Search

Your search keyword '"Ramilowski, Jordan A."' showing total 146 results
Start Over Author "Ramilowski, Jordan A."
146 results on '"Ramilowski, Jordan A."'

2. Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting

Author

Aizawa, Yoshihiro, Takada, Kentaro, Aoyama, Jun, Sano, Daisuke, Yamanaka, Shoji, Seki, Masahide, Kuze, Yuta, Ramilowski, Jordan A., Okuda, Ryo, Ueno, Yasuharu, Nojima, Yusuke, Inayama, Yoshiaki, Hatakeyama, Hiromitsu, Hatano, Takashi, Takahashi, Hideaki, Nishimura, Goshi, Fujii, Satoshi, Suzuki, Yutaka, Taniguchi, Hideki, and Oridate, Nobuhiko

Published
2023
Full Text
View/download PDF

3. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Author

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A, Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C, FANTOM consortium, Chatelain, Clément, Carninci, Piero, de Hoon, Michiel JL, Wasserman, Wyeth W, Bréhélin, Laurent, and Lecellier, Charles-Henri

Subjects
FANTOM consortium, Animals, Humans, Mice, Neurodegenerative Diseases, Computational Biology, Base Sequence, Microsatellite Repeats, Polymorphism, Genetic, Genome, Human, Transcription Initiation Site, Enhancer Elements, Genetic, Promoter Regions, Genetic, High-Throughput Nucleotide Sequencing, Transcription Initiation, Genetic, A549 Cells, Deep Learning, Neural Networks, Computer, Clinical Research, Human Genome, Genetics, Generic health relevance
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

Published
2021

4. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Author

Yip, Chi Wai, Hon, Chung-Chau, Yasuzawa, Kayoko, Sivaraman, Divya M., Ramilowski, Jordan A., Shibayama, Youtaro, Agrawal, Saumya, Prabhu, Anika V., Parr, Callum, Severin, Jessica, Lan, Yan Jun, Dostie, Josée, Petri, Andreas, Nishiyori-Sueki, Hiromi, Tagami, Michihira, Itoh, Masayoshi, López-Redondo, Fernando, Kouno, Tsukasa, Chang, Jen-Chien, Luginbühl, Joachim, Kato, Masaki, Murata, Mitsuyoshi, Yip, Wing Hin, Shu, Xufeng, Abugessaisa, Imad, Hasegawa, Akira, Suzuki, Harukazu, Kauppinen, Sakari, Yagi, Ken, Okazaki, Yasushi, Kasukawa, Takeya, de Hoon, Michiel, Carninci, Piero, and Shin, Jay W.

Published
2022
Full Text
View/download PDF

5. Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers

Author

Jikuya, Ryosuke, Murakami, Koichi, Nishiyama, Akira, Kato, Ikuma, Furuya, Mitsuko, Nakabayashi, Jun, Ramilowski, Jordan A., Hamanoue, Haruka, Maejima, Kazuhiro, Fujita, Masashi, Mitome, Taku, Ohtake, Shinji, Noguchi, Go, Kawaura, Sachi, Odaka, Hisakazu, Kawahara, Takashi, Komeya, Mitsuru, Shinoki, Risa, Ueno, Daiki, Ito, Hiroki, Ito, Yusuke, Muraoka, Kentaro, Hayashi, Narihiko, Kondo, Keiichi, Nakaigawa, Noboru, Hatano, Koji, Baba, Masaya, Suda, Toshio, Kodama, Tatsuhiko, Fujii, Satoshi, Makiyama, Kazuhide, Yao, Masahiro, Shuch, Brian M., Schmidt, Laura S., Linehan, W. Marston, Nakagawa, Hidewaki, Tamura, Tomohiko, and Hasumi, Hisashi

Published
2022
Full Text
View/download PDF

6. Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Chatelain, Clément, Carninci, Piero, de Hoon, Michiel J. L., Wasserman, Wyeth W., Bréhélin, Laurent, and Lecellier, Charles-Henri

Published
2022
Full Text
View/download PDF

7. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Author

Lizio, Marina, Harshbarger, Jayson, Abugessaisa, Imad, Noguchi, Shuei, Kondo, Atsushi, Severin, Jessica, Mungall, Chris, Arenillas, David, Mathelier, Anthony, Medvedeva, Yulia A, Lennartsson, Andreas, Drabløs, Finn, Ramilowski, Jordan A, Rackham, Owen, Gough, Julian, Andersson, Robin, Sandelin, Albin, Ienasescu, Hans, Ono, Hiromasa, Bono, Hidemasa, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair RR, Kasukawa, Takeya, and Kawaji, Hideya

Subjects
Genetics, Generic health relevance, Animals, Computational Biology, Databases, Genetic, Gene Expression Profiling, Genomics, Humans, Mammals, Search Engine, Software, Web Browser, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

Published
2017

8. Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia

Author

Hashimoto, Mari, Saito, Yoriko, Nakagawa, Ryo, Ogahara, Ikuko, Takagi, Shinsuke, Takata, Sadaaki, Amitani, Hanae, Endo, Mikiko, Yuki, Hitomi, Ramilowski, Jordan A., Severin, Jessica, Manabe, Ri-ichiroh, Watanabe, Takashi, Ozaki, Kokoro, Kaneko, Akiko, Kajita, Hiroshi, Fujiki, Saera, Sato, Kaori, Honma, Teruki, Uchida, Naoyuki, Fukami, Takehiro, Okazaki, Yasushi, Ohara, Osamu, Shultz, Leonard D., Yamada, Makoto, Taniguchi, Shuichi, Vyas, Paresh, de Hoon, Michiel, Momozawa, Yukihide, and Ishikawa, Fumihiko

