cran: STAR | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.15237

Metabolic heterogeneity signature of primary treatment-naïve prostate cancer
Cited by: 16
Author(s): Dong Lin, Susan Ettinger, Sifeng Qu, Hui Xue, Noushin Nabavi, Si‐Sun Choi, Robert H. Bell, Fan Mo, Anne Haegert, Peter W. Gout, Neil Fleshner, Martin Gleave, Michael Pollak, Colin C. Collins, Yuzhuo Wang
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.18117

Notch signaling regulates metabolic heterogeneity in glioblastoma stem cells
Cited by: 55
Author(s): N. Sumru Bayın, Joshua D. Frenster, Rajeev Sen, Sheng Si, Aram S. Modrek, Nataliya Galifianakis, Igor Dolgalev, Valerio Ortenzi, Irineu Illa-Bochaca, Anadjeet Khahera, Jonathan Serrano, Luis Chiriboga, David Zagzag, John G. Golfinos, Werner Doyle, Aristotelis Tsirigos, Adriana Heguy, Mitchell Chesler, Mary Helen Barcellos‐Hoff, Matija Snuderl, Dimitris G. Placantonakis
Software Mentions: 2
Published: about 9 years ago

10.18632/oncotarget.20260

The conjugated antimetabolite 5-FdU-ECyd and its cellular and molecular effects on platinum-sensitive vs. -resistant ovarian cancer cells in vitro
Cited by: 5
Author(s): Sarah Schott, Pauline Wimberger, Barbara Klink, Konrad Grützmann, Julian Puppe, Ulrike Sophie Wauer, Daniel Martin Klotz, Evelin Schröck, Jan Dominik Kuhlmann
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.19283

Aberrantly activated Cox-2 and Wnt signaling interact to maintain cancer stem cells in glioblastoma
Cited by: 32
Author(s): Megan Wu, Jennifer Guan, Chris Li, Simon J Gunter, Labeeba Nusrat, S. C. Ng, Karan Dhand, Cindi M. Morshead, Albert Kim, Sunit Das
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.22159

Regulatory T cells characterized by low Id3 expression are highly suppressive and accumulate during chronic infection
Cited by: 7
Author(s): Katharina S. Rauch, Miriam Hils, Alexandra J. Menner, Mikael Sigvardsson, Susana Minguet, Peter Aichele, Christian Schachtrup, Christian Schachtrup
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.22867

Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling
Cited by: 32
Author(s): Masashi Fujita, Nagahide Matsubara, Ikuo Matsuda, Kazuhiro Maejima, Ayako Oosawa, Tomoki Yamano, Akihiro Fujimoto, Mayuko Furuta, Kaoru Nakano, Aya Oku‐Sasaki, Hiroko Tanaka, Yuichi Shiraishi, Raúl Nicolás Mateos, Kenta Nakai, Satoru Miyano, Naohiro Tomita, Seiichi Hirota, Hiroki Ikeuchi, Hidewaki Nakagawa
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.24341

Methotrexate sensitizes drug-resistant metastatic melanoma cells to BRAF V600E inhibitors dabrafenib and encorafenib
Cited by: 8
Author(s): Kayleigh C. Ross, Kevin F Chin, Dae-Hwan Kim, Christopher D. Marion, Timothy Yen, Vikram Bhattacharjee
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.24422

Human tripartite motif protein 52 is required for cell context-dependent proliferation
Cited by: 11
Author(s): Stefan Benke, Benedikt Agerer, Linda Haas, Martin Stöger, Alexander Lercher, Lisa Gabler, Izabella Kiss, Sara Scinicariello, Walter Berger, Andréas Bergthaler, Anna C. Obenauf, Gijs A. Versteeg
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.24862

ONC201 kills breast cancer cellsin vitroby targeting mitochondria
Cited by: 70
Author(s): Yoshimi Endo Greer, Natalie Porat-Shliom, Kunio Nagashima, Christina H. Stuelten, Dan Crooks, Vishal N. Kopardé, Sarah L. Gilbert, Celia Islam, Ashley Ubaldini, Yun Ji, Luca Gattinoni, Ferri Soheilian, Xiantao Wang, Markus Hafner, Jyoti Shetty, Bao Tran, Parthav Jailwala, Maggie Cam, Martin Lang, Donna Voeller, William C. Reinhold, Vinodh N. Rajapakse, Yves Pommier, Roberto Weigert, W. Marston Linehan, Stanley Lipkowitz
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.24808

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia
Cited by: 1
Author(s): Frida Danielsson, Erik Fasterius, Devin P. Sullivan, Linnea Hases, Kemal Sanli, Cheng Cheng Zhang, Adil Mardinoğlu, Cristina Al-Khalili, Mikael Huss, Mathias Uhlén, Cecilia Williams, Emma Lundberg
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.25188

