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: CAGE
https://packages.ecosyste.ms/registries/pypi.org/packages/CAGE
A generic and fairly complete cellular automata simulation engine.
3 versions
Latest release: over 1 year ago
Papers Mentioning CAGE 101
10.12688/f1000research.18456.1
A step-by-step guide to analyzing CAGE data using R/BioconductorCited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago
10.1186/s12859-019-3029-5
CAGEfightR: analysis of 5′-end data using R/BioconductorCited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago
10.3389/fgene.2020.580580
Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago
10.1186/s12859-017-1651-7
Zipper plot: visualizing transcriptional activity of genomic regionsCited by: 5
Author(s): Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, Pieter Mestdagh
Software Mentions: 9
Published: over 7 years ago
10.1371/journal.ppat.1007852
The landscape of transcription initiation across latent and lytic KSHV genomesCited by: 11
Author(s): Xiang Ye, Yang Zhao, John Karijolich
Software Mentions: 6
Published: over 5 years ago
10.1016/j.molcel.2021.02.034
POINT technology illuminates the processing of polymerase-associated intact nascent transcriptsCited by: 44
Author(s): Rui Sousa-Luís, Geneviève Dujardin, Inna Zukher, Hiroshi Kimurâ, Carika Weldon, Maria Carmo‐Fonseca, Nick J. Proudfoot, Takayuki Nojima
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-018-25748-3
Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: over 6 years ago
10.1186/1471-2105-15-144
MOIRAI: a compact workflow system for CAGE analysisCited by: 62
Author(s): Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann
Software Mentions: 5
Published: over 10 years ago
10.1186/s13059-014-0560-6
Gateways to the FANTOM5 promoter level mammalian expression atlasCited by: 634
Author(s): Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J. Mungall, Peter Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D. Diehl, Emmanuel Dimont, Tom C. Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Ono Hiromasa, Michael Rehli, Albin Sandelin, Erik Schultes, Peter A.C. ’t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W. Wright, Carsten O. Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji
Software Mentions: 5
Published: almost 10 years ago
10.3389/fgene.2021.649619
Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in CancerCited by: 21
Author(s): Anshika Chowdhary, Venkata Satagopam, Reinhard Schneider
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-018-4564-6
Characterization of the human RFX transcription factor family by regulatory and target gene analysisCited by: 57
Author(s): Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Santosh Misra, Carsten O. Daub, Juha Kere, Peter Swoboda
Software Mentions: 4
Published: over 6 years ago
10.3389/fgene.2014.00035
The analytical landscape of static and temporal dynamics in transcriptome dataCited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: almost 11 years ago
10.1186/1471-2164-15-982
Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injuryCited by: 19
Author(s): Masayuki Yasuda, Yuji Tanaka, Koji M. Nishiguchi, Morin Ryu, S. Tsuda, Kouichi Maruyama, Toru Nakazawa
Software Mentions: 4
Published: about 10 years ago
10.1186/s12864-020-07334-y
scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasetsCited by: 9
Author(s): Hongyu Liu, N M Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-021-88743-1
Identification of candidate PAX2-regulated genes implicated in human kidney developmentCited by: 6