Published
2021
Full Text
View/download PDF

9. Annotation of nuclear lncRNAs based on chromatin interactions.

Author

Agrawal, Saumya, Buyan, Andrey, Severin, Jessica, Koido, Masaru, Alam, Tanvir, Abugessaisa, Imad, Chang, Howard Y., Dostie, Josée, Itoh, Masayoshi, Kere, Juha, Kondo, Naoto, Li, Yunjing, Makeev, Vsevolod J., Mendez, Mickaël, Okazaki, Yasushi, Ramilowski, Jordan A., Sigorskikh, Andrey I., Strug, Lisa J., Yagi, Ken, and Yasuzawa, Kayoko

Subjects
RNA-protein interactions, LINCRNA, CHROMATIN, GENE enhancers, WEB portals, HUMAN genome
Abstract

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

12. Fractal Weyl law behavior in an open, chaotic Hamiltonian system

Author

Ramilowski, Jordan A., Prado, S. D., Borondo, F., and Farrelly, David

Subjects
Quantum Physics, Nonlinear Sciences - Chaotic Dynamics
Abstract

We numerically show fractal Weyl law behavior in an open Hamiltonian system that is described by a smooth potential and which supports numerous above-barrier resonances. This behavior holds even relatively far away from the classical limit. The complex resonance wave functions are found to be localized on the fractal classical repeller., Comment: 4 pages, 3 figures. to appear in Phys Rev E

Published
2009
Full Text
View/download PDF

16. Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting

Author

Aizawa, Yoshihiro, primary, Takada, Kentaro, additional, Aoyama, Jun, additional, Sano, Daisuke, additional, Yamanaka, Shoji, additional, Seki, Masahide, additional, Kuze, Yuta, additional, Ramilowski, Jordan A., additional, Okuda, Ryo, additional, Ueno, Yasuharu, additional, Nojima, Yusuke, additional, Inayama, Yoshiaki, additional, Hatakeyama, Hiromitsu, additional, Hatano, Takashi, additional, Takahashi, Hideaki, additional, Nishimura, Goshi, additional, Fujii, Satoshi, additional, Suzuki, Yutaka, additional, Taniguchi, Hideki, additional, and Oridate, Nobuhiko, additional

Published
2022
Full Text
View/download PDF

17. Experimental models of salivary gland cancer established using organoid culture and patient-derived xenografting

Author

Aizawa, Yoshihiro, primary, Takada, Kentaro, additional, Aoyama, Jun, additional, Sano, Daisuke, additional, Yamanaka, Shoji, additional, Seki, Masahide, additional, Kuze, Yuta, additional, Ramilowski, Jordan, additional, Okuda, Ryo, additional, Ueno, Yasuharu, additional, Nojima, Yusuke, additional, Inayama, Yoshiaki, additional, Hatakeyama, Hiromitsu, additional, Hatano, Takashi, additional, Takahashi, Hideaki, additional, Nishimura, Goshi, additional, Fujii, Satoshi, additional, Suzuki, Yutaka, additional, Taniguchi, Hideki, additional, and Oridate, Nobuhiko, additional

Published
2022
Full Text
View/download PDF

18. An atlas of human long non-coding RNAs with accurate 5′ ends

Author

Hon, Chung-Chau, Ramilowski, Jordan A., Harshbarger, Jayson, Bertin, Nicolas, Rackham, Owen J. L., Gough, Julian, Denisenko, Elena, Schmeier, Sebastian, Poulsen, Thomas M., Severin, Jessica, Lizio, Marina, Kawaji, Hideya, Kasukawa, Takeya, Itoh, Masayoshi, Burroughs, Maxwell A., Noma, Shohei, Djebali, Sarah, Alam, Tanvir, Medvedeva, Yulia A., Testa, Alison C., Lipovich, Leonard, Yip, Chi-Wai, Abugessaisa, Imad, Mendez, Mickaël, Hasegawa, Akira, Tang, Dave, Lassmann, Timo, Heutink, Peter, Babina, Magda, Wells, Christine A., Kojima, Soichi, Nakamura, Yukio, Suzuki, Harukazu, Daub, Carsten O., de Hoon, Michiel J. L., Arner, Erik, Hayashizaki, Yoshihide, Carninci, Piero, and Forrest, Alistair R. R.

Published
2017
Full Text
View/download PDF

19. Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Author

Yip, Chi Wai, primary, Hon, Chung-Chau, additional, Yasuzawa, Kayoko, additional, Sivaraman, Divya M., additional, Ramilowski, Jordan A., additional, Shibayama, Youtaro, additional, Agrawal, Saumya, additional, Prabhu, Anika V., additional, Parr, Callum, additional, Severin, Jessica, additional, Lan, Yan Jun, additional, Dostie, Josée, additional, Petri, Andreas, additional, Nishiyori-Sueki, Hiromi, additional, Tagami, Michihira, additional, Itoh, Masayoshi, additional, López-Redondo, Fernando, additional, Kouno, Tsukasa, additional, Chang, Jen-Chien, additional, Luginbühl, Joachim, additional, Kato, Masaki, additional, Murata, Mitsuyoshi, additional, Yip, Wing Hin, additional, Shu, Xufeng, additional, Abugessaisa, Imad, additional, Hasegawa, Akira, additional, Suzuki, Harukazu, additional, Kauppinen, Sakari, additional, Yagi, Ken, additional, Okazaki, Yasushi, additional, Kasukawa, Takeya, additional, de Hoon, Michiel, additional, Carninci, Piero, additional, and Shin, Jay W., additional

