, Jonas Reeb, Sujana Ghosh, Lindsay R. Stolzenburg, Saleh Tamim, Jozef Lazar, J. Wade Davis, Howard J. Jacob
Publikováno v:
BMC medical genomics. 15(1)
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is address
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-12 (2020)
BMC Bioinformatics
BMC Bioinformatics
Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-syn
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8bb22056f641ca8cce71d7b3a402a65b
https://doi.org/10.1101/859603
https://doi.org/10.1101/859603
Autor:
Renzhi Cao, Alice C. McHardy, Cen Wan, Jonathan G. Lees, Vedrana Vidulin, Alex Warwick Vesztrocy, Huy N Nguyen, Devon Johnson, Ian Sillitoe, Alessandro Petrini, Richard Bonneau, Hans Moen, Peter L. Freddolino, Rui Fa, Alfredo Benso, Jianlin Cheng, Indika Kahanda, Qizhong Mao, Zihan Zhang, Chenguang Zhao, Rebecca L. Hurto, Predrag Radivojac, Stefano Di Carlo, Sayoni Das, Suwisa Kaewphan, Sabeur Aridhi, Alan Medlar, Casey S. Greene, Constance J. Jeffery, Christophe Dessimoz, Jose Manuel Rodriguez, Gianfranco Politano, Michele Berselli, Jia-Ming Chang, Deborah A. Hogan, Julian Gough, Tunca Doğan, David T. Jones, Claire O'Donovan, Volkan Atalay, Paolo Fontana, Feng Zhang, Shuwei Yao, Robert Hoehndorf, Olivier Lichtarge, Alex W. Crocker, Ahmet Sureyya Rifaioglu, Rabie Saidi, Farrokh Mehryary, Neven Sumonja, Yang Zhang, Florian Boecker, Jie Hou, Christine A. Orengo, Matteo Re, Natalie Thurlby, Chengxin Zhang, Stefano Pascarelli, Alberto Paccanaro, Hafeez Ur Rehman, Yuxiang Jiang, Mohammad R. K. Mofrad, Naihui Zhou, Asa Ben-Hur, Steven E. Brenner, Martti Tolvanen, Filip Ginter, Mark N. Wass, Patricia C. Babbitt, David W. Ritchie, George Georghiou, Stefano Toppo, Caleb Chandler, Larry Davis, Da Chen Emily Koo, Itamar Borukhov, Petri Törönen, Rengul Cetin-Atalay, Fabio Fabris, Haixuan Yang, Kai Hakala, Silvio C. E. Tosatto, Domenico Cozzetto, Slobodan Vucetic, Balint Z. Kacsoh, Luke W Sagers, Alex A. Freitas, Tapio Salakoski, Fran Supek, Alfonso E. Romero, Angela D. Wilkins, Elaine Zosa, Shanshan Zhang, Yotam Frank, Jonathan B. Dayton, Jeffrey M. Yunes, Pier Luigi Martelli, Dallas J. Larsen, Giuliano Grossi, Alexandra J. Lee, Marco Mesiti, Yi-Wei Liu, Jonas Reeb, Damiano Piovesan, Sean D. Mooney, Magdalena Antczak, Erica Suh, Marco Falda, Marie-Dominique Devignes, Castrense Savojardo, Zheng Wang, Danielle A Brackenridge, Peter W. Rose, Enrico Lavezzo, Dane Jo, Ronghui You, Tomislav Šmuc, Liam J. McGuffin, Michael L. Tress, Ilya Novikov, Adrian M. Altenhoff, Burkhard Rost, Miguel Amezola, Mateo Torres, Prajwal Bhat, Wen-Hung Liao, Meet Barot, Marco Notaro, Suyang Dai, Giorgio Valentini, Jari Björne, Nevena Veljkovic, Wei-Cheng Tseng, Po-Han Chi, Alperen Dalkiran, Maxat Kulmanov, Nafiz Hamid, Aashish Jain, Branislava Gemovic, Alexandre Renaux, Ashton Omdahl, Daniel B. Roche, Vladimir Perovic, Iddo Friedberg, Daisuke Kihara, Giovanni Bosco, Gage S. Black, Saso Dzeroski, Liisa Holm, Marco Frasca, Michal Linial, Ehsaneddin Asgari, Tatyana Goldberg, Maria Jesus Martin, Vladimir Gligorijević, Marco Carraro, Shanfeng Zhu, Radoslav Davidovic, Timothy Bergquist, Hai Fang, José M. Fernández, Giuseppe Profiti, Weidong Tian, Imane Boudellioua, Kimberley A. Lewis, Seyed Ziaeddin Alborzi, Rita Casadio
The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that fe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4041959032930476de14481a887bcd78