The critical role that STAT3 plays in glioma-initiating cells: STAT3 addiction in glioma
Cited by: 41
Author(s): Debolina Ganguly, Meiyun Fan, Chuan Yang, Blazej Zbytek, David Finkelstein, Martine F. Roussel, Lawrence M. Pfeffer
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.27234

Assessment of circularized E7 RNA, GLUT1, and PD-L1 in anal squamous cell carcinoma
Cited by: 20
Author(s): Bahir Chamseddin, Eunice E. Lee, Jiwoong Kim, Xiaowei Zhan, Rong Yang, Kathleen M. Murphy, Cheryl Lewis, Gregory A. Hosler, Suntrea T.G. Hammer, Richard C. Wang
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.27511

hPCL3S promotes proliferation and migration of androgen-independent prostate cancer cells
Cited by: 5
Author(s): Souhila Abdelfettah, Gaylor Boulay, Marion Dubuissez, Nathalie Spruyt, Sara P. Garcia, Shruthi Rengarajan, Ingrid Loison, Xavier Leroy, Miguel N. Rivera, Dominique Leprince
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.27637

Inhibition of the RUNX1-CBFβ transcription factor complex compromises mammary epithelial cell identity: a phenotype potentially stabilized by mitotic gene bookmarking
Cited by: 6
Author(s): Joshua T. Rose, Eliana Moskovitz, Joseph R. Boyd, Jonathan A. R. Gordon, Nicole A. Bouffard, Andrew J. Fritz, Anuradha Illendula, John H. Bushweller, Jane B. Lian, Janet L. Stein, Sayyed K. Zaidi
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.27679

Induction of phenotypic changes in HER2-postive breast cancer cells in vivo and in vitro
Cited by: 2
Author(s): Anastasia Frank-Kamenetskii, Julia Mook, Meredith Reeves, Corinne A. Boulanger, Thomas J. Meyer, Lauren E. Ragle, H. Caroline Jordan, Gilbert H. Smith, Brian W. Booth
Software Mentions: 2
Published: almost 6 years ago

10.18632/oncotarget.27693

Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma
Cited by: 9
Author(s): Neetu Singh, Dinesh Kumar Sahu, Ratnesh Kumar Tripathi, Archana Mishra, Hari Shyam, Pratap Shankar, Mayank Jain, Nawazish Alam, Anil Kumar, Abhishek Mishra, Rebecca Chowdhry, Anjana Singh, Sudeep Gupta, Divya Mehrotra, Preeti Agarwal, Madhu Mati Goel, Arun Chaturvedi, Saurabh Agarwal, Manish Kumar Bajpai, Devendra K. Gupta, Madan Lal Brahma Bhatt, Ravi Kant
Software Mentions: 2
Published: almost 6 years ago

10.18632/oncotarget.27906

Characterization of the inflammatory microenvironment and hepatic macrophage subsets in experimental hepatocellular carcinoma models
Cited by: 10
Author(s): Helena Degroote, Sander Lefere, Astrid Vandierendonck, Bart Vanderborght, Tim Meese, Filip Van Nieuwerburgh, Xavier Verhelst, Anja Geerts, Hans Van Vlierberghe, Lindsey Devisscher
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.27955

Genome wide DNA methylation landscape reveals glioblastoma’s influence on epigenetic changes in tumor infiltrating CD4+ T cells
Cited by: 13
Author(s): Marpe Bam, Sreenivasulu Chintala, Kaleigh Fetcko, Brooke Carmen Williamsen, Seema Siraj, Sheng Liu, Jun Wan, Xiaoling Xuei, Yunlong Liu, Adam Leibold, Mahua Dey
Software Mentions: 2
Published: about 5 years ago

10.18632/oncotarget.28056

The antitumoral effects of chemerin are independent from leukocyte recruitment and mediated by inhibition of neoangiogenesis
Cited by: 7
Author(s): Ingrid Dubois-Vedrenne, Diana D.A.D. Al Delbany, Olivier De Henau, Virginie Robert, Maxime Vernimmen, Francina Langa, Anne Lefort, Frédérick Libert, Valérie Wittamer, Marc Parmentier
Software Mentions: 2
Published: almost 5 years ago

10.3390/jpm11050330

The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology
Cited by: 1
Author(s): Sigve Nakken, Wolfgang Lilleby, Marta D. Switlyk, Karen E. Knudsen, Oscar Lilleby, Sen Zhao, Fatemeh Kaveh, Per Olaf Ekstrøm, Alfonso Urbanucci, Eivind Hovig
Software Mentions: 2
Published: about 5 years ago

10.1186/s13023-021-01679-7

Proteomics analysis of a human brain sample from a mucolipidosis type IV patient reveals pathophysiological pathways
Cited by: 10
Author(s): Ayelet Vardi, Amir Pri-Or, Noa Wigoda, Yulia Grishchuk, Anthony H. Futerman
Software Mentions: 2
Published: over 5 years ago

