cran: STAR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-88671-0

Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period
Cited by: 0
Author(s): Arnaud Beddok, Gaëlle Pérot, Sophie Le Guellec, Noémie Thébault, Alexandre Coutté, Henri Sevestre, Bruno Chauffert, Frédéric Chibon
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-04356-7

Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains
Cited by: 28
Author(s): Qianhui Yu, Zhisong He
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-04333-0

Hypoxia is a Key Driver of Alternative Splicing in Human Breast Cancer Cells
Cited by: 52
Author(s): Jian Han, Jia Li, Jeongwon Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Software Mentions: 1
Published: over 9 years ago

10.3390/cells9102175

Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
Cited by: 11
Author(s): Adam J. Poe, Mangesh Kulkarni, Aleksandra Leszczynska, Jie Tang, Ruchi Shah, Yasaman Jami‐Alahmadi, Jason Wang, Andrei A. Kramerov, Vasu Punj, Alexander V. Ljubimov, Mehrnoosh Saghizadeh
Software Mentions: 1
Published: about 6 years ago

10.3390/cells10020399

Aldehyde Dehydrogenase, a Therapeutic Target in Chordoma: Analysis in 3D Cellular Models
Cited by: 4
Author(s): Marie-Anaïs Locquet, Anne-Lise Dechaume, Paul Berchard, Lhorra Abbes, Daniel Pissaloux, Franck Tirode, Inês Ramos, Julie Bedoucha, Julie Valantin, Marie Karanian, Raul Perret, Olivier Gille, Jean‐Yves Blay, Aurélie Dutour
Software Mentions: 1
Published: over 5 years ago

10.3390/cells10092306

Overexpression of Msx1 in Mouse Lung Leads to Loss of Pulmonary Vessels Following Vascular Hypoxic Injury
Cited by: 0
Author(s): James West, Anandharajan Rathinasabapathy, Xinping Chen, Sheila Shay, Shanti Gladson, Megha Talati
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-02520-7

Tropospheric Warming Over The Past Two Decades
Cited by: 20
Author(s): Benjamin D. Santer, Susan Solomon, F. J. Wentz, Qiang Fu, Stephen Po‐Chedley, C. A. Mears, Jeffrey F. Painter, C. Bonfils
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-90047-3

From multi-omics integration towards novel genomic interaction networks to identify key cancer cell line characteristics
Cited by: 2
Author(s): T. J. M. Kuijpers, J. C. S. Kleinjans, Danyel Jennen
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-89927-5

Predicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool
Cited by: 3
Author(s): Carlos Wert-Carvajal, Rubén J. Sánchez-García, José Ramón Macías, Rebeca Sanz‐Pamplona, Almudena Méndez Pérez, Ramón Alemany, Esteban Veiga, C.O.S. Sorzano, Arrate Muñoz-Barrutia
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-01377-0

Transcriptomic response of durum wheat to nitrogen starvation
Cited by: 103
Author(s): Pasquale Luca Curci, Riccardo Aiese Cigliano, Diana L. Zuluaga, Michela Janni, Walter Sanseverino, Gabriella Sonnante
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-01165-w

Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
Cited by: 7
Author(s): Zhibiao Mai, Chuan-Le Xiao, Jingjie Jin, Gong Zhang
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-90798-z

Transcriptome analysis of MBD5-associated neurodevelopmental disorder (MAND) neural progenitor cells reveals dysregulation of autism-associated genes
Cited by: 4
Author(s): Sureni V Mullegama, Stephen P. Klein, Stephen R. Williams, Jeffrey W. Innis, Frank J. Probst, Chad R. Haldeman-Englert, Julián A. Martínez-Agosto, Ying Yang, Yuchen Tian, Sarah H. Elsea, Toshihiko Ezashi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-00801-9

Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum
Cited by: 13
Author(s): Sherwin Chan, Jun-Hong Ch’ng, Mats Wahlgren, Jessada Thutkawkorapin
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-00575-0

Eμ and 3′RR IgH enhancers show hierarchic unilateral dependence in mature B-cells
Cited by: 17
Author(s): Alexis Saintamand, Christelle Vincent-Fabert, Marie Marquet, Nour Ghazzaui, Virginie Magnone, Eric Pinaud, Michel Cogné, Yves Denizot
Software Mentions: 1
Published: over 9 years ago

