Search

Your search keyword '"Schoof, Heiko"' showing total 218 results
Start Over Author "Schoof, Heiko"
218 results on '"Schoof, Heiko"'

2. AFDP: An Automated Function Description Prediction Approach to Improve Accuracy of Protein Function Predictions

Author

Jozashoori, Samaneh, Jozashoori, Amir, and Schoof, Heiko

Subjects
Quantitative Biology - Genomics
Abstract

With the rapid growth in high-throughput biological sequencing technologies and subsequently the amount of produced omics data, it is essential to develop automated methods to annotate the functionality of unknown genes and proteins. There are developed tools such as AHRD applying known proteins characterization to annotate unknown ones. Some other algorithms such as eggNOG apply orthologous groups of proteins to detect the most probable function. However, while the available tools focus on the detection of the most similar characterization, they are not able to generalize and integrate information from multiple homologs while maintaining accuracy. Here, we devise AFDP, an integrated approach for protein function prediction which benefits from the combination of two available tools, AHRD and eggNOG, to predict the functionality of novel proteins and produce more precise human readable descriptions by applying our stCFExt algorithm. StCFExt creates function descriptions applying available manually curated descriptions in swiss-prot. Using a benchmark dataset we show that the annotations predicted by our approach are more accurate than eggNOG and AHRD annotations.

Published
2019

3. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico

Subjects
Human Genome, Networking and Information Technology R&D (NITRD), Genetics, Generic health relevance, Animals, Biofilms, Candida albicans, Drosophila melanogaster, Genome, Bacterial, Genome, Fungal, Humans, Locomotion, Memory, Long-Term, Molecular Sequence Annotation, Pseudomonas aeruginosa, Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

Published
2019

4. ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

Author

Kirschner, Gwendolyn K., Rosignoli, Serena, Guo, Li, Vardanega, Isaia, Imani, Jafargholi, Altmüller, Janine, Milner, Sara G., Balzano, Raffaella, Nagel, Kerstin A., Pflugfelder, Daniel, Forestan, Cristian, Bovina, Riccardo, Koller, Robert, Stöcker, Tyll G., Mascher, Martin, Simmonds, James, Uauy, Cristobal, Schoof, Heiko, Tuberosa, Roberto, Salvi, Silvio, and Hochholdinger, Frank

Published
2021

6. Suberin deficiency and its effect on the transport physiology of young poplar roots

Author

Grünhofer, Paul, primary, Heimerich, Ines, additional, Pohl, Svenja, additional, Oertel, Marlene, additional, Meng, Hongjun, additional, Zi, Lin, additional, Lucignano, Kevin, additional, Bokhari, Syed Nadeem Hussain, additional, Guo, Yayu, additional, Li, Ruili, additional, Lin, Jinxing, additional, Fladung, Matthias, additional, Kreszies, Tino, additional, Stöcker, Tyll, additional, Schoof, Heiko, additional, and Schreiber, Lukas, additional

Published
2024
Full Text
View/download PDF

8. Isolation and characterization of the gene HvFAR1 encoding acyl‐CoA reductase from the cer‐za.227 mutant of barley (Hordeum vulgare) and analysis of the cuticular barrier functions

Author

Müller, Yannic, primary, Patwari, Payal, additional, Stöcker, Tyll, additional, Zeisler‐Diehl, Viktoria, additional, Steiner, Ulrike, additional, Campoli, Chiara, additional, Grewe, Lea, additional, Kuczkowska, Magdalena, additional, Dierig, Maya Marita, additional, Jose, Sarah, additional, Hetherington, Alistair M., additional, Acosta, Ivan F., additional, Schoof, Heiko, additional, Schreiber, Lukas, additional, and Dörmann, Peter, additional

Published
2023
Full Text
View/download PDF

17. Report on the annual joint meeting of the DPG-Working Group "Nematology" and the Working Group "Free Living Nematodes"

Author

Daub, Matthias, Hakl, Ulrike, Rueß, Liliane, Elashry, Abdelnaser, Ahmadinegad, Nahal, Blümel, Roman, Altmüller, Janine, Schoof, Heiko, Grundler, Florian MW, Kiewnick, Sebastian, van Heese, Evelyn, Frey, Jürg E, Hallmann, Johannes, Wolf, Stefanie, Lüth, Peter, Baklawa, Mohamed, Niere, Björn, Heuer, Holger, Massoud, Samia, Gutbrod, Philipp, Siddique, Shahid, vom Dorp, Katharina, Wever, Vera, Dörmann, Peter, Grundler, Florian, Preiß, Uwe, Augustin, Bernd, and Sturhan, Dieter