Author(s): Yuta Yamamura, Kengo Furuichi, Yuji Murakawa, Shigeki Hirabayashi, Masahito Yoshihara, Keisuke Sako, Shinji Kitajima, Tadashi Toyama, Yasunori Iwata, Norihiko Sakai, Kazuyoshi Hosomichi, Philip M. Murphy, Atsushi Tajima, Keisuke Okita, Kenji Osafune, Shuichi Kaneko, Takashi Wada
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1008050
Cross-species regulatory sequence activity predictionCited by: 89
Author(s): David R. Kelley
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pbio.2002887
Systematic analysis of transcription start sites in avian developmentCited by: 33
Author(s): Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galán, Peter Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, María A. Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng
Software Mentions: 3
Published: about 7 years ago
10.5811/westjem.2017.7.34373
Effectiveness of SBIRT for Alcohol Use Disorders in the Emergency Department: A Systematic ReviewCited by: 105
Author(s): Isabel A. Barata, Jamie Shandro, Margaret Montgomery, Robin Polansky, Carolyn J. Sachs, Herbert C. Duber, Lindsay Weaver, Alan Heins, Heather S. Owen, Elaine B. Josephson, Wendy Macias‐Konstantopoulos
Software Mentions: 3
Published: about 7 years ago
10.1038/s41598-020-57811-3
Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE dataCited by: 14
Author(s): Γεώργιος Γεωργακίλας, Nikos Perdikopanis, Artemis G. Hatzigeorgiou
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12859-016-1349-2
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory functionCited by: 14
Author(s): Rezvan Ehsani, Shahram Bahrami, Finn Drabløs
Software Mentions: 3
Published: about 8 years ago
10.1038/s41598-019-54180-4
A framework for identification of on- and off-target transcriptional responses to drug treatmentCited by: 23
Author(s): Yi Huang, Masaaki Furuno, Takahiro Arakawa, Satoshi Takizawa, Michiel de Hoon, Harukazu Suzuki, Erik Arner
Software Mentions: 3
Published: almost 5 years ago
10.1128/JVI.02394-20
CAGE-Seq Reveals that HIV-1 Latent Infection Does Not Trigger Unique Cellular Responses in a Jurkat T Cell ModelCited by: 1
Author(s): Hiroyuki Matsui, Kotaro Shirakawa, Yoshinobu Konishi, Shigeki Hirabayashi, Anamaria Daniela Sarca, Hirofumi Fukuda, Ryosuke Nomura, Emani Stanford, Yoshihito Horisawa, Yasuhiro Kazuma, Tadahiko Matsumoto, Hiroyuki Yamazaki, Yuji Murakawa, Emilie Battivelli, Eric Verdin, Yoshio Koyanagi, Akifumi Takaori‐Kondo
Software Mentions: 3
Published: over 3 years ago
10.1038/srep17978
Identifying transcription start sites and active enhancer elements using BruUV-seqCited by: 26
Author(s): Brian Magnuson, Artur Veloso, Killeen S. Kirkconnell, Leonardo Carmo de Andrade Lima, Michelle T. Paulsen, Emily A. Ljungman, Karan Bedi, J.K. Prasad, Thomas E. Wilson, Mats Ljungman
Software Mentions: 3
Published: almost 9 years ago
10.1186/s12864-015-2111-2
Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genomeCited by: 15
Author(s): Christelle Robert, Ronan Kapétanovic, Dario Beraldi, Michael Watson, Alan Archibald, David Hume
Software Mentions: 3
Published: about 9 years ago
10.1186/s12864-019-5650-0
Selective translational usage of TSS and core promoters revealed by translatome sequencingCited by: 2
Author(s): Hua Li, Longchuan Bai, Hongmei Li, Xinhui Li, Yani Kang, Ningbo Zhang, Jingyong Sun, Zongshu Shao
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-015-1670-6
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sitesCited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: over 9 years ago
10.1038/sdata.2017.163
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous systemCited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: about 7 years ago