10.3390/cells10061356

Continuous Inflammatory Stimulation Leads via Metabolic Plasticity to a Prometastatic Phenotype in Triple-Negative Breast Cancer Cells
Cited by: 4
Author(s): Dina Morein, Linor Rubinstein-Achiasaf, Hadar Brayer, Orly Dorot, Edward Pichinuk, Hagar Ben-Yaakov, Tsipi Meshel, Metsada Pasmanik‐Chor, Adit Ben‐Baruch
Software Mentions: 1
Published: over 5 years ago

10.1038/srep46440

LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes
Cited by: 8
Author(s): Hyung Chan Suh, Touati Benoukraf, S. Pavithra, Tong Yin, Qi Cao, Jonathan Said, Stephen Lee, Raymond Boon Tar Lim, Henry Yang, Jacqueline Salotti, Peter F. Johnson, Vikas Madan, H. Phillip Koeffler
Software Mentions: 1
Published: over 9 years ago

10.1038/srep43745

Dietary restriction protects against diethylnitrosamine-induced hepatocellular tumorigenesis by restoring the disturbed gene expression profile
Cited by: 16
Author(s): Ting Duan, Wenjie Sun, Mohan Zhang, Juan Ge, Yansu He, Jun Zhang, Yifan Zheng, Wei Yang, Han‐Ming Shen, Jun Yang, Xinqiang Zhu, Peilin Yu
Software Mentions: 1
Published: over 9 years ago

10.1038/srep40214

Aminophylline suppresses stress-induced visceral hypersensitivity and defecation in irritable bowel syndrome
Cited by: 16
Author(s): Teita Asano, Ken Ichiro Tanaka, Arisa Tada, Hikaru Shimamura, Rikako Tanaka, Hiroki Maruoka, Mitsuko Takenaga, Tohru Mizushima
Software Mentions: 1
Published: almost 10 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: almost 10 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: almost 10 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: almost 10 years ago

10.1038/s41598-021-90510-1

Human induced pluripotent stem cell derived hepatocytes provide insights on parenteral nutrition associated cholestasis in the immature liver
Cited by: 4
Author(s): T. Hang Nghiem-Rao, Courtney Pfeifer, Michelle Asuncion, Joshua Nord, Daniel J. Schill, Kirthi Pulakanti, Shailendra B. Patel, Lisa Ann Cirillo, Sridhar Rao
Software Mentions: 1
Published: over 5 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: almost 10 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: about 10 years ago

10.3390/cells8050461

The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae
Cited by: 16
Author(s): L. V. Trilisenko, Anton Zvonarev, Airat Valiakhmetov, Aleksey A. Penin, Irina A. Eliseeva, V. G. Ostroumov, Ivan V. Kulakovskiy, T. V. Kulakovskaya
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-92529-w

The ATF6β-calreticulin axis promotes neuronal survival under endoplasmic reticulum stress and excitotoxicity
Cited by: 8
Author(s): Dinh Thi Nguyen, Thuong Manh Le, Tsuyoshi Hattori, Mika Takarada-Iemata, Hiroshi Ishii, Jureepon Roboon, Takashi Tamatani, Takayuki Kannon, Kazuyoshi Hosomichi, Atsushi Tajima, Shusuke Taniuchi, Masato Miyake, Seiichi Oyadomari, Takashi Tanaka, Nobuo Kato, Shunsuke Saito, Kazutoshi Mori, Osamu Hori
Software Mentions: 1
Published: over 5 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: about 10 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: about 10 years ago

10.3390/nu11051081

Transcriptomic Analysis of MAPK Signaling in NSC-34 Motor Neurons Treated with Vitamin E
Cited by: 7
Author(s): Luigi Chiricosta, Agnese Gugliandolo, Giuseppe Tardiolo, Placido Bramantı, Emanuela Mazzon
Software Mentions: 1
Published: over 7 years ago

10.3390/cells9081806

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences
Cited by: 16
Author(s): Annie Robic, Julie Demars, Christa Kühn
Software Mentions: 1
Published: about 6 years ago

