pypi: CAGE | Projects | Ecosyste.ms: Papers

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited 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/Bioconductor
Cited 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 regions
Cited 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 genomes
Cited 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 transcripts
Cited 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/Cas9
Cited 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 analysis
Cited 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 atlas
Cited 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 Cancer
Cited 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 analysis
Cited 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 data
Cited 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 injury
Cited by: 19
Author(s): Masayuki Yasuda, Yuji Tanaka, Koji M. Nishiguchi, Morin Ryu, S. Tsuda, Kouichi Maruyama, Toru Nakazawa
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-020-07334-y

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets
Cited 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 development
Cited 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 prediction
Cited 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 development
Cited 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 Review
Cited 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 data
Cited 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 function
Cited by: 14
Author(s): Rezvan Ehsani, Shahram Bahrami, Finn Drabløs
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-54180-4

A framework for identification of on- and off-target transcriptional responses to drug treatment
Cited 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 Model
Cited 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-seq
Cited 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 genome
Cited by: 15
Author(s): Christelle Robert, Ronan Kapétanovic, Dario Beraldi, Michael Watson, Alan Archibald, David Hume
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-019-5650-0

Selective translational usage of TSS and core promoters revealed by translatome sequencing
Cited 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 sites
Cited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited 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 blood
Cited 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 Space
Cited by: 15
Author(s): Anca F. Savulescu, Caron Jacobs, Yutaka Negishi, L. Davignon, Musa M. Mhlanga
Software Mentions: 3
Published: about 4 years ago

10.3389/fncel.2019.00391

The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Progenitor Cells
Cited 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: in vivo and in silico metabolic and genome engineering
Cited 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 assemblies
Cited 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 lung
Cited 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 Gears
Cited 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 lincRNAs
Cited 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 Occur
Cited by: 8
Author(s): Ulf Schaefer, Rimantas Kodzius, Kai Cui, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic
Software Mentions: 2
Published: almost 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 angiogenesis
Cited 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 stroke
Cited 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 inhibitors
Cited 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 Cells
Cited 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 miRNAs
Cited 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 ZAP
Cited 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 Australia
Cited 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 dog
Cited 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 brain
Cited 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 analyses
Cited 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: almost 8 years ago

10.1186/s13045-018-0673-6

Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies
Cited by: 30
Author(s): Nonthaphat Kent Wong, Chien‐Ling Huang, Rabiul Islam, Shea Ping Yip
Software Mentions: 2
Published: almost 6 years ago

10.1189/jlb.6TA1014-477RR

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells
Cited 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 Thrombosis
Cited by: 61
Author(s): Léa Plantureux, Diane Mège, Lydie Crescence, Françoise Dignat-George, Christophe Dubois, Laurence Panicot‐Dubois
Software Mentions: 1
Published: almost 6 years ago

10.1111/dar.12193

Alcohol brief interventions practice following training for multidisciplinary health and social care teams: A qualitative interview study
Cited 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 duringMycobacterium tuberculosisInfection
Cited 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 Genomics
Cited 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 gene
Cited 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 differentiation
Cited 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

Flavobacterium branchiophilum and F. succinicans associated with bacterial gill disease in rainbow trout Oncorhynchus mykiss (Walbaum) in water recirculation aquaculture systems
Cited 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 chromatin
Cited 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 consortia
Cited 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 dataset
Cited 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 survey
Cited 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 Carbonate
Cited 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 CD36
Cited 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 regions
Cited 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 E2F1
Cited 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 Genome
Cited 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 Activation
Cited 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 transcripts
Cited 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 Ireland
Cited 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 transcripts
Cited 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 contexts
Cited 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 Design
Cited 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 cancer
Cited 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 development
Cited 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 engineering
Cited 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 transcription
Cited 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 Carcinoma
Cited 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 consortium
Cited 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 CAGEscan
Cited 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 DNAs
Cited 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 significance
Cited 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 clusters
Cited 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 PTEN 5′ leader identifies a major AUU initiated proteoform
Cited 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 era
Cited 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-seq
Cited 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 isoform
Cited 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 Biology
Cited by: 11
Author(s): Priscila Grynberg, Thomas Abeel, Pedro Lopes, Geoff Macintyre, Lorena Pantano Rubiño
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-15-S17-S1

Orthology-driven mapping of bidirectional promoters in human and mouse genomes
Cited 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 development
Cited 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 Diseases
Cited 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 differentiation
Cited 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 Disease
Cited 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 projects
Cited 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 disease
Cited 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 Way
Cited 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 retroviruses
Cited 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 RNAs
Cited 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 Yeast
Cited 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 translation
Cited 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 Usage
Cited 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 Sequencer
Cited 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 glioma
Cited 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

Projects: pypi: CAGE

Papers Mentioning CAGE 101