10.1186/s12864-017-3863-7
A high-quality annotated transcriptome of swine peripheral bloodCited by: 7
Author(s): Haibo Li, Timothy P. L. Smith, Dan Nonneman, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 3
Published: over 7 years ago
10.3389/fmolb.2020.00209
Pinpointing Cell Identity in Time and SpaceCited by: 15
Author(s): Anca F. Savulescu, Caron Jacobs, Yutaka Negishi, L. Davignon, Musa M. Mhlanga
Software Mentions: 3
Published: over 4 years ago
10.3389/fncel.2019.00391
The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Progenitor CellsCited by: 11
Author(s): Katarzyna Kośla, Elżbieta Płuciennik, Ewa Styczeń-Binkowska, Magdalena Nowakowska, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 3
Published: about 5 years ago
10.1042/EBC20180045
Genome-driven cell engineering review: <i>in vivo</i> and <i>in silico</i> metabolic and genome engineeringCited by: 11
Author(s): Sophie Landon, Joshua Rees-Garbutt, Lucia Marucci, Claire Grierson
Software Mentions: 3
Published: over 5 years ago
10.1038/sdata.2017.107
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assembliesCited by: 58
Author(s): Imad Abugessaisa, Shuhei Noguchi, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Marina Lizio, Jessica Severin, Piero Carninci, Hideya Kawaji, Takeya Kasukawa
Software Mentions: 2
Published: about 7 years ago
10.1186/s12885-016-2792-1
Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lungCited by: 37
Author(s): Kazuya Takamochi, Hiroko Ohmiya, Masayoshi Itoh, Kaoru Mogushi, Tsuyoshi Saito, Kieko Hara, Keiko Mitani, Yasushi Kogo, Yasunari Yamanaka, Jun Kawai, Yoshihide Hayashizaki, Shiaki Oh, Kenji Suzuki, Hideya Kawaji
Software Mentions: 2
Published: about 8 years ago
10.3390/ma14174848
An Efficient Approach to the Five-Axis Flank Milling of Non-Ferrous Spiral Bevel GearsCited by: 5
Author(s): Hao Xu, Yuansheng Zhou, Yi He, Jinyuan Tang
Software Mentions: 2
Published: about 3 years ago
10.1016/j.molcel.2016.11.029
Distinctive Patterns of Transcription and RNA Processing for Human lincRNAsCited by: 208
Author(s): Margarita Schlackow, Takayuki Nojima, Tomás Gomes, Ashish Dhir, Maria Carmo‐Fonseca, Nick J. Proudfoot
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0013934
High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot OccurCited by: 8
Author(s): Ulf Schaefer, Rimantas Kodzius, Kai Cui, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic
Software Mentions: 2
Published: about 14 years ago
10.1371/journal.pone.0208952
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesisCited by: 7
Author(s): Łukasz Huminiecki
Software Mentions: 2
Published: over 5 years ago
10.1016/j.ebiom.2019.03.035
SUMOylation promotes survival and integration of neural stem cell grafts in ischemic strokeCited by: 32
Author(s): Joshua D. Bernstock, Luca Peruzzotti‐Jametti, Tommaso Leonardi, Nunzio Vicario, Daniel Ye, Yang-ja Lee, Dragan Maric, Kory R. Johnson, Yongshan Mou, Aletta van den Bosch, Mark S. Winterbone, Gregory K. Friedman, R. J. M. Franklin, John M. Hallenbeck, Stefano Pluchino
Software Mentions: 2
Published: over 5 years ago
10.1186/s13072-015-0043-3
Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitorsCited by: 32
Author(s): Andreas Lennartsson, Peter Arner, Michela Fagiolini, Alka Saxena, Robin Andersson, Hazuki Takahashi, Yukihiko Noro, Judy Sng, Albin Sandelin, Takao K. Hensch, Piero Carninci
Software Mentions: 2
Published: almost 9 years ago
10.3389/fonc.2020.00316
Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer CellsCited by: 0
Author(s): Ru Chen, Aiko Sugiyama, Naoyuki Kataoka, Masahiro Sugimoto, Shoko Yokoyama, Akira Fukuda, Shigeo Takaishi, Hiroshi Seno