Published
2022
Full Text
View/download PDF

20. Single-Cell Transcriptomes of Hereditary Kidney Cancers Underscore Genetically Defined Tumor Characteristics and Microenvironment

Author

Jikuya, Ryosuke, primary, Murakami, Koichi, additional, Nishiyama, Akira, additional, Kato, Ikuma, additional, Furuya, Mitsuko, additional, Nakabayashi, Jun, additional, Ramilowski, Jordan A., additional, Hamanoue, Haruka, additional, Maejima, Kazuhiro, additional, Fujita, Masashi, additional, Mitome, Taku, additional, Ohtake, Shinji, additional, Noguchi, Go, additional, Kawaura, Sachi, additional, Odaka, Hisakazu, additional, Kawahara, Takashi, additional, Komeya, Mitsuru, additional, Shinoki, Risa, additional, Ueno, Daiki, additional, Ito, Hiroki, additional, Ito, Yusuke, additional, Muraoka, Kentaro, additional, Hayashi, Narihiko, additional, Kondo, Keiichi, additional, Nakaigawa, Noboru, additional, Hatano, Koji, additional, Baba, Masaya, additional, Suda, Toshio, additional, Kodama, Tatsuhiko, additional, Fujii, Satoshi, additional, Nakagawa, Hidewaki, additional, Tamura, Tomohiko, additional, Makiyama, Kazuhide, additional, Yao, Masahiro, additional, Shuch, Brian M., additional, Schmidt, Laura S., additional, Linehan, W. Marston, additional, and Hasumi, Hisashi, additional

Published
2022
Full Text
View/download PDF

21. Novel Preclinical Human Salivary Gland Cancer Models Established Using Organoid Culture And Patient-Derived Xenografting

Author

Aizawa, Yoshihiro, primary, Takada, Kentaro, additional, Aoyama, Jun, additional, Sano, Daisuke, additional, Yamanaka, Shoji, additional, Seki, Masahide, additional, Kuze, Yuta, additional, Ramilowski, Jordan, additional, Okuda, Ryo, additional, Ueno, Yasuharu, additional, Nojima, Yusuke, additional, Inayama, Yoshiaki, additional, Hatakeyama, Hiromitsu, additional, Hatano, Takashi, additional, Takahashi, Hideaki, additional, Nishimura, Goshi, additional, Fujii, Satoshi, additional, Suzuki, Yutaka, additional, Taniguchi, Hideki, additional, and Oridate, Nobuhiko, additional

Published
2021
Full Text
View/download PDF

23. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
Full Text
View/download PDF

24. Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F., Parkinson, Nicholas J., Petri, Andreas, Roos, Leonie, Severin, Jessica, Yasuzawa, Kayoko, Abugessaisa, Imad, Akalin, Altuna, Antonov, Ivan V., Arner, Erik, Bonetti, Alessandro, Bono, Hidemasa, Borsari, Beatrice, Brombacher, Frank, Cameron, Christopher J.F., Cannistraci, Carlo V., Cardenas, Ryan, Cardon, Melissa, Chang, Howard, Dostie, Josée, Ducoli, Luca, Favorov, Alexander V., Fort, Alexandre, Garrido, Diego, Gil, Noa, Gimenez, Juliette, Guler, Reto, Handoko, Lusy, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Kosuke, Hayatsu, Norihito, Heutink, Peter, Hirose, Tetsuro, Imada, Eddie L., Itoh, Masayoshi, Kaczkowski, Bogumil, Kanhere, Aditi S., Kawabata, Emily, Kawaji, Hideya, Kawashima, Tsugumi, Kelly, S. Thomas, Kojima, Miki, Kondo, Naoto, Koseki, Haruhiko, Kouno, Tsukasa, Kratz, Anton, Kurowska-Stolarska, Mariola S., Kwon, Andrew Tae Jun, Leek, Jeffrey T., Lennartsson, Andreas, Lizio, Marina, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod, Marchionni, Luigi, Medvedeva, Yulia A., Minoda, Aki, Müller, Ferenc, Muñoz-Aguirre, Manuel, Murata, Mitsuyoshi, Nishiyori, Hiromi, Nitta, Kazuhiro R., Noguchi, Shuhei, Noro, Yukihiko, Nurtdinov, Ramil N., Okazaki, Yasushi, Orlando, Valerio, Paquette, Denis, Parr, Callum J.C., Rackham, Owen J.L., Rizzu, Patrizia, Sánchez Martinez, Diego Fernando, Sandelin, Albin, Sanjana, Pillay, Semple, Colin A.M., Shibayama, Youtaro, Sivaraman, Divya M., Szumowski, Suzannah C., Tagami, Michihira, Taylor, Martin S., Terao, Chikashi, Thodberg, Malte, Thongjuea, Supat, Tripathi, Vidisha, Ulitsky, Igor, Verardo, Roberto, Vorontsov, Ilya E., Yamamoto, Chinatsu, Baillie, J. Kenneth, Forrest, Alistair R.R., Guigó, Roderic, Hoffman, Michael, Hon, Chungchau, Kasukawa, Takeya, Kauppinen, Sakari, Kere, Jura, Lenhard, Boris, Schneider, Claudio, Suzuki, Harukazu, Yagi, Ken, de Hoon, Michiel J.L., Shin, Jay W., and Carninci, Piero