10.1128/JVI.02102-20

Segment-Specific Kinetics of mRNA, cRNA, and vRNA Accumulation during Influenza Virus Infection
Cited by: 21
Author(s): Thu T Phan, Elizabeth J. Fay, Zion Lee, Stephanie L. Aron, Wei Shou Hu, Ryan A. Langlois
Software Mentions: 2
Published: about 5 years ago

10.1128/JVI.00319-20

Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication
Cited by: 3
Author(s): Bing Shao Chia, Bo Li, Ang Cui, Thomas Eisenhaure, Raktima Raychowdhury, David Lieb, Nir Hacohen
Software Mentions: 2
Published: over 5 years ago

10.1186/s12967-018-1578-4

PBMC fixation and processing for Chromium single-cell RNA sequencing
Cited by: 95
Author(s): Jinguo Chen, Foo Cheung, Rongye Shi, Huizhi Zhou, Wenrui Lu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12967-017-1350-1

Transforming growth factor beta (TGF-β) in adolescent chronic fatigue syndrome
Cited by: 14
Author(s): Vegard Bruun Wyller, Chinh Bkrong Nguyen, Judith Krey Ludviksen, Tom Eirik Mollnes
Software Mentions: 2
Published: over 8 years ago

10.1038/srep39094

Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle
Cited by: 21
Author(s): Anne-Laure Bougé, Eva M. Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, M. Kœnig, Mireille Claustres, Sylvie Tuffery‐Giraud
Software Mentions: 1
Published: over 9 years ago

10.1038/srep38624

Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome
Cited by: 25
Author(s): Assaf Malik, Vered Domankevich, Lijuan Han, Xiaodong Fang, Abraham B. Korol, Aaron Avivi, Imad Shams
Software Mentions: 1
Published: over 9 years ago

10.1038/srep37412

Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1
Cited by: 20
Author(s): Savita Sankar, Dhananjay Yellajoshyula, Bo Zhang, Bryan W. Teets, Nicole B. Rockweiler, Kristen L. Kroll
Software Mentions: 1
Published: over 9 years ago

10.1038/srep37235

Nitrogen-induced metabolic changes and molecular determinants of carbon allocation in Dunaliella tertiolecta
Cited by: 49
Author(s): Kenneth Wei Min Tan, Huixin Lin, Hui Shen, Yuan Kun Lee
Software Mentions: 1
Published: over 9 years ago

10.1038/srep35228

Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes
Cited by: 17
Author(s): Jing‐Woei Li, Heung‐Man Lee, Ying Wang, Amy Hin-Yan Tong, Kevin Y. Yip, Stephen Kwok‐Wing Tsui, Si Lok, Risa Ozaki, Andrea O. Y. Luk, Alice Pik‐Shan Kong, Wing–Yee So, C. Ronald, Juliana C.N. Chan, Ting-Fung Chan
Software Mentions: 1
Published: over 9 years ago

10.1038/srep34863

Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin
Cited by: 35
Author(s): Pablo Sandoval, J’Neka S. Claxton, Jae Woo Lee, Fahad Saeed, Jason D. Hoffert, Mark A. Knepper
Software Mentions: 1
Published: over 9 years ago

10.1038/srep33209

STAR: a simple TAL effector assembly reaction using isothermal assembly
Cited by: 13
Author(s): Sabine Gogolok, Claudia Garcia-Diaz, Steven M. Pollard
Software Mentions: 1
Published: almost 10 years ago

10.18632/oncotarget.26808

Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer
Cited by: 9
Author(s): Jessica Kaufmann, Nicolas Wentzensen, Titus J. Brinker, Niels Grabe
Software Mentions: 1
Published: over 7 years ago

10.1038/srep30311

Transcriptome sequencing wide functional analysis of human mesenchymal stem cells in response to TLR4 ligand
Cited by: 26
Author(s): Sun Hwa Kim, Amitabh Das, Jin Choul Chai, Bert Binas, Mi Ran Choi, Kyoung Sun Park, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep26200

Possible mechanisms of host resistance to Haemonchus contortus infection in sheep breeds native to the Canary Islands
Cited by: 57
Author(s): Zhengyu Guo, J. González, Julia N. Hernández, Tom N. McNeilly, Yolanda Corripio-Miyar, David Frew, Tyler Morrison, Peng Yu, Robert W. Li
Software Mentions: 1
Published: about 10 years ago

10.1038/srep22177

Evolution of the assassin’s arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea)
Cited by: 33
Author(s): Junxia Zhang, Eric R. L. Gordon, Michael Forthman, Wei Song Hwang, Kimberly K. O. Walden, Daniel R. Swanson, Kevin P. Johnson, Rudolf Meier, Christiane Weirauch
Software Mentions: 1
Published: over 10 years ago