Software Mentions: 2
Published: over 4 years ago
10.1186/gb-2013-14-8-r84
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAsCited by: 102
Author(s): Annalisa Marsico, Matthew R. Huska, Julia Lasserre, Haiyang Hu, Dubravka Vučićević, Anne Musahl, Ulf Andersson Ørom, Martin Vingron
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12977-019-0500-3
HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAPCited by: 18
Author(s): Paola Miyazato, Misaki Matsuo, Benjy J.Y. Tan, Michiyo Tokunaga, Hiroo Katsuya, Saiful Islam, Jumpei Ito, Yuji Murakawa, Yorifumi Satou
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13722-018-0108-2
Standardised alcohol screening in primary health care services targeting Aboriginal and Torres Strait Islander peoples in AustraliaCited by: 15
Author(s): M. Mofizul Islam, Helen Tosin Oni, K. S. Kylie Lee, Noel Hayman, Scott Wilson, Kristie Harrison, Beth Hummerston, Rowena Ivers, Katherine M. Conigrave
Software Mentions: 2
Published: over 6 years ago
10.1038/sdata.2017.173
Monitoring transcription initiation activities in rat and dogCited by: 6
Author(s): Marina Lizio, Abdul Kadir Mukarram, Mizuho Ohno, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Chung-Chau Hon, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji
Software Mentions: 2
Published: almost 7 years ago
10.1038/srep25039
Characterization of piRNAs across postnatal development in mouse brainCited by: 34
Author(s): Yanal Ghosheh, Loqmane Seridi, Tae Woo Ryu, Hazuki Takahashi, Valerio Orlando, Piero Carninci, Timothy Ravasi
Software Mentions: 2
Published: over 8 years ago
10.1038/srep37324
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analysesCited by: 29
Author(s): Chih-Yu Chen, Wenqiang Shi, Bradley P. Balaton, Allison Matthews, Yifeng Li, David J. Arenillas, Anthony Mathelier, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Carolyn J. Brown, Wyeth W. Wasserman
Software Mentions: 2
Published: about 8 years ago
10.1186/s13045-018-0673-6
Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategiesCited by: 30
Author(s): Nonthaphat Kent Wong, Chien‐Ling Huang, Rabiul Islam, Shea Ping Yip
Software Mentions: 2
Published: about 6 years ago
10.1189/jlb.6TA1014-477RR
Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cellsCited by: 21
Author(s): Anagha Joshi, Christopher Pooley, Tom C. Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis B. H. Geijtenbeek, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Yoshihide Hayashizaki, Piero Carninci, Michael Rehli, David Hume
Software Mentions: 2
Published: over 9 years ago
10.3390/cancers10110441
Impacts of Cancer on Platelet Production, Activation and Education and Mechanisms of Cancer-Associated ThrombosisCited by: 61
Author(s): Léa Plantureux, Diane Mège, Lydie Crescence, Françoise Dignat-George, Christophe Dubois, Laurence Panicot‐Dubois
Software Mentions: 1
Published: about 6 years ago
10.1111/dar.12193
Alcohol brief interventions practice following training for multidisciplinary health and social care teams: A qualitative interview studyCited by: 13
Author(s): Niamh Fitzgerald, Heather Molloy, Fiona MacDonald, Jim McCambridge
Software Mentions: 1
Published: about 10 years ago
10.1128/mBio.02550-18
Biphasic Dynamics of Macrophage Immunometabolism during<i>Mycobacterium tuberculosis</i>InfectionCited by: 92
Author(s): Lanbo Shi, Qi Jiang, Yuri Bushkin, Selvakumar Subbian, Sanjay Tyagi
Software Mentions: 1
Published: over 5 years ago
10.3390/e22090942
Models of the Gene Must Inform Data-Mining Strategies in GenomicsCited by: 5