Abstract

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2., Genome Research, 30 (7), ISSN:1088-9051, ISSN:1549-5469

Published
2020

25. Comparative transcriptomics of primary cells in vertebrates

Author

Alam, Tanvir, Agrawal, Saumya, Severin, Jessica, Young, Robert S., Andersson, Robin, Arner, Erik, Hasegawa, Akira, Lizio, Marina, Ramilowski, Jordan A., Abugessaisa, Imad, Ishizu, Yuri, Noma, Shohei, Tarui, Hiroshi, Taylor, Martin S., Lassmann, Timo, Itoh, Masayoshi, Kasukawa, Takeya, Kawaji, Hideya, Marchionni, Luigi, Sheng, Guojun, Forrest, Alistair R. R., Khachigian, Levon M., Hayashizaki, Yoshihide, Carninci, Piero, de Hoon, Michiel J. L., Alam, Tanvir, Agrawal, Saumya, Severin, Jessica, Young, Robert S., Andersson, Robin, Arner, Erik, Hasegawa, Akira, Lizio, Marina, Ramilowski, Jordan A., Abugessaisa, Imad, Ishizu, Yuri, Noma, Shohei, Tarui, Hiroshi, Taylor, Martin S., Lassmann, Timo, Itoh, Masayoshi, Kasukawa, Takeya, Kawaji, Hideya, Marchionni, Luigi, Sheng, Guojun, Forrest, Alistair R. R., Khachigian, Levon M., Hayashizaki, Yoshihide, Carninci, Piero, and de Hoon, Michiel J. L.

Abstract

Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

Published
2020

26. Systematic identification of cis-interacting lncRNAs and their targets

Author

Agrawal, Saumya, primary, Kulakovskiy, Ivan V., additional, Severin, Jessica, additional, Koido, Masaru, additional, Alam, Tanvir, additional, Abugessaisa, Imad, additional, Buyan, Andrey, additional, Chang, Howard Y., additional, Dostie, Josee, additional, Itoh, Masayoshi, additional, Kere, Juha, additional, Kondo, Naoto, additional, Li, Yunjing, additional, Makeev, Vsevolod J., additional, Mendez, Mickaël, additional, Okazaki, Yasushi, additional, Ramilowski, Jordan A., additional, Sigorskikh, Andrey I., additional, Strug, Lisa J., additional, Yagi, Ken, additional, Yasuzawa, Kayoko, additional, Yip, Chi Wai, additional, Hon, Chung Chau, additional, Hoffman, Michael M., additional, Terao, Chikashi, additional, Kasukawa, Takeya, additional, Shin, Jay W., additional, Carninci, Piero, additional, and de Hoon, Michiel JL, additional

Published
2021
Full Text
View/download PDF

27. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Author

Abugessaisa, Imad, primary, Ramilowski, Jordan A, additional, Lizio, Marina, additional, Severin, Jesicca, additional, Hasegawa, Akira, additional, Harshbarger, Jayson, additional, Kondo, Atsushi, additional, Noguchi, Shuhei, additional, Yip, Chi Wai, additional, Ooi, Jasmine Li Ching, additional, Tagami, Michihira, additional, Hori, Fumi, additional, Agrawal, Saumya, additional, Hon, Chung Chau, additional, Cardon, Melissa, additional, Ikeda, Shuya, additional, Ono, Hiromasa, additional, Bono, Hidemasa, additional, Kato, Masaki, additional, Hashimoto, Kosuke, additional, Bonetti, Alessandro, additional, Kobayashi, Norio, additional, Shin, Jay, additional, de Hoon, Michiel, additional, Hayashizaki, Yoshihide, additional, Carninci, Piero, additional, Kawaji, Hideya, additional, and Kasukawa, Takeya, additional