10.1038/s41419-019-1799-3

Mitofusin 1 is required for female fertility and to maintain ovarian follicular reserve
Cited by: 60
Author(s): Man Zhang, Muhammed Burak Bener, Zongliang Jiang, Tianren Wang, Ecem Esencan, Richard T. Scott, Tamás L. Horváth, Emre Seli
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.66808

Expansion of CD10neg neutrophils and CD14+HLA-DRneg/low monocytes driving proinflammatory responses in patients with acute myocardial infarction
Cited by: 18
Author(s): Daniela Fraccarollo, Jonas Neuser, Julian Möller, Christian Riehle, Paolo Galuppo, Johann Bauersachs
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41419-018-0796-2

CCL5-deficiency enhances intratumoral infiltration of CD8+ T cells in colorectal cancer
Cited by: 48
Author(s): Shengbo Zhang, Ming Zhong, Chao Wang, Yanjie Xu, Wei‐Qiang Gao, Yan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1093/gigascience/gix081

Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
Cited by: 8
Author(s): Koen Kole, Yutaro Komuro, Jan Provazník, Jelena Pistolic, Vladimı́r Beneš, Paul Tiesinga, Tansu Celikel
Software Mentions: 1
Published: almost 9 years ago

10.1093/gigascience/giy010

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)
Cited by: 37
Author(s): Matteo Buti, Marco Moretto, Elena Barghini, Flavia Mascagni, Lucia Natali, Matteo Brilli, Alexandre Lomsadze, Paolo Sonego, L. Giongo, Michael Alonge, Riccardo Velasco, Claudio Varotto, Nada Šurbanovski, Mark Borodovsky, J. A. Ward, Kristof Engelen, Andrea Cavallini, Alessandro Cestaro, Daniel J. Sargent
Software Mentions: 1
Published: over 9 years ago

10.1093/gigascience/giy008

Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning
Cited by: 12
Author(s): Bradley M. Colquitt, David G. Mets, Michael S. Brainard
Software Mentions: 1
Published: over 8 years ago

10.1093/gigascience/gix122

VaDiR: an integrated approach to Variant Detection in RNA
Cited by: 14
Author(s): Lisa Neums, Seiji Suenaga, Peter Beyerlein, Sara Anders, Devin C. Koestler, Andrea Mariani, Jeremy Chien
Software Mentions: 1
Published: over 8 years ago

10.1093/gigascience/gix035

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
Cited by: 45
Author(s): Reuben W. Nowell, Benjamin Elsworth, Vicencio Oostra, Bas J. Zwaan, Christopher W. Wheat, Marjo Saastamoinen, Ilik J. Saccheri, Arjen E Van’t Hof, Bethany R. Wasik, Heidi Connahs, Muhammad Aslam, Sujai Kumar, Richard Challis, Antónia Monteiro, Paul M. Brakefield, Mark Blaxter
Software Mentions: 1
Published: about 9 years ago

10.1093/gigascience/gix012

RED-ML: a novel, effective RNA editing detection method based on machine learning
Cited by: 27
Author(s): Heng Xiong, Dongbing Liu, Qiye Li, Mengyue Lei, Liqin Xu, Liang Wu, Zongji Wang, Shancheng Ren, Wangsheng Li, Min Xia, Lihua Lü, Haorong Lu, Yong Hou, Shida Zhu, Xin Liu, Ying Sun, Jian Wang, Huanming Yang, Kui Wu, Xun Xu, Leo J. Lee
Software Mentions: 1
Published: over 9 years ago

10.1186/s13742-015-0105-2

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
Cited by: 2
Author(s): Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves‐Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1004448

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
Cited by: 8
Author(s): Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi‐Juan Hu, Zhaohui S. Qin
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41419-019-1946-x

The stem cell-associated transcription co-factor, ZNF521, interacts with GLI1 and GLI2 and enhances the activity of the Sonic hedgehog pathway
Cited by: 15
Author(s): Stefania Scicchitano, Marco Giordano, Valeria Lucchino, Ylenia Montalcini, Emanuela Chiarella, Annamaria Aloisio, Bruna Codispoti, Pietro Zoppoli, Valentina Melocchi, Fabrizio Bianchi, Enrico De Smaele, Maria Mesuraca, Giovanni Morrone
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.gpb.2020.10.005

Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients
Cited by: 384
Author(s): Zheng Zhao, Kenan Zhang, Qiangwei Wang, Guanzhang Li, Fan Zeng, Ying Zhang, Fan Wu, Rui‐Chao Chai, Zheng Wang, Chuanbao Zhang, Wei Zhang, Zhaoshi Bao, Tao Jiang
Software Mentions: 1
Published: over 5 years ago