Author(s): Łukasz Huminiecki
Software Mentions: 1
Published: about 4 years ago
10.1186/1756-8935-5-2
Knockdown of menin affects pre-mRNA processing and promoter fidelity at the interferon-gamma inducible IRF1 geneCited by: 5
Author(s): Lauren B Auriemma, Shaili Shah, Lara M. Linden, Melissa A. Henriksen
Software Mentions: 1
Published: almost 13 years ago
10.1186/1756-8935-6-S1-P53
Genome-wide analysis of promoter and enhancer usage in hematopoietic stem cell differentiationCited by: 0
Author(s): Annarita Miccio, Clelia Peano, Oriana Romano, Guidantonio Malagoli Tagliazucchi, Luca Petiti, Ingrid Cifola, Ermanno Rizzi, Marco Severgnini, Silvio Bicciato, Gianluca De Bellis, Fulvio Mavilio
Software Mentions: 1
Published: over 11 years ago
10.1111/jfd.12249
<i>Flavobacterium branchiophilum</i> and <i>F. succinicans</i> associated with bacterial gill disease in rainbow trout <i>Oncorhynchus mykiss</i> (Walbaum) in water recirculation aquaculture systemsCited by: 47
Author(s): Christopher Good, John Davidson, Gregory D. Wiens, Timothy J. Welch, Steven T. Summerfelt
Software Mentions: 1
Published: over 10 years ago
10.1002/bies.201100084
Long non‐coding RNA modifies chromatinCited by: 175
Author(s): Alka Saxena, Piero Carninci
Software Mentions: 1
Published: about 13 years ago
10.1038/s12276-020-0409-x
An era of single-cell genomics consortiaCited by: 12
Author(s): Yoshinari Ando, Andrew Tae-Jun Kwon, Jay W. Shin
Software Mentions: 1
Published: about 4 years ago
10.1186/1752-0509-6-S2-S7
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative datasetCited by: 57
Author(s): Shingo Kikugawa, Kensaku Nishikata, Katsuhiko Murakami, Yoshiharu Sato, Mami Suzuki, Md. Altaf-Ul-Amin, Shigehiko Kanaya, Tadashi Imanishi
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2458-13-178
Exploring knowledge, attitudes, and practices related to alcohol in Mongolia: a national population-based surveyCited by: 46
Author(s): Alessandro Demaio, Otgontuya Dugee, Maximilian de Courten, Ib Christian Bygbjerg, Enkhtuya Palam, Dan Wolf Meyrowitsch
Software Mentions: 1
Published: over 11 years ago
10.3389/fchem.2020.593602
Regioselective Radical Reaction of Monometallofullerene Y@C2v(9)-C82 With N-arylbenzamidine Mediated by Silver CarbonateCited by: 1
Author(s): Jia Li, Pengyuan Yu, Peng Xiang Lai, Jun Zou, Zhe Liu, Xiu-Guang Yi, Wei Wang, Changwang Pan
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2199-7-8
Alternative promoter usage of the membrane glycoprotein CD36Cited by: 50
Author(s): Malin Andersen, Boris Lenhard, Carl Whatling, Per Eriksson, Jacob Odeberg
Software Mentions: 1
Published: over 18 years ago
10.1186/1471-2199-11-64
L1CAM expression in endometrial carcinomas is regulated by usage of two different promoter regionsCited by: 36
Author(s): Marco Pfeifer, Uwe Schirmer, Claudia Geismann, Heiner Schäfer, Susanne Sebens, Peter Altevogt
Software Mentions: 1
Published: about 14 years ago
10.1186/1471-2199-9-30
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1Cited by: 26
Author(s): Barbara Maenz, Paul Hekerman, Eva M. Vela, Juan Galceran, Walter Becker
Software Mentions: 1
Published: almost 17 years ago
10.3389/fgene.2016.00026
Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human GenomeCited by: 26
Author(s): Michael J. Milligan, Erin Harvey, Albert D. Yu, Ashleigh L. Morgan, Daniela L. Smith, Eden Zhang, Jonathan F. Berengut, Jothini Sivananthan, Radhini Subramaniam, Aleksandra Skoric, Scott P. Collins, Caio Damski, Kevin V. Morris, Leonard Lipovich
Software Mentions: 1
Published: over 8 years ago
10.3389/fimmu.2015.00370
The Many Alternative Faces of Macrophage ActivationCited by: 222