Published
2012

20. Legume Genome Evolution Viewed through the Medicago truncatula and Lotus japonicus Genomes

Author

Cannon, Steven B., Sterck, Lieven, Rombauts, Stephane, Sato, Shusei, Cheung, Foo, Gouzy, Jérôme, Wang, Xiaohong, Mudge, Joann, Vasdewani, Jayprakash, Scheix, Thomas, Spannagl, Manuel, Monaghan, Erin, Nicholson, Christine, Humphray, Sean J., Schoof, Heiko, Mayer, Klaus F. X., Rogers, Jane, Quétier, Francis, Oldroyd, Giles E., Debellé, Frédéric, Cook, Douglas R., Retzel, Ernest F., Roe, Bruce A., Town, Christopher D., Tabata, Satoshi, van de Peer, Yves, and Young, Nevin D.

Published
2006
Full Text
View/download PDF

22. ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF-containing protein that controls root growth angle in barley and wheat

Author

Kirschner, K. Gwendolyn, Rosignoli, Serena, Guo, Li, Vardanega, Isaia, Imani, Jafargholi, Altmueller, Janine, Milner, G. Sara, Balzano, Raffaella, Nagel, A. Kerstin, Pflugfelder, Daniel, Forestan, Cristian, Bovina, Riccardo, Koller, Robert, Stoecker, G. Tyll, Mascher, Martin, Simmonds, James, Uauy, Cristobal, Schoof, Heiko, Tuberosa, Roberto, Salvi, Silvio, Hochholdinger, Frank, Kirschner, K. Gwendolyn, Rosignoli, Serena, Guo, Li, Vardanega, Isaia, Imani, Jafargholi, Altmueller, Janine, Milner, G. Sara, Balzano, Raffaella, Nagel, A. Kerstin, Pflugfelder, Daniel, Forestan, Cristian, Bovina, Riccardo, Koller, Robert, Stoecker, G. Tyll, Mascher, Martin, Simmonds, James, Uauy, Cristobal, Schoof, Heiko, Tuberosa, Roberto, Salvi, Silvio, and Hochholdinger, Frank

Abstract

The root growth angle defines how roots grow toward the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience, and, as a consequence, yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin-independent higher responsiveness to gravity compared to wild-type plants. We cloned the EGT2 gene by a combination of bulked-segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain-containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA sequencing, we observed that seven expansin genes were transcriptionally down-regulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals.

Published
2021

23. PEP1 regulates perennial flowering in Arabis alpina

Author

Wang, Renhou, Farrona, Sara, Vincent, Coral, Joecker, Anika, Schoof, Heiko, Turck, Franziska, Alonso-Blanco, Carlos, Coupland, George, and Albani, Maria C.

Subjects
Flowering trees -- Research, Perennials -- Research, Plant physiological ecology -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Research
Abstract

Annual plants complete their life cycle in one year and initiate flowering only once, whereas perennials live for many years and flower repeatedly. How perennials undergo repeated cycles of vegetative [...]

Published
2009

28. ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIVE containing protein that controls root growth angle in barley and wheat

Author

Kirschner, Gwendolyn K., primary, Rosignoli, Serena, additional, Vardanega, Isaia, additional, Guo, Li, additional, Imani, Jafargholi, additional, Altmüller, Janine, additional, Milner, Sara G., additional, Balzano, Raffaella, additional, Nagel, Kerstin A., additional, Pflugfelder, Daniel, additional, Forestan, Cristian, additional, Bovina, Riccardo, additional, Koller, Robert, additional, Stöcker, Tyll G., additional, Mascher, Martin, additional, Simmonds, James, additional, Uauy, Cristobal, additional, Schoof, Heiko, additional, Tuberosa, Roberto, additional, Salvi, Silvio, additional, and Hochholdinger, Frank, additional

Published
2021
Full Text
View/download PDF

32. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
Full Text
View/download PDF