Published
2020
Full Text
View/download PDF

29. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., primary, Yip, Chi Wai, additional, Agrawal, Saumya, additional, Chang, Jen-Chien, additional, Ciani, Yari, additional, Kulakovskiy, Ivan V., additional, Mendez, Mickaël, additional, Ooi, Jasmine Li Ching, additional, Ouyang, John F., additional, Parkinson, Nick, additional, Petri, Andreas, additional, Roos, Leonie, additional, Severin, Jessica, additional, Yasuzawa, Kayoko, additional, Abugessaisa, Imad, additional, Akalin, Altuna, additional, Antonov, Ivan V., additional, Arner, Erik, additional, Bonetti, Alessandro, additional, Bono, Hidemasa, additional, Borsari, Beatrice, additional, Brombacher, Frank, additional, Cameron, Christopher J.F., additional, Cannistraci, Carlo Vittorio, additional, Cardenas, Ryan, additional, Cardon, Melissa, additional, Chang, Howard, additional, Dostie, Josée, additional, Ducoli, Luca, additional, Favorov, Alexander, additional, Fort, Alexandre, additional, Garrido, Diego, additional, Gil, Noa, additional, Gimenez, Juliette, additional, Guler, Reto, additional, Handoko, Lusy, additional, Harshbarger, Jayson, additional, Hasegawa, Akira, additional, Hasegawa, Yuki, additional, Hashimoto, Kosuke, additional, Hayatsu, Norihito, additional, Heutink, Peter, additional, Hirose, Tetsuro, additional, Imada, Eddie L., additional, Itoh, Masayoshi, additional, Kaczkowski, Bogumil, additional, Kanhere, Aditi, additional, Kawabata, Emily, additional, Kawaji, Hideya, additional, Kawashima, Tsugumi, additional, Kelly, S. Thomas, additional, Kojima, Miki, additional, Kondo, Naoto, additional, Koseki, Haruhiko, additional, Kouno, Tsukasa, additional, Kratz, Anton, additional, Kurowska-Stolarska, Mariola, additional, Kwon, Andrew Tae Jun, additional, Leek, Jeffrey, additional, Lennartsson, Andreas, additional, Lizio, Marina, additional, López-Redondo, Fernando, additional, Luginbühl, Joachim, additional, Maeda, Shiori, additional, Makeev, Vsevolod J., additional, Marchionni, Luigi, additional, Medvedeva, Yulia A., additional, Minoda, Aki, additional, Müller, Ferenc, additional, Muñoz-Aguirre, Manuel, additional, Murata, Mitsuyoshi, additional, Nishiyori, Hiromi, additional, Nitta, Kazuhiro R., additional, Noguchi, Shuhei, additional, Noro, Yukihiko, additional, Nurtdinov, Ramil, additional, Okazaki, Yasushi, additional, Orlando, Valerio, additional, Paquette, Denis, additional, Parr, Callum J.C., additional, Rackham, Owen J.L., additional, Rizzu, Patrizia, additional, Martinez, Diego Fernando Sánchez, additional, Sandelin, Albin, additional, Sanjana, Pillay, additional, Semple, Colin A.M., additional, Shibayama, Youtaro, additional, Sivaraman, Divya M., additional, Suzuki, Takahiro, additional, Szumowski, Suzannah C., additional, Tagami, Michihira, additional, Taylor, Martin S., additional, Terao, Chikashi, additional, Thodberg, Malte, additional, Thongjuea, Supat, additional, Tripathi, Vidisha, additional, Ulitsky, Igor, additional, Verardo, Roberto, additional, Vorontsov, Ilya E., additional, Yamamoto, Chinatsu, additional, Young, Robert S., additional, Baillie, J. Kenneth, additional, Forrest, Alistair R.R., additional, Guigó, Roderic, additional, Hoffman, Michael M., additional, Hon, Chung Chau, additional, Kasukawa, Takeya, additional, Kauppinen, Sakari, additional, Kere, Juha, additional, Lenhard, Boris, additional, Schneider, Claudio, additional, Suzuki, Harukazu, additional, Yagi, Ken, additional, de Hoon, Michiel J.L., additional, Shin, Jay W., additional, and Carninci, Piero, additional

Published
2020
Full Text
View/download PDF

31. Comparative transcriptomics of primary cells in vertebrates

Author

Alam, Tanvir, primary, Agrawal, Saumya, additional, Severin, Jessica, additional, Young, Robert S., additional, Andersson, Robin, additional, Arner, Erik, additional, Hasegawa, Akira, additional, Lizio, Marina, additional, Ramilowski, Jordan A., additional, Abugessaisa, Imad, additional, Ishizu, Yuri, additional, Noma, Shohei, additional, Tarui, Hiroshi, additional, Taylor, Martin S., additional, Lassmann, Timo, additional, Itoh, Masayoshi, additional, Kasukawa, Takeya, additional, Kawaji, Hideya, additional, Marchionni, Luigi, additional, Sheng, Guojun, additional, R.R. Forrest, Alistair, additional, Khachigian, Levon M., additional, Hayashizaki, Yoshihide, additional, Carninci, Piero, additional, and de Hoon, Michiel J.L., additional

Published
2020
Full Text
View/download PDF

32. Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

Author

Pawlak, Michal, primary, Kedzierska, Katarzyna Z., additional, Migdal, Maciej, additional, Nahia, Karim Abu, additional, Ramilowski, Jordan A., additional, Bugajski, Lukasz, additional, Hashimoto, Kosuke, additional, Marconi, Aleksandra, additional, Piwocka, Katarzyna, additional, Carninci, Piero, additional, and Winata, Cecilia L., additional

Published
2020
Full Text
View/download PDF

33. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

Author

Pawlak, Michal, primary, Kedzierska, Katarzyna Z., additional, Migdal, Maciej, additional, Nahia, Karim Abu, additional, Ramilowski, Jordan A., additional, Bugajski, Lukasz, additional, Hashimoto, Kosuke, additional, Marconi, Aleksandra, additional, Piwocka, Katarzyna, additional, Carninci, Piero, additional, and Winata, Cecilia L., additional

Published
2019
Full Text
View/download PDF

34. Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development

Author

Pawlak, Michal, primary, Kedzierska, Katarzyna Z., additional, Migdal, Maciej, additional, Abu Nahia, Karim, additional, Ramilowski, Jordan A., additional, Bugajski, Lukasz, additional, Hashimoto, Kosuke, additional, Marconi, Aleksandra, additional, Piwocka, Katarzyna, additional, Carninci, Piero, additional, and Winata, Cecilia L., additional

Published
2018
Full Text
View/download PDF

35. Physical and functional interaction among Irf8enhancers during dendritic cell differentiation

Author

Yamasaki, Takaya, Nishiyama, Akira, Kurogi, Nagomi, Nishimura, Koutarou, Nishida, Shion, Kurotaki, Daisuke, Ban, Tatsuma, Ramilowski, Jordan A., Ozato, Keiko, Toyoda, Atsushi, and Tamura, Tomohiko

Abstract

The production of type 1 conventional dendritic cells (cDC1s) requires high expression of the transcription factor IRF8. Three enhancers at the Irf83′ region function in a differentiation stage-specific manner. However, whether and how these enhancers interact physically and functionally remains unclear. Here, we show that the Irf83′ enhancers directly interact with each other and contact the Irf8gene body during cDC1 differentiation. The +56 kb enhancer, which functions from multipotent progenitor stages, activates the other 3′ enhancers through an IRF8-dependent transcription factor program, that is, in trans. Then, the +32 kb enhancer, which operates in cDC1-committed cells, reversely acts in cison the other 3′ enhancers to maintain the high expression of Irf8. Indeed, mice with compound heterozygous deletion of the +56 and +32 kb enhancers are unable to generate cDC1s. These results illustrate how multiple enhancers cooperate to induce a lineage-determining transcription factor gene during cell differentiation.