Author(s): David Hume
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-8-298
Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcriptsCited by: 92
Author(s): Inge Seim, Christopher Collet, Adrian C. Herington, Lisa K. Chopin
Software Mentions: 1
Published: about 17 years ago
10.1186/2049-3258-71-29
Socio-demographic correlates of six indicators of alcohol consumption: survey findings of students across seven universities in England, Wales and Northern IrelandCited by: 40
Author(s): Walid El Ansari, René Šebeňa, Christiane Stock
Software Mentions: 1
Published: about 11 years ago
10.1186/gb-2007-8-3-r42
CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcriptsCited by: 3
Author(s): Shintaro Katayama, Mutsumi Kanamori-Katayama, Kazumi Yamaguchi, Piero Carninci, Yoshihide Hayashizaki
Software Mentions: 1
Published: almost 18 years ago
10.1186/gb-2012-13-9-r53
Modeling gene expression using chromatin features in various cellular contextsCited by: 239
Author(s): Xianjun Dong, Melissa C. Greven, Anshul Kundaje, Sarah Djebali, James Brown, Chao Cheng, T Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng
Software Mentions: 1
Published: almost 13 years ago
10.2196/13614
The Use of Smart Devices by Care Providers in Emergency Departments: Cross-Sectional Survey DesignCited by: 9
Author(s): Mohamad Alameddine, Hussein Soueidan, Maha Makki, Hani Tamim, Eveline Hitti
Software Mentions: 1
Published: over 5 years ago
10.1186/gb-2013-14-7-r73
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancerCited by: 77
Author(s): Georges St. Laurent, Dmitry Shtokalo, Biao Dong, Michael Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J. Triche, Timothy A. McCaffrey, Wendiong Xiao, Philipp Kapranov
Software Mentions: 1
Published: almost 12 years ago
10.1186/s12864-017-3834-z
Relatively frequent switching of transcription start sites during cerebellar developmentCited by: 26
Author(s): Peter Zhang, Emmanuel Dimont, Thomas Ha, Douglas J. Swanson, Winston Hide, Dan Goldowitz
Software Mentions: 1
Published: over 7 years ago
10.1186/s13059-017-1223-1
Millstone: software for multiplex microbial genome analysis and engineeringCited by: 5
Author(s): Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen, George M. Church
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-015-1485-5
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcriptionCited by: 25
Author(s): Susanne Bornelöv, Jan Komorowski, Claes Wadelius
Software Mentions: 1
Published: over 9 years ago
10.1128/JVI.01625-16
Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular CarcinomaCited by: 25
Author(s): Kübra Altinel, Kosuke Hashimoto, Wei Yu, Christine Neuveut, Ishita Gupta, Ana Maria Suzuki, Alexandre Dos Santos, Pierrick Moreau, Xiaoling Tian, Soichi Kojima, Sachi Kato, Yasuhiro Takikawa, Isao Hidaka, Masahito Shimizu, Tomokazu Matsuura, Akihito Tsubota, Hitoshi Ikeda, Sumiko Nagoshi, Harukazu Suzuki, Marie‐Louise Michel, Didier Samuel, Marie Annick Buendia, J Faivre, Piero Carninci
Software Mentions: 1
Published: almost 8 years ago
10.7554/eLife.52155
The single-cell eQTLGen consortiumCited by: 133
Author(s): Monique G. P. van der Wijst, DH de Vries, Hilde E. Groot, Gosia Trynka, Chung-Chau Hon, Marc Jan Bonder, Oliver Stegle, Martijn C. Nawijn, Youssef Idaghdour, Pim van der Harst, Ye Cj, Joseph E. Powell, Theis Fj, Ahmed Mahfouz, Matthias Heinig, Lude Franke
Software Mentions: 1
Published: over 4 years ago
10.1038/sdata.2017.147
Linking FANTOM5 CAGE peaks to annotations with CAGEscanCited by: 15