10.3390/cells9071683

Inter-Tumor Heterogeneity—Melanomas Respond Differently to GM-CSF-Mediated Activation
Cited by: 10
Author(s): Adi Moshe, Sivan Izraely, Orit Sagi‐Assif, Sapir Malka, Shlomit Ben‐Menachem, Tsipi Meshel, Metsada Pasmanik‐Chor, Dave S. B. Hoon
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-91358-1

Neoantigens elicit T cell responses in breast cancer
Cited by: 13
Author(s): Takafumi Morisaki, Makoto Kubo, Masayo Umebayashi, Poh Yin Yew, Satoshi Yoshimura, Jae-Hyun Park, Kazuma Kiyotani, Masaya Kai, Mai Yamada, Yoshinao Oda, T. Morisaki, Masafumi Nakamura
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-93180-1

Florigen governs shoot regeneration
Cited by: 4
Author(s): Yaarit Kutsher, Michal Fisler, Adi Faigenboim, Moshe Reuveni
Software Mentions: 1
Published: over 5 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: over 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: over 10 years ago

10.3390/cells9030783

A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma
Cited by: 8
Author(s): Marianna Szemes, Zsombor Melegh, Jacob Bellamy, Alexander Greenhough, Madhu Kollareddy, Daniel Catchpoole, Karim Malik
Software Mentions: 1
Published: over 6 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

10.3390/cells9010162

Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN)
Cited by: 6
Author(s): Tian-Li Duan, Han Yi Jiao, Guang‐Jun He, Yong-Bin Yan
Software Mentions: 1
Published: almost 7 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: about 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: almost 9 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: over 9 years ago

10.3390/cells9102333

Tafazzin Mutation Affecting Cardiolipin Leads to Increased Mitochondrial Superoxide Anions and Mitophagy Inhibition in Barth Syndrome
Cited by: 12
Author(s): Patrice X. Petit, Hector Ardilla-Osorio, Lucile Penalvia, Nathan Earl Rainey
Software Mentions: 1
Published: about 6 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

10.3390/nu11040709

High Levels of Prebiotic Resistant Starch in Diet Modulate Gene Expression and Metabolomic Profile in Pancreatic Cancer Xenograft Mice
Cited by: 9
Author(s): Concetta Panebianco, Antonio Villani, Valerio Pazienza
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.28768

Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation
Cited by: 26
Author(s): Chee Wai Chua, Nusrat J Epsi, Eva Leung, Shouhong Xuan, Ming Lei, Bo I Li, Sarah K. Bergren, Hanina Hibshoosh, Antonina Mitrofanova, Michael M. Shen
Software Mentions: 1
Published: almost 9 years ago

10.3390/cells9020516

Transcriptional and Ultrastructural Analyses Suggest Novel Insights into Epithelial Barrier Impairment in Celiac Disease
Cited by: 7
Author(s): Agnieszka Sowińska, Yasser Morsy, E. Czarnowska, Beata Oralewska, Ewa Konopka, Marek Woynarowski, Sylwia Szymańska, Maria Ejmont, Michael Scharl, Joanna B. Bierła, Marcin Wawrzyniak, Božena Cukrowská
Software Mentions: 1
Published: over 6 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

10.1016/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: about 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: about 7 years ago

10.1038/s41598-021-95630-2

Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior
Cited by: 11
Author(s): Kathleen M Hudson, Emily Shiver, Jianshi Yu, Sanya Mehta, Dereje D. Jima, Maureen A. Kane, Heather B. Patisaul, Michael Cowley
Software Mentions: 1
Published: about 5 years ago

10.1016/j.cels.2021.04.006

Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity
Cited by: 16
Author(s): Joanna M. Chustecki, Daniel J. Gibbs, George W. Bassel, Iain G. Johnston
Software Mentions: 1
Published: over 5 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

10.1371/journal.pgen.1007206

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC
Cited by: 7
Author(s): Xin Bai, Ji An An Jia, Meng Fang, Shipeng Chen, Xiaotao Liang, Shanfeng Zhu, Shuqin Zhang, Jianfeng Feng, Fengzhu Sun, Chunfang Gao
Software Mentions: 1
Published: over 8 years ago

10.1016/j.cels.2018.02.004

Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction
Cited by: 61