10.1016/j.gpb.2016.02.003

Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts
Cited by: 74
Author(s): Tobias Jakobi, Lisa F. Czaja-Hasse, Richard Reinhardt, Christoph Dieterich
Software Mentions: 1
Published: almost 10 years ago

10.5808/GI.2020.18.1.e10

Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms
Cited by: 29
Author(s): Karl R. Franke, Erin L. Crowgey
Software Mentions: 1
Published: over 6 years ago

10.5808/GI.2019.17.3.e32

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing
Cited by: 29
Author(s): Sol A Jeon, Jong‐Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong‐Sung Kim, Jin Cheon Kim, Seon‐Young Kim
Software Mentions: 1
Published: almost 7 years ago

10.5808/GI.2019.17.1.e3

Identification of ERBB Pathway-Activated Cells in Triple-Negative Breast Cancer
Cited by: 8
Author(s): Soo Young Cho
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.28652

Host proteostasis modulates influenza evolution
Cited by: 30
Author(s): Angela M Phillips, Luna O Gonzalez, Emmanuel E Nekongo, Anna I. Ponomarenko, Sean M. McHugh, Vincent Butty, Stuart S. Levine, Yu‐Shan Lin, Leonid A. Mirny, Matthew D. Shoulders
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.59303

One-shot analysis of translated mammalian lncRNAs with AHARIBO
Cited by: 13
Author(s): L. Minati, Claudia Firrito, Alessia Del Piano, Alberto Peretti, Simone Sidoli, Daniele Peroni, Romina Belli, Francesco Gandolfi, Alessandro Romanel, Paola Bernabò, Jacopo Zasso, Alessandro Quattrone, Graziano Guella, Fabio Lauria, Gabriella Viero, Massimiliano Clamer
Software Mentions: 1
Published: over 5 years ago

10.1186/s13073-020-00746-1

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
Cited by: 21
Author(s): Francesc Muyas, Luís Zapata, Roderic Guigó, Stephan Ossowski
Software Mentions: 1
Published: about 6 years ago

10.1038/s41419-020-2257-y

Lipid desaturation-associated endoplasmic reticulum stress regulates MYCN gene expression in hepatocellular carcinoma cells
Cited by: 30
Author(s): Xian‐Yang Qin, Ting Su, Wenkui Yu, Soichi Kojima
Software Mentions: 1
Published: over 6 years ago

10.1186/s12967-021-02837-y

The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure
Cited by: 23
Author(s): Anbang He, Yangyun Zou, Cheng Wan, Jing Zhao, Qiong Zhang, Zhongyuan Yao, Tian Fen, Hong Wu, Xi Huang, Jing Fu, Chunxu Hu, Yue Sun, Lanbo Xiao, Tianli Yang, Zhaojuan Hou, Xin Dong, Sijia Lü, Yanping Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s13073-019-0635-9

TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression
Cited by: 41
Author(s): Quanyi Zhao, Robert Wirka, Trieu Nguyen, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic, Thomas Quertermous
Software Mentions: 1
Published: about 7 years ago

10.1038/s41419-020-2536-7

The HMGB1-RAGE axis modulates the growth of autophagy-deficient hepatic tumors
Cited by: 14
Author(s): Bilon Khambu, Honghai Hong, Sheng Liu, Gang Liu, Xiaoyun Chen, Zheng Dong, Jun Wan, Xiao Ming Yin
Software Mentions: 1
Published: about 6 years ago

10.1038/s41419-020-02754-w

The longevity-associated variant of BPIFB4 improves a CXCR4-mediated striatum–microglia crosstalk preventing disease progression in a mouse model of Huntington’s disease
Cited by: 14
Author(s): Alba Di Pardo, Elena Ciaglia, Monica Cattaneo, Anna Maciąg, Francesco Montella, Valentina Lopardo, Anna Ferrario, Francesco Villa, Michele Madonna, Enrico Amico, Albino Carrizzo, Antonio L. Damato, Giuseppe Pepe, Federico Marracino, Alberto Auricchio, Carmine Vecchione, Vittorio Maglione, Annibale Alessandro Puca
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13073-018-0567-9

Single-cell transcriptome analysis of lineage diversity in high-grade glioma
Cited by: 157
Author(s): Jinzhou Yuan, Hanna Mendes Levitin, Véronique Frattini, Erin C. Bush, Deborah Boyett, Jorge Samanamud, Michele Ceccarelli, Athanassios Dovas, George Zanazzi, Peter Canoll, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter A. Sims
Software Mentions: 1
Published: almost 8 years ago

10.1038/cddis.2016.188

MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3
Cited by: 26
Author(s): Philip Hallenborg, Majken Siersbæk, Iñigo Barrio-Hernandez, Ronni Nielsen, Karsten Kristiansen, Susanne Mandrup, Lars Grøntved, Blagoy Blagoev
Software Mentions: 1
Published: about 10 years ago