Author(s): Nicolas Bertin, Mickaël Mendez, Akira Hasegawa, Marina Lizio, Imad Abugessaisa, Jessica Severin, Mizuho Sakai-Ohno, Timo Lassmann, Takeya Kasukawa, Hideya Kawaji, Yoshihide Hayashizaki, Alistair R.R. Forrest, Charles Plessy
Software Mentions: 1
Published: about 7 years ago
10.1186/1471-2164-9-574
Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAsCited by: 82
Author(s): Fumihito Miura, Noriko Kawaguchi, Mikio Yoshida, Chihiro Uematsu, Keiji Kito, Yoshiyuki Sakaki, Takashi Ito
Software Mentions: 1
Published: almost 16 years ago
10.1002/cjp2.213
Transcription start site‐level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significanceCited by: 1
Author(s): Kei Sano, Takuo Hayashi, Yoshiyuki Suehara, Masaki Hosoya, Kazuya Takamochi, Shinji Kohsaka, Satsuki Kishikawa, Monami Kishi, Satomi Saito, Fumiyuki Takahashi, Kazuo Kaneko, Kenji Suzuki, Takashi Yao, Muneaki Ishijima, Tsuyoshi Saito
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2148-11-226
Conversion events in gene clustersCited by: 11
Author(s): Giltae Song, Chih-Hao Hsu, Cathy Riemer, Yu Zhang, Hie Lim Kim, Federico G. Hoffmann, Louxin Zhang, Ross C. Hardison, Eric D. Green, Webb Miller
Software Mentions: 1
Published: over 13 years ago
10.1098/rsob.150203
Systematic analysis of the <i>PTEN</i> 5′ leader identifies a major AUU initiated proteoformCited by: 38
Author(s): Ioanna Tzani, Ivaylo P. Ivanov, Dmitry E. Andreev, Ruslan I. Dmitriev, Kellie Dean, Pavel V. Baranov, John F. Atkins, Gary Loughran
Software Mentions: 1
Published: over 8 years ago
10.1098/rsob.190221
A practical view of fine-mapping and gene prioritization in the post-genome-wide association eraCited by: 73
Author(s): Roeland Broekema, Olivier B. Bakker, Iris Jonkers
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41598-017-04520-z
A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seqCited by: 128
Author(s): Bin Li, Tao Qing, Jiaquan Zhu, Zhiping Wen, Ying Yu, Ryutaro Fukumura, Yuanting Zheng, Yoichi Gondo, Leming Shi
Software Mentions: 1
Published: over 7 years ago
10.1186/1741-7007-6-31
A cryptic promoter in the first exon of the SPG4gene directs the synthesis of the 60-kDa spastin isoformCited by: 41
Author(s): Giuseppe Mancuso, Elena I. Rugarli
Software Mentions: 1
Published: over 16 years ago
10.1186/1471-2105-12-S11-A1
Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational BiologyCited by: 11
Author(s): Priscila Grynberg, Thomas Abeel, Pedro Lopes, Geoff Macintyre, Lorena Pantano Rubiño
Software Mentions: 1
Published: about 13 years ago
10.1186/1471-2105-15-S17-S1
Orthology-driven mapping of bidirectional promoters in human and mouse genomesCited by: 9
Author(s): Mary Qu Yang, Laura Elnitski
Software Mentions: 1
Published: almost 10 years ago
10.1038/s41598-020-61693-w
microRNA-875-5p plays critical role for mesenchymal condensation in epithelial-mesenchymal interaction during tooth developmentCited by: 11
Author(s): Keita Funada, Keigo Yoshizaki, Kouji Miyazaki, Han Xue, Tomomi Yuta, Tian Tian, Kanji Mizuta, Yao Fu, Tsutomu Iwamoto, Aya Yamada, Ichiro Takahashi, Satoshi Fukumoto
Software Mentions: 1
Published: over 4 years ago
10.1007/s12035-018-1465-2
Antisense Transcription in Loci Associated to Hereditary Neurodegenerative DiseasesCited by: 18
Author(s): S. Zucchelli, Stefania Fedele, Paolo Vatta, Raffaella Calligaris, Peter Heutink, Patrizia Rizzu, Masayoshi Itoh, Francesca Persichetti, Claudio Santoro, Hideya Kawaji, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Stefano Gustincich
Software Mentions: 1
Published: almost 6 years ago
10.15252/msb.20156492
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiationCited by: 302