33. The Medicago genome provides insight into the evolution of rhizobial symbioses

Author

Young, Nevin D., Debellé, Frédéric, Oldroyd, Giles E. D., Geurts, Rene, Cannon, Steven B., Udvardi, Michael K., Benedito, Vagner A., Mayer, Klaus F. X., Gouzy, Jérôme, Schoof, Heiko, Van de Peer, Yves, Proost, Sebastian, Cook, Douglas R., Meyers, Blake C., Spannagl, Manuel, Cheung, Foo, De Mita, Stéphane, Krishnakumar, Vivek, Gundlach, Heidrun, Zhou, Shiguo, Mudge, Joann, Bharti, Arvind K., Murray, Jeremy D., Naoumkina, Marina A., Rosen, Benjamin, Silverstein, Kevin A. T., Tang, Haibao, Rombauts, Stephane, Zhao, Patrick X., Zhou, Peng, Barbe, Valérie, Bardou, Philippe, Bechner, Michael, Bellec, Arnaud, Berger, Anne, Bergès, Hélène, Bidwell, Shelby, Bisseling, Ton, Choisne, Nathalie, Couloux, Arnaud, Denny, Roxanne, Deshpande, Shweta, Dai, Xinbin, Doyle, Jeff J., Dudez, Anne-Marie, Farmer, Andrew D., Fouteau, Stéphanie, Franken, Carolien, Gibelin, Chrystel, Gish, John, Goldstein, Steven, González, Alvaro J., Green, Pamela J., Hallab, Asis, Hartog, Marijke, Hua, Axin, Humphray, Sean J., Jeong, Dong-Hoon, Jing, Yi, Jöcker, Anika, Kenton, Steve M., Kim, Dong-Jin, Klee, Kathrin, Lai, Hongshing, Lang, Chunting, Lin, Shaoping, Macmil, Simone L., Magdelenat, Ghislaine, Matthews, Lucy, McCorrison, Jamison, Monaghan, Erin L., Mun, Jeong-Hwan, Najar, Fares Z., Nicholson, Christine, Noirot, Céline, O’Bleness, Majesta, Paule, Charles R., Poulain, Julie, Prion, Florent, Qin, Baifang, Qu, Chunmei, Retzel, Ernest F., Riddle, Claire, Sallet, Erika, Samain, Sylvie, Samson, Nicolas, Sanders, Iryna, Saurat, Olivier, Scarpelli, Claude, Schiex, Thomas, Segurens, Béatrice, Severin, Andrew J., Sherrier, Janine D., Shi, Ruihua, Sims, Sarah, Singer, Susan R., Sinharoy, Senjuti, Sterck, Lieven, Viollet, Agnès, Wang, Bing-Bing, Wang, Keqin, Wang, Mingyi, Wang, Xiaohong, Warfsmann, Jens, Weissenbach, Jean, White, Doug D., White, Jim D., Wiley, Graham B., Wincker, Patrick, Xing, Yanbo, Yang, Limei, Yao, Ziyun, Ying, Fu, Zhai, Jixian, Zhou, Liping, Zuber, Antoine, Dénarié, Jean, Dixon, Richard A., May, Gregory D., Schwartz, David C., Rogers, Jane, Quétier, Francis, Town, Christopher D., and Roe, Bruce A.

Published
2011
Full Text
View/download PDF

34. BonnMu: A Sequence-Indexed Resource of Transposon-Induced Maize Mutations for Functional Genomics Studies

Author

Marcon, Caroline, primary, Altrogge, Lena, additional, Win, Yan Naing, additional, Stöcker, Tyll, additional, Gardiner, Jack M., additional, Portwood, John L., additional, Opitz, Nina, additional, Kortz, Annika, additional, Baldauf, Jutta A., additional, Hunter, Charles T., additional, McCarty, Donald R., additional, Koch, Karen E., additional, Schoof, Heiko, additional, and Hochholdinger, Frank, additional

Published
2020
Full Text
View/download PDF

37. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes

Author

Schoof, Heiko, Lenhard, Michael, Haecker, Achim, Mayer, Klaus F.X., Jurgens, Gerd, and Laux, Thomas

Subjects
Meristem -- Genetic aspects, Genetic regulation -- Research, Biological sciences
Abstract

Two gene groups form a feedback loop in the meristem of Arabidopsis. The CLAVATA1, 2, and 3 (CLV) genes inhibit the WUS gene, which induces meristem cell identity and expression of CLV3.