10.7554/eLife.13374

Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation
Cited by: 404
Author(s): Xinde Zheng, Leah Boyer, Mingji Jin, Jérôme Mertens, Yongsung Kim, Li Ma, Michael W. Hamm, Fred H. Gage, Tony Hunter
Software Mentions: 1
Published: about 10 years ago

10.1186/s13073-015-0152-4

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
Cited by: 71
Author(s): Patrick Deelen, Daria V. Zhernakova, Mark de Haan, Marijke van der Sijde, Marc Jan Bonder, Juha Karjalainen, K. Joeri van der Velde, Kristin M. Abbott, Jingyuan Fu, Cisca Wijmenga, Richard J. Sinke, Morris A. Swertz, Lude Franke
Software Mentions: 1
Published: over 11 years ago

10.1093/gbe/evab178

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae
Cited by: 5
Author(s): Chris J. Hulatt, René H. Wijffels, Matthew C. Posewitz
Software Mentions: 1
Published: almost 5 years ago

10.1093/gbe/evaa235

A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis
Cited by: 27
Author(s): Eiichi Shoguchi, Girish Beedessee, Kanako Hisata, Isao Tada, Haruhi Narisoko, Noriyuki Satoh, Masanobu Kawachi, Chuya Shinzato
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-021-03041-8

Platelet transcriptome profiles provide potential therapeutic targets for elderly acute myelocytic leukemia patients
Cited by: 2
Author(s): Bao Ji-zhang, Xinhua Zhao, Jiahui Lü, Zhaoyang Hu, Minghui Hu, Xiaoxia Hu, Libing Wang, Qi Hu, Wei Sun, Jie Wang, Hailin Chen, Hao Lü, Changgui Li, Jianing Xu, Yongming Zhou, Weiliang Zhu
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.27570

A 3D biofabricated cutaneous squamous cell carcinoma tissue model with multi-channel confocal microscopy imaging biomarkers to quantify antitumor effects of chemotherapeutics in tissue
Cited by: 15
Author(s): James Browning, Paige Derr, Kristy Derr, Nicole Doudican, Sam Michael, Samantha R. Lish, Nicholas A. Taylor, James G. Krueger, Marc Ferrer, John A. Carucci, Daniel S. Gareau
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.65482

Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
Cited by: 27
Author(s): Brian R. Lee, Agata Budzillo, Kristen Hadley, Jeremy A. Miller, Tim Jarsky, Katherine Baker, DiJon Hill, Lisa Kim, Rusty Mann, Lindsay Ng, Aaron Oldre, Ram Rajanbabu, Jessica Trinh, Sara Vargas, Thomas Braun, Rachel Dalley, Nathan W. Gouwens, Brian Kalmbach, Tae Kyung Kim, Kimberly A. Smith, Gilberto Soler-Llavina, Staci A. Sorensen, Bosiljka Tasic, Jonathan T. Ting, Ed Lein, Hongkui Zeng, Gabe J. Murphy, Jim Berg
Software Mentions: 1
Published: almost 5 years ago

10.1093/gbe/evaa195

Comprehensive Transcriptome of the Maize Stalk Borer,Busseola fusca, from Multiple Tissue Types, Developmental Stages, and Parasitoid Wasp Exposures
Cited by: 1
Author(s):
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pbio.2002623

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation
Cited by: 39
Author(s): Lauren Brady, Hejia Wang, Caleb M. Radens, Yue Bi, Milan Radovich, Amit Maity, Cristina Ivan, Mircea Ivan, Yoseph Barash, Constantinos Koumenis
Software Mentions: 1
Published: almost 9 years ago

10.1093/gbe/evz176

Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly
Cited by: 4
Author(s): Lars Höök, Luis Leal, Venkat Talla, Niclas Backström
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evz141

The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus
Cited by: 25
Author(s): Nikola Palevich, Paul Maclean, Abdul Baten, Richard W. Scott, David M Leathwick
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.09207

SPOP mutation leads to genomic instability in prostate cancer
Cited by: 142
Author(s): Gunther Boysen, Christopher E. Barbieri, Davide Prandi, Mirjam Blattner, Sung-Suk Chae, Arun Dahija, Srilakshmi Nataraj, Dennis Huang, Clarisse Marotz, Limei Xu, Julie Huang, Paola Lecca, Sagar Chhangawala, Liu D, Pengbo Zhou, Andrea Sboner, Johann S. de Bono, Francesca Demichelis, Yariv Houvras, Mark A. Rubin
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-021-02434-8

Specific splice junction detection in single cells with SICILIAN
Cited by: 12
Author(s): Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic, Julia Salzman
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13059-021-02399-8