Author(s): James S. Fraser, Carmelo Ferrai, Andrea M. Chiariello, Markus Schueler, Tiago Rito, Giovanni Laudanno, Mariano Barbieri, Benjamin L. Moore, Dorothee Kraemer, Stuart Aitken, Shaoping Xie, Kelly J. Morris, Masayoshi Itoh, Hideya Kawaji, Ines S. Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Colin A. Semple, Josée Dostie, Ana Pombo, Mario Nicodemi
Software Mentions: 1
Published: almost 9 years ago
10.3390/microorganisms9061339
Epigenetic Silencing of MicroRNA-126 Promotes Cell Growth in Marek’s DiseaseCited by: 2
Author(s): Isabelle Gennart, Astrid Petit, L. Wiggers, Srđan Pejaković, Nicolas Dauchot, Sylvie Laurent, Damien Coupeau, Benoît Muylkens
Software Mentions: 1
Published: over 3 years ago
10.1007/s00335-015-9593-8
Paradigm shifts in genomics through the FANTOM projectsCited by: 91
Author(s): Michiel de Hoon, Jay W. Shin, Piero Carninci
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pcbi.1005934
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human diseaseCited by: 15
Author(s): J Kenneth Baillie, Andrew D. Bretherick, C.S. Haley, Sara Clohisey, Alan Gray, Lucile Neyton, Jeffrey C. Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, James B. Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten O. Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, Damian J. Mole, Vladimir B. Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A. Wells, Nir Hacohen, Tom C. Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, David Hume
Software Mentions: 1
Published: over 6 years ago
10.1155/2018/8285653
Genetic Variant rs755622 Regulates Expression of the Multiple Sclerosis Severity Modifier D-Dopachrome Tautomerase in a Sex-Specific WayCited by: 11
Author(s): Zhijie Han, Jiaojiao Qu, Jin Zhao, Xiao Zou
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pgen.1008471
Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retrovirusesCited by: 8
Author(s): Melvyn W. Yap, George R. Young, Renata Varnaitė, Sergé Morand, Jonathan P. Stoye
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-2105-16-S8-A7
Evolution of 3'UTR-associated RNAsCited by: 1
Author(s): Jan Engelhardt, Peter F. Stadler
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0144677
Tor Signaling Regulates Transcription of Amino Acid Permeases through a GATA Transcription Factor Gaf1 in Fission YeastCited by: 15
Author(s): Yan Ma, Ning Ma, Qingbin Liu, Yue Qi, Ri-ichiroh Manabe, Tomoyuki Furuyashiki
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0183229
Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translationCited by: 21
Author(s): Hazuki Takahashi, Ana Kozhuharova, Harshita Sharma, Masakazu Hirose, Tetsuo Ohyama, Francesca Fasolo, Toshio Yamazaki, Diego Cotella, Claudio Santoro, S. Zucchelli, Stefano Gustincich, Piero Carninci
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pone.0144176
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter UsageCited by: 1
Author(s): Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Peter Arner, Alistair R.R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, Mariko Okada‐Hatakeyama, Jessica C. Mar
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0030809
Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule SequencerCited by: 22
Author(s): Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Yoshihide Hayashizaki
Software Mentions: 1
Published: almost 13 years ago
10.7150/thno.54150
Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant gliomaCited by: 4
Author(s): Jun Xiao, Xiaoyan Jin, Chunlong Zhang, Haozhe Zou, Zhenghong Chang, Nan Han, Xia Li, Yunpeng Zhang, Yongsheng Li
Software Mentions: 1
Published: almost 4 years ago