Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: TopHat
https://packages.ecosyste.ms/registries/pypi.org/packages/TopHat
TopHat Platform
3 versions
Latest release: over 11 years ago
9 downloads last month
Papers Mentioning TopHat 5,017
10.7554/eLife.02948
Two-signal requirement for growth-promoting function of Yap in hepatocytesCited by: 51
Author(s): Tian Su, Tanya Bondar, Xu Zhou, Cuiling Zhang, Hang He, Ruslan Medzhitov
Software Mentions: 1
Published: over 9 years ago
10.7554/eLife.19573
Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thalianaCited by: 44
Author(s): Urszula Piskurewicz, Mayumi Iwasaki, Daichi Susaki, Christian Megies, Tetsu Kinoshita, Luis Lopez‐Molina
Software Mentions: 1
Published: over 7 years ago
10.7554/eLife.27706
Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesisCited by: 30
Author(s): Stephin J. Vervoort, Olivier G. de Jong, M. Guy Roukens, Cynthia L Frederiks, Jeroen F. Vermeulen, Ana Rita Lourenço, Laura Bella, Ana Tufegdžić Vidaković, José Luís Sandoval, Cathy B. Moelans, Miranda van Amersfoort, Margaret J. Dallman, Alejandra Bruna, Carlos Caldas, Edward E. S. Nieuwenhuis, Elsken van der Wall, Patrick W.B. Derksen, Paul van Diest, Marianne C. Verhaar, Eric Lam, Michal Mokrý, Paul J. Coffer
Software Mentions: 1
Published: over 5 years ago
10.7554/eLife.14330
A feedback amplification loop between stem cells and their progeny promotes tissue regeneration and tumorigenesisCited by: 51
Author(s): Jun Chen, Na Xu, Huagnwei Huang, Tao Cai, Rongwen Xi
Software Mentions: 1
Published: about 8 years ago
10.7554/eLife.10567
Embryonic attenuated Wnt/β-catenin signaling defines niche location and long-term stem cell fate in hair follicleCited by: 51
Author(s): Zijian Xu, Wenjie Wang, Kaiju Jiang, Yu Zhou, Huagnwei Huang, Fengchao Wang, Bin Zhou, Ting Chen
Software Mentions: 1
Published: over 8 years ago
10.18632/oncotarget.25451
Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamideCited by: 5
Author(s): Kokiladevi Alagarswamy, Ken‐ichi Shinohara, Shihori Takayanagi, Masaki Fukuyo, Atsushi Okabe, Bahityar Rahmutulla, Natsumi Yoda, Rui Qin, Naoki Shiga, Masahiro Sugiura, Hiroaki Sato, K Kita, Takayoshi Suzuki, Tetsuhiro Nemoto, Atsushi Kaneda
Software Mentions: 1
Published: almost 6 years ago
10.18632/oncotarget.26177
Mutant TP53 modulates metastasis of triple negative breast cancer through adenosine A2b receptor signalingCited by: 12
Author(s): Eisuke Horigome, Michiru Fujieda, Tadashi Handa, Ayaka Katayama, Masashi Ito, Ami Ichihara, Daiki Tanaka, Navchaa Gombodorj, Shinji Yoshiyama, Arito Yamane, Keiichi Yamada, Jun Horiguchi, Kazuo Shinozuka, Tetsunari Oyama, Masahiko Nishiyama, Susumu Rokudai
Software Mentions: 1
Published: over 5 years ago
10.1113/jphysiol.2014.278994
Ionotropic GABA and glycine receptor subunit composition in human pluripotent stem cell‐derived excitatory cortical neuronesCited by: 14
Author(s): Owain T. James, Matthew R. Livesey, Jingdan Qiu, Owen Dando, Bilada Bilican, Ghazal Haghi, Rinku Rajan, Karen Burr, Giles E. Hardingham, Siddharthan Chandran, Peter C. Kind, David J. A. Wyllie
Software Mentions: 1
Published: over 9 years ago
10.1186/s40101-020-00242-w
NOD-like receptors mediate inflammatory lung injury during plateau hypoxia exposureCited by: 8
Author(s): Haiyan Wang, Xue Lin, Xiongming Pu
Software Mentions: 1
Published: over 3 years ago
10.1093/jrr/rrz057
Reprogramming and differentiation-dependent transcriptional alteration of DNA damage response and apoptosis genes in human induced pluripotent stem cellsCited by: 13
Author(s): Mikio Shimada, Kaima Tsukada, Nozomi Kagawa, Yoshihisa Matsumoto
Software Mentions: 1
Published: over 4 years ago
10.1098/rsob.170119
The requirement of Mettl3-promoted <i>MyoD</i> mRNA maintenance in proliferative myoblasts for skeletal muscle differentiationCited by: 66
Author(s): Kensuke Kudou, Tetsuro Komatsu, Jumpei Nogami, Kazuhira Maehara, Akihito Harada, Hiroshi Saeki, Eiji Oki, Yoshihiko Maehara, Yasuyuki Ohkawa
Software Mentions: 1
Published: over 6 years ago
10.1098/rsob.180029
Cultured cells and wing disc size of silkworm can be controlled by the Hippo pathwayCited by: 9
Author(s): Zi Liang, Yingjie Lu, Ying Qian, Liyuan Zhu, Sulan Kuang, Fei Chen, Yongjie Feng, Xiaolong Hu, Guangwen Cao, Renyu Xue, Chengliang Gong
Software Mentions: 1
Published: almost 6 years ago
10.1186/s13023-016-0439-6
Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disabilityCited by: 23
Author(s): Valerie V. Maduro, Barbara N. Pusey, Praveen F. Cherukuri, Paul Atkins, Christèle du Souich, Rosemarie Rupps, Marjolaine M. Limbos, David R. Adams, Samarth Bhatt, Patrice Eydoux, Amanda Links, Anna Lehman, May Christine V. Malicdan, Christopher E. Mason, Marie Morimoto, James C. Mullikin, Andrew Sear, Clara van Karnebeek, Paweł Stankiewicz, William A. Gahl, Camilo Toro, Cornelius F. Boerkoel
Software Mentions: 1
Published: about 8 years ago
10.1128/JVI.01335-20
Mapping the Human Herpesvirus 6B TranscriptomeCited by: 3
Author(s): Annie Gravel, Wes Sanders, Éric Fournier, Arnaud Droit, Nathaniel J. Moorman, Louis Flamand
Software Mentions: 1
Published: about 3 years ago
10.1186/s12967-018-1749-3
Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysmsCited by: 27
Author(s): Vincent M. Tutino, Kerry E. Poppenberg, Lü Li, Hussain Shallwani, Kaiyu Jiang, James N. Jarvis, Yijun Sun, Kenneth V. Snyder, Elad I. Levy, Adnan H. Siddiqui, John Kolega
Software Mentions: 1
Published: over 5 years ago
10.1186/s12935-018-0618-8
SOX2OT knockdown derived changes in mitotic regulatory gene network of cancer cellsCited by: 6
Author(s): Marie Saghaeian Jazi, Nader Mansour Samaei, Seyed Javad Mowla, Babak Arefnezhad, Morteza Kouhsar
Software Mentions: 1
Published: over 5 years ago