LIQA: long-read isoform quantification and analysis
Cited by: 37
Author(s): Yu Hu, Fang Li, Xuelian Chen, Jiang Zhong, Mingyao Li, Kai Wang
Software Mentions: 1
Published: about 5 years ago

10.1186/s13059-021-02350-x

Intergenic RNA mainly derives from nascent transcripts of known genes
Cited by: 13
Author(s): Antonella Federico, Julian A. Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Software Mentions: 1
Published: about 5 years ago

10.1186/s13059-020-02180-3

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Cited by: 89
Author(s): Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jèssica Gómez‐Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo‐Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frías, Marta Gut, Toni Gabaldón, Alberto Pallavicini, Carlos Canchaya, Beatriz Novoa, Tyler Alioto, David Posada, António Figueras
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.2004718

Polarization-resolved microscopy reveals a muscle myosin motor-independent mechanism of molecular actin ordering during sarcomere maturation
Cited by: 40
Author(s): Olivier Loison, Manuela Weitkunat, Aynur Kaya-Çopur, Camila Nascimento Alves, Till Matzat, Maria L. Spletter, Stefan Luschnig, Sophie Brasselet, Pierre-François Lenne, Frank Schnorrer
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-020-02094-0

Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
Cited by: 52
Author(s): Qingxin Song, Atsumi Ando, Ning Jiang, Yoko Ikeda, Z Jeffrey Chen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2020.00982

RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer
Cited by: 67
Author(s): Yan Xie, Juan Li, Peilong Li, Ning Li, Ying Zhang, Helen Binang, Yinghui Zhao, Weili Duan, Yingjie Chen, Yunshan Wang, Du Li, Chuanxin Wang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12967-018-1495-6

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer
Cited by: 14
Author(s): Pascale Kündig, Charlotte Giesen, Hartland W. Jackson, Bernd Bodenmiller, Bärbel Papassotirolopus, Sandra N. Freiberger, Catharine Aquino, Lennart Opitz, Zsuzsanna Varga
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.47702

The alternative regenerative strategy of bearded dragon unveils the key processes underlying vertebrate tooth renewal
Cited by: 22
Author(s): Lotta Salomies, Julia Eymann, Imran Khan, Nicolas Di-Poı̈
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.47098

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation
Cited by: 204
Author(s): David McSwiggen, Anders S. Hansen, Sheila S Teves, Hervé Marie-Nelly, Yvonne Hao, Alec Heckert, Dinesh Vyas, Claire Dugast-Darzacq, Robert Tjian, Xavier Darzacq
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2020.632187

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects
Cited by: 14
Author(s): Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-020-02371-3

Decidual CD8+T cells exhibit both residency and tolerance signatures modulated by decidual stromal cells
Cited by: 18
Author(s): Lu Liu, Xixi Huang, Chunfang Xu, Chunqin Chen, Weijie Zhao, Da‐Jin Li, Liping Li, Li Wang, Meirong Du
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.28021

Actionability evaluation of biliary tract cancer by genome transcriptome analysis and Asian cancer knowledgebase
Cited by: 4
Author(s): Yuki Okawa, Nobutaka Ebata, Nayoung K.D. Kim, Masashi Fujita, Kazuhiro Maejima, Shota Sasagawa, Tõru Nakamura, Woong-Yang Park, Satoshi Hirano, Hidewaki Nakagawa
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41419-021-04146-0

The long non-coding RNA HOTAIRM1 promotes tumor aggressiveness and radiotherapy resistance in glioblastoma
Cited by: 18
Author(s): Ulvi Ahmadov, Daniel Picard, Jasmin Bartl, Manuela Silginer, Marija Trajkovic‐Arsic, Nan Qin, Lena Blümel, Marietta Wolter, Jonathan Lim, David Pauck, Alina M Winkelkotte, Marlen Melcher, Maike Langini, Viktoria Marquardt, Felix Sander, Anja Stefanski, Sascha Steltgens, Christina Hassiepen, Anna Kaufhold, Frank Meyer, Annette Seibt, Lara Kleinesudeik, Anika Hain, Carsten Münk, Christiane B. Knobbe-Thomsen, Alexander Schramm, Ute Fischer, Gabriel Leprivier, Kai Stühler, Simone Fulda, Jens T. Siveke, Felix Distelmaier, Arndt Borkhardt, Michael Weller, Guido Reifenberger, Marc Remke
Software Mentions: 1
Published: almost 5 years ago