Published
2024
Full Text
View/download PDF

36. Quantum solvation dynamics of HCN in a helium-4 droplet.

Author

Mikosz, Aleksandra A., Ramilowski, Jordan A., and Farrelly, David

Subjects
*ULTRACOLD neutrons, *SUPERFLUIDITY, *NANOSCIENCE, *HELIUM at low temperatures, *SOLVENTS, *MONTE Carlo method, *SOLVATION, *ANGULAR momentum (Nuclear physics)
Abstract

Ultracold nanodroplets of helium-4, containing several thousands of He atoms, offer considerable promise as microscopic cryogenic chambers. Potential applications include the creation of tailor-made chemical or biomolecular complexes and studies of superfluidity in nanoscale systems. Recent experiments have succeeded in interrogating droplets of quantum solvent which consist of as few as 1–20 helium-4 atoms and which contain a single solute molecule. This allows the transition from a floppy, but essentially molecular, complex to a dissolved molecule to be followed and, surprisingly, the transition is found to occur quite rapidly, in some cases for as few as N=7–20 solvent atoms. For example, in experiments on helium-4 droplets seeded with CO molecules [Tang and McKellar, J. Chem. Phys. 119, 754 (2003)], two series of transitions are observed which correlate with the a-type (ΔK=0) and b-type (ΔK=±1) lines of the binary complex, CO–He (K is the quantum number associated with the projection of the total angular momentum onto the vector connecting the atom and the molecular center of mass). The a-type series, which evolves from the end-over-end rotational motion of the CO–He binary complex, saturates to the nanodroplet limit for as few as 10–15 helium-4 atoms, i.e., the effective moment of inertia of the molecule converges to its asymptotic (solvated) value quite rapidly. In contrast, the b-type series, which evolves from the free-molecule rotational mode, disappears altogether for N≈7 atoms. Similar behavior is observed in recent computational studies of HCN(4He)N droplets [Paolini et al., J. Chem. Phys. 123, 114306 (2005)]. In this article the quantum solvation of HCN in small helium-4 droplets is studied using a new fixed-node diffusion Monte Carlo (DMC) procedure. In this approach a Born-Oppenheimer-type separation of radial and angular motions is introduced as a means of computing nodal surfaces of the many-body wave functions which are required in the fixed-node DMC method. Excited rotational energies are calculated for HCN(4He)N droplets with N=1–20: the adiabatic node approach also allows concrete physical mechanisms to be proposed for the predicted disappearance of the b-type series as well as the rapid convergence of the a-type series to the nanodroplet limit with increasing N. The behavior of the a-type series is traced directly to the mechanics of angular momentum coupling—and decoupling—between identical bosons and the molecular rotor. For very small values of N there exists significant angular momentum coupling between the molecule and the helium atoms: at N≈10 solvation appears to be complete as evidenced by significant decoupling of the molecule and solvent angular momenta. The vanishing of the b-type series is predicted to be a result of increasing He–He repulsion as the number of solvent atoms increases. [ABSTRACT FROM AUTHOR]

Published
2006
Full Text
View/download PDF

37. Update of the FANTOM web resource:high resolution transcriptome of diverse cell types in mammals

Author

Lizio, Marina, Harshbarger, Jayson, Abugessaisa, Imad, Noguchi, Shuei, Kondo, Atsushi, Severin, Jessica, Mungall, Chris, Arenillas, David, Mathelier, Anthony, Medvedeva, Yulia A., Lennartsson, Andreas, Drabløs, Finn, Ramilowski, Jordan A., Rackham, Owen, Gough, Julian, Andersson, Robin, Sandelin, Albin Gustav, Ienasescu, Hans-Ioan, Ono, Hiromasa, Bono, Hidemasa, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair R. R., Kasukawa, Takeya, Kawaji, Hideya, Lizio, Marina, Harshbarger, Jayson, Abugessaisa, Imad, Noguchi, Shuei, Kondo, Atsushi, Severin, Jessica, Mungall, Chris, Arenillas, David, Mathelier, Anthony, Medvedeva, Yulia A., Lennartsson, Andreas, Drabløs, Finn, Ramilowski, Jordan A., Rackham, Owen, Gough, Julian, Andersson, Robin, Sandelin, Albin Gustav, Ienasescu, Hans-Ioan, Ono, Hiromasa, Bono, Hidemasa, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair R. R., Kasukawa, Takeya, and Kawaji, Hideya

Abstract

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

Published
2017

38. Planar to linear structural transition in small boron-carbon mixed clusters: [C.sub.x][B.sub.5-x.sup.-] (x = 1-5)

Author

Lei-Ming Wang, Averkiev, Boris B., Ramilowski, Jordan A., Wei Huang, Lai-Sheng Wang, and Boldyrev, Alexander I.