Published
2000

39. MOESM2 of The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Naihui Zhou, Yuxiang Jiang, Bergquist, Timothy, Lee, Alexandra, Balint Kacsoh, Crocker, Alex, Lewis, Kimberley, Georghiou, George, Nguyen, Huy, Md Nafiz Hamid, Davis, Larry, Tunca Dogan, Atalay, Volkan, Rifaioglu, Ahmet, Dalkıran, Alperen, Rengul Cetin Atalay, Chengxin Zhang, Hurto, Rebecca, Freddolino, Peter, Zhang, Yang, Prajwal Bhat, Supek, Fran, Fernández, José, Gemovic, Branislava, Perovic, Vladimir, Davidović, Radoslav, Sumonja, Neven, Veljkovic, Nevena, Ehsaneddin Asgari, Mofrad, Mohammad, Profiti, Giuseppe, Castrense Savojardo, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Indika Kahanda, Thurlby, Natalie, McHardy, Alice, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex, Antczak, Magdalena, Fabris, Fabio, Wass, Mark, Hou, Jie, Jianlin Cheng, Wang, Zheng, Romero, Alfonso, Paccanaro, Alberto, Haixuan Yang, Goldberg, Tatyana, Chenguang Zhao, Holm, Liisa, Törönen, Petri, Medlar, Alan, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Po-Han Chi, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter, Dessimoz, Christophe, Vidulin, Vedrana, Saso Dzeroski, Sillitoe, Ian, Sayoni Das, Lees, Jonathan Gill, Jones, David, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Vesztrocy, Alex Warwick, Rodriguez, Jose Manuel, Tress, Michael, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel, Reeb, Jonas, Ritchie, David, Sabeur Aridhi, Alborzi, Seyed Ziaeddin, Marie-Dominique Devignes, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Meet Barot, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio, Carraro, Marco, Piovesan, Damiano, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Vucetic, Slobodan, Black, Gage, Jo, Dane, Suh, Erica, Dayton, Jonathan, Larsen, Dallas, Omdahl, Ashton, McGuffin, Liam, Brackenridge, Danielle, Babbitt, Patricia, Yunes, Jeffrey, Fontana, Paolo, Zhang, Feng, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Wen-Hung Liao, Liu, Yi-Wei, Pascarelli, Stefano, Yotam Frank, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Carlo, Stefano Di, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Suwisa Kaewphan, Björne, Jari, Moen, Hans, Tolvanen, Martti, Salakoski, Tapio, Kihara, Daisuke, Aashish Jain, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven, Orengo, Christine, Jeffery, Constance, Bosco, Giovanni, Hogan, Deborah, Martin, Maria, O’Donovan, Claire, Mooney, Sean, Greene, Casey, Radivojac, Predrag, and Friedberg, Iddo

Subjects
Pharmacology, FOS: Biological sciences, Genetics, Molecular Biology, 69999 Biological Sciences not elsewhere classified, Developmental Biology
Abstract

Additional file 2 Review History.

Published
2019
Full Text
View/download PDF

47. Structural insights into the function of the core-circadian factor TIMING OF CAB2 EXPRESSION 1 (TOC1)

Author

Plümer Michael, Schoof Heiko, Kolmos Elsebeth, and Davis Seth J

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background The plant circadian clock has at its core a feedback loop that includes TIMING OF CAB2 EXPRESSION 1 (TOC1). This protein has an as of yet unknown biochemical activity. It has been noted that the extreme amino-terminus of this protein is distantly related in sequence to response regulators (RR), and thus TOC1 is a member of the so-called pseudo response regulator (PRR) family. As well, the extreme carboxy-terminus has a small sequence stretch related to the other PRRs and CONSTANS (CO)-like proteins, and this peptide stretch has been termed the CCT (for CONSTANS, CONSTANS-LIKE, TOC1) domain. Methods To extend further our understanding of the TOC1 protein, we performed a ROSETTA structural prediction on TOC1 orthologues from four plant species. Phylogenetic interpretations assisted in model construction. Results From our models, we suggest that TOC1 is a three-domain protein: TOC1 has an amino-terminal signaling-domain related to response receivers, a carboxy-terminal domain that could participate both in metal binding and in transcriptional regulation, and a linker domain that connects the two. Conclusion The models we present should prove useful in future hypothesis-driven biochemical analyses to test the predictions that TOC1 is a multi-domain signaling component of the plant circadian clock.