10.1007/s11104-017-3265-2

Depth of soil compaction predominantly affects rice yield reduction by reproductive-stage drought at varietal screening sites in Bangladesh, India, and Nepal
Cited by: 10
Author(s): Suresh Prasad Singh, Abhinav Jain, M. S. Anantha, Santosh Raj Tripathi, Subarna Sharma, Santosh Kumar, A. Prasad, Bhawana Sharma, Biswajit Karmakar, Rudra Bhattarai, Surojit Das, Satish Kumar Singh, V. V. Shenoy, R. Chandra Babu, S. Robin, Padmini Swain, J. L. Dwivedi, Ram Baran Yadaw, Nimai Prasad Mandal, T. Ram, K. K. Mishra, Satish Verulkar, Tamal Lata Aditya, Krishna Prasad K, Puvvada Perraju, Ram Krishna Mahato, Sheetal Sharma, K. Anitha Raman, Arvind Kumar, Amelia Henry
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.59166

Metabolic but not transcriptional regulation by PKM2 is important for natural killer cell responses
Cited by: 17
Author(s): Jessica Walls, Jeffrey Subleski, Erika M. Palmieri, Marieli Gonzalez-Cotto, Clair M. Gardiner, Daniel W. McVicar, David K. Finlay
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2021.612354

Inhibition of HSP90 as a Strategy to Radiosensitize Glioblastoma: Targeting the DNA Damage Response and Beyond
Cited by: 10
Author(s): Michael Orth, Valérie Albrecht, Karin Seidl, Linda Kinzel, Kristian Unger, Julia Heß, Lisa Kreutzer, Na Sun, Benjamin Stegen, Alexander Nieto, Jessica Maas, Nicolas Winssinger, Anna A. Friedl, Axel Walch, Claus Belka, Horst Zitzelsberger, Maximilian Niyazi, Kirsten Lauber
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2021.622244

Patient-Derived Nasopharyngeal Cancer Organoids for Disease Modeling and Radiation Dose Optimization
Cited by: 11
Author(s): Sasidharan Swarnalatha Lucky, Martin Law, Man Tin Lui, Jamie Mong, Jin Shi, Sidney Yu, Do Kun Yoon, Shih Kien Djeng, Ji‐Guang Wang, Chwee Ming Lim, Min Tan
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.49117

The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay
Cited by: 132
Author(s): Karole N. D’Orazio, Colin Chih-Chien Wu, Niladri K. Sinha, Raphaël Loll-Krippleber, Grant W. Brown, Rachel Green
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2019.01120

Epstein-Barr Virus BART Long Non-coding RNAs Function as Epigenetic Modulators in Nasopharyngeal Carcinoma
Cited by: 43
Author(s): Rob J. A. Verhoeven, S. Y. Tong, Bobo Wing-Yee Mok, Jiayan Liu, Songtao He, Jingfeng Zong, Yixin Chen, Sai‐Wah Tsao, Maria Li Lung, Honglin Chen
Software Mentions: 1
Published: over 6 years ago

10.3389/fonc.2020.01498

Immune-Related Gene Expression and Cytokine Secretion Is Reduced Among African American Colon Cancer Patients
Cited by: 26
Author(s): Jenny Paredes, Jovanny Zabaleta, Jone Garai, Ping Ji, Sayed Imtiaz, Marzia Spagnardi, Joussette I. Alvarado, Li Li, Mubarak Akadri, Kaylene Barrera, María Muñoz-Sagastibelza, Raavi Gupta, Mohamed Alshal, Maksim Agaronov, Henry Talus, Xuefeng Wang, John M. Carethers, Jennie L. Williams, Laura Martello
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2015.00016

Therapeutic Re-Activation of Protein Phosphatase 2A in Acute Myeloid Leukemia
Cited by: 23
Author(s): Kavitha Ramaswamy, Barbara Spitzer, Alex Kentsis
Software Mentions: 1
Published: over 11 years ago

10.3389/fonc.2020.611467

Identification of STRBP as a Novel JAK2 Fusion Partner Gene in a Young Adult With Philadelphia Chromosome-Like B-Lymphoblastic Leukemia
Cited by: 4
Author(s): Xinyue Zhang, Haiping Dai, Zheng Li, Jia Yin, Xingping Lang, Chen Yang, Sheng Xiao, Mingqing Zhu, Dandan Liu, Hong Liu, Hongjie Shen, Depei Wu, Xiaowen Tang
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2020.01203

A Greedy Algorithm-Based Stem Cell LncRNA Signature Identifies a Novel Subgroup of Lung Adenocarcinoma Patients With Poor Prognosis
Cited by: 3
Author(s): Seema Khadirnaikar, Annesha Chatterjee, Pranjal Kumar, Sudhanshu Shukla
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2019.01279

Fry Is Required for Mammary Gland Development During Pregnant Periods and Affects the Morphology and Growth of Breast Cancer Cells
Cited by: 6
Author(s): Yan Liu, Xushen Chen, Zhihong Gong, Hao Zhang, Fudong Fan, Xiaojiang Tang, Jie Wang, Peng Xu, Helmut Zarbl, Xuefeng Ren
Software Mentions: 1
Published: over 6 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759