Subjects
Organoboron compounds -- Structure, Organoboron compounds -- Chemical properties, Phase transformations (Statistical physics) -- Analysis, Photoelectron spectroscopy -- Usage, Chemistry
Abstract

Boron/carbon (B/C) mixed clusters containing five atoms ([C.sub.x][B.sub.5-x.sup.-] (x = 1-5)) are analyzed, which have displayed a planar to linear structural transition as a function of the C content. The planar-to-linear transition has occurred between x = 2 and 3, where the global minimum structures of the B-rich clusters, C[B.sub.4.sup.-] and [C.sub.2][B.sub.3.sup.-], are planar, similar to [B.sub.5.sup.-], and those of the C-rich clusters, [C.sub.3][B.sub.2.sup.-] and [C.sub.4][B.sup.-], are linear, similar to [C.sub.5.sup.-].

Published
2010

39. Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human

Author

Ramilowski, Jordan A., Goldberg, Tatyana, Harshbarger, Jayson, Kloppmann, Edda, Lizio, Marina, Satagopam, Venkata P., Itoh, Masayoshi, Kawaji, Hideya, Carninci, Piero, Rost, Burkhard, and Forrest, Alistair R. R.

Subjects
Evolution, Molecular, Animals, Humans, Receptors, Cell Surface, Cell Communication, Ligands, Corrigenda, Software
Abstract

Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand-receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1-CSF1R interacting pair.

Published
2016

40. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Author

Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R R, Huminiecki, Lukasz, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati Bhatt, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun ichi, Geijtenbeek, Teunis B., Gibson, Andrew, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori, Mutsumi Katayama, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan sim, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao, Sayaka Sato, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada, Mariko Hatakeyama, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A C, Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide, Hubrecht Institute for Developmental Biology and Stem Cell Research, Barton, Nick H, Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Male, Medical and Health Sciences, Essential, Models, Gene expression, Databases, Genetic, Biology (General), Non-U.S. Gov't, X-linked recessive inheritance, X chromosome, Cells, Cultured, Regulation of gene expression, Genetics, Sex Characteristics, Dosage compensation, Tumor, Cultured, Genes, Essential, Genome, Agricultural and Biological Sciences(all), General Neuroscience, Research Support, Non-U.S. Gov't, Biological Sciences, Organ Specificity, Female, General Agricultural and Biological Sciences, Research Article, Human, X Chromosome, Retroelements, QH301-705.5, Neuroscience(all), 1.1 Normal biological development and functioning, Cells, Down-Regulation, Biology, Research Support, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Cell Line, Databases, Genetic, Species Specificity, Underpinning research, Immunology and Microbiology(all), Cell Line, Tumor, Journal Article, Animals, Humans, Comparative Study, Gene, Chromosomes, Human, X, Autosome, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Models, Genetic, Biochemistry, Genetics and Molecular Biology(all), Genome, Human, Mammalian, Human Genome, Chromosomes, Mammalian, Genes, Gene Expression Regulation, Human genome, FANTOM consortium, Developmental Biology
Abstract

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution., Laurence Hurst, Lukasz Huminiecki, and the FANTOM5 consortium propose a new explanation for the peculiar expression properties of genes on the human X chromosome, based on the premise that very high expression levels cannot be achieved on a haploid-expressed chromosome., Author Summary Genes located on the human X chromosome are not a random mix of genes: they tend to be expressed in relatively few tissues or are specific for a particular set of tissues, e.g., brain regions. Prior attempts to explain this skewed gene content have hypothesized that the X chromosome might be peculiar because it has to balance mutations that are advantageous to one sex but deleterious to the other, or because it has to shut down during the process of sperm manufacture in males. Here we suggest and test a third possible explanation: that genes on the X chromosome are limited in their transcription levels and thus tend to be genes that are lowly or specifically expressed. We consider the suggestion that since these genes can only be expressed from one chromosome, as males only have one X, the ability to express a gene at very high rates is limited owing to potential transcriptional traffic jams. As predicted, we find that human X-located genes have maximal expression rates far below that of genes residing on autosomes. When we look at genes that have moved onto or off the X chromosome during recent evolution, we find the maximal expression is higher when not on the X chromosome. We also find that X-located genes that are relatively highly expressed are not able to increase their expression level further. Our model explains both the enrichment for tissue specificity and the paucity of certain tissues with X-located genes. Genes underrepresented on the X are either expressed in many tissues—such genes tend to have high maximal expression—or are from tissues that require a lot of transcription (e.g., fast secreting tissues like the liver). Just as many of the findings cannot be explained by the two earlier models, neither can the traffic jam model explain all the peculiar features of the genes found on the X chromosome. Indeed, we find evidence of a reproduction-related bias in X-located genes, even after allowing for the traffic jam problem.

Published
2015

41. Rotational structure of small [super 4]He clusters seeded with HF, HCl, and HBr molecules

Author

Ramilowski, Jordan A., Mikosz, Aleksandra A., Farrelly, David, Jose Luis Cagide Fajin, and Fernandez, Berta

Subjects
Monte Carlo method -- Analysis, Hafnium -- Structure, Hafnium -- Electric properties, Hafnium -- Chemical properties, Anisotropy -- Analysis, Potential energy -- Research, Chemicals, plastics and rubber industries
Abstract

Diffusion Monte Carlo calculations are used for studying the ground and excited rotational states of HX[([super 4]He).sub.N], complexes with N

Published
2007

42. Genomics dissection of the zebrafish heart

Author

Pawlak, Michal, primary, Kedzierska, Katarzyna, additional, Bugajski, Lukasz, additional, Hashimoto, Kosuke, additional, Ramilowski, Jordan, additional, Marconi, Aleksandra, additional, Carninci, Piero, additional, Piwocka, Katarzyna, additional, and Winata, Cecilia, additional

Published
2017
Full Text
View/download PDF

43. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Author

Lizio, Marina, primary, Harshbarger, Jayson, additional, Abugessaisa, Imad, additional, Noguchi, Shuei, additional, Kondo, Atsushi, additional, Severin, Jessica, additional, Mungall, Chris, additional, Arenillas, David, additional, Mathelier, Anthony, additional, Medvedeva, Yulia A., additional, Lennartsson, Andreas, additional, Drabløs, Finn, additional, Ramilowski, Jordan A., additional, Rackham, Owen, additional, Gough, Julian, additional, Andersson, Robin, additional, Sandelin, Albin, additional, Ienasescu, Hans, additional, Ono, Hiromasa, additional, Bono, Hidemasa, additional, Hayashizaki, Yoshihide, additional, Carninci, Piero, additional, Forrest, Alistair R.R., additional, Kasukawa, Takeya, additional, and Kawaji, Hideya, additional

Published
2016
Full Text
View/download PDF

44. A draft network of ligand–receptor-mediated multicellular signalling in human

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Ramilowski, Jordan, Goldberg, Tatyana, Harshbarger, Jayson, Kloppman, Edda, Lizio, Marina, Satagopam, Venkata, Itoh, Masayoshi, Kawaji, Hideya, Carninci, Rost, Burkhard, Forrest, Alistair, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Ramilowski, Jordan, Goldberg, Tatyana, Harshbarger, Jayson, Kloppman, Edda, Lizio, Marina, Satagopam, Venkata, Itoh, Masayoshi, Kawaji, Hideya, Carninci, Rost, Burkhard, and Forrest, Alistair

Abstract

Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand–receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1–CSF1R interacting pair.

Published
2015

46. Dynamics of van der Waals Clusters: Theoretical and Computational Studies

Author

Ramilowski, Jordan Aleksander

Subjects
theoretical studies, computational studies, van der Waals clusters, Physical Chemistry
Abstract

The marriage of two very powerful techniques – cryogenic matrix isolation spectroscopy and seeded supersonic molecular beams – has led to the development of a novel type of cryogenic matrix isolation spectroscopy in ultracold, near 0 K, He droplets. The technique known as helium nanodroplet isolation (HENDI) has seen tremendeous experimental interest over the past 20 years; this in turn has resulted in the availability of spectroscopic data for many molecules and clusters embedded in He clusters. The experimental findings have motivated a large number of theoretical calculations. This dissertation focuses on theoretical and computational studies of the rotational dynamics of weakly bound van der Waals clusters with its main theme being the dynamics of molecules and small molecular dimers embedded in superfluid 4He nanodroplets. The single molecular dopant systems studied were clusters of HCN-(He)N, HX-(He)N, where X = F, Cl, Br as well as NH3-(He)N, with N = 1 ≈ 20. Ground and excited state calculations were performed using the rigid body diffusion Monte Carlo (RBDMC) algorithm. For the excited state calculations a new approach was developed: adiabatic-node DMC (ANDMC). The ANDMC method was used to study the renormalization of molecular rotational constants in He droplets. It revealed that the dynamics depend on a delicate interplay between the gas phase rotational constant value and the anisotropies in the potential energy interaction between the He atom and the dopant. Also presented are the results of the first DMC simulations of the ammonia dimer doped into a small droplet of 4He. Further, a new approach to finding nodal surfaces for DMC simulations was developed that involved using a genetic algorithm (GA). This method was implemented to systematically and automatically compute nodal surfaces of excited states of the HCN-4He complex and of the interchange tunneling splitting in the hydrogen-bonded HCl-HCl complex. The classical rotational dynamics of HX-4He complexes with X = F, Cl, Br, CN were studied to gain insight into quantum simulations and revealed highly chaotic dynamics for states with J > 0. Fractal Weyl law behavior in an open, chaotic Hamiltonian system is the subject of the final chapter.

Published
2010
Full Text
View/download PDF

47. A promoter-level mammalian expression atlas

Author

Forest, Alistair R.R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michiel J.L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab Alam, Albanese, Davide, Altschule, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun Ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Sui, Shannan J Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri Ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Morais, David A Lima, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A C, Tagami, Michihira, Tagami, Naoko Takahashi, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering, Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Lenhard Vladimir B, Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide, Forest, Alistair R.R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michiel J.L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab Alam, Albanese, Davide, Altschule, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A. Maxwell, Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun Ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Sui, Shannan J Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri Ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Morais, David A Lima, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A C, Tagami, Michihira, Tagami, Naoko Takahashi, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering, Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Lenhard Vladimir B, Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Abstract

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly â ̃ housekeepingâ ™, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Published
2014

48. Fractal Weyl law behavior in an open Hamiltonian system

Author

Ramilowski, Jordan A., Prado, Sandra Denise, Borondo Rodríguez, Florentino, and Farrelly, David

Subjects
Funcoes de ondas, Fractais, Caos, Ressonancia
Abstract

We numerically show fractal Weyl law behavior in an open Hamiltonian system that is described by a smooth potential and which supports numerous above-barrier resonances. This behavior holds even relatively far away from the classical limit. The complex resonance wave functions are found to be localized on the fractal classical repeller.

Published
2009

Catalog

Books, media, physical & digital resources
See catalog results