Published
2008
Full Text
View/download PDF

48. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

Author

Bruggmann Rémy, Meksem Khalid, Paal Jürgen, Ishihara Hirofumi, Viehöver Prisca, Jöcker Anika, Ballvora Agim, Schoof Heiko, Weisshaar Bernd, and Gebhardt Christiane

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.

Published
2007
Full Text
View/download PDF

49. Charting Small RNA Landscape – an Exciting Journey in the Postgenomic Era

Author

Schoof, Heiko (Prof. Dr.), Mewes, Hans-Werner (Prof. Dr.), Wang, Yu, Schoof, Heiko (Prof. Dr.), Mewes, Hans-Werner (Prof. Dr.), and Wang, Yu

Abstract

This thesis focuses on small regulatory RNAs, which include microRNA (miRNA) and small interfering RNA (siRNA). Using computational methods, I investigated not only the biogenesis of small RNAs, but also the regulatory roles of them. The work covered miRNA gene identification, miRNA promoter analysis, viral small interfering RNA (vsRNA) population analysis and miRNA target interactions. The model organisms studied in this thesis are Arabidopsis thaliana, Sorghum bicolor, 9 plant viruses and Homo sapiens. The phylogenetic heterogeneity of these organisms suggests wide spread regulatory roles of small RNAs in various formats of life., In dieser Doktorarbeit wurden kleine regulatorische RNA-Moleküle, insbesondere sogenannte Mikro-RNAs (miRNAs) und kleine interferierende RNAs (siRNAs) bearbeitet. Unter Verwendung computer-gestützter Analysen evaluierte ich neben der Biogenese auch die regulatorischen Rollen kleiner RNAs. Die Studien umfassen die Identifizierung von miRNA Genen und deren Promoteranalysen, die Untersuchung viraler siRNA-Populationen sowie die Interaktionen von miRNAs mit Zielgenen. Die in dieser Arbeit untersuchten Arten umfassen die Ackerschmalwand (Arabidopsis thaliana), die Hirse (Sorghum bicolor), 9 Pflanzenviren und den Menschen (Homo sapiens). Die grosse phylogenetische Vielfalt, die die untersuchten Organismen abdecken, unterstreicht die Bedeutung und weite Verbreitung kleiner RNA-Moleküle und deren regulatorischen Wirkungen.

Published
2018

50. Charting Small RNA Landscape – an Exciting Journey in the Postgenomic Era

Author

Mewes, Hans-Werner (Prof. Dr.), Schoof, Heiko (Prof. Dr.), Wang, Yu, Mewes, Hans-Werner (Prof. Dr.), Schoof, Heiko (Prof. Dr.), and Wang, Yu

Abstract

This thesis focuses on small regulatory RNAs, which include microRNA (miRNA) and small interfering RNA (siRNA). Using computational methods, I investigated not only the biogenesis of small RNAs, but also the regulatory roles of them. The work covered miRNA gene identification, miRNA promoter analysis, viral small interfering RNA (vsRNA) population analysis and miRNA target interactions. The model organisms studied in this thesis are Arabidopsis thaliana, Sorghum bicolor, 9 plant viruses and Homo sapiens. The phylogenetic heterogeneity of these organisms suggests wide spread regulatory roles of small RNAs in various formats of life., In dieser Doktorarbeit wurden kleine regulatorische RNA-Moleküle, insbesondere sogenannte Mikro-RNAs (miRNAs) und kleine interferierende RNAs (siRNAs) bearbeitet. Unter Verwendung computer-gestützter Analysen evaluierte ich neben der Biogenese auch die regulatorischen Rollen kleiner RNAs. Die Studien umfassen die Identifizierung von miRNA Genen und deren Promoteranalysen, die Untersuchung viraler siRNA-Populationen sowie die Interaktionen von miRNAs mit Zielgenen. Die in dieser Arbeit untersuchten Arten umfassen die Ackerschmalwand (Arabidopsis thaliana), die Hirse (Sorghum bicolor), 9 Pflanzenviren und den Menschen (Homo sapiens). Die grosse phylogenetische Vielfalt, die die untersuchten Organismen abdecken, unterstreicht die Bedeutung und weite Verbreitung kleiner RNA-Moleküle und deren regulatorischen Wirkungen.

Published
2018

Catalog

Books, media, physical & digital resources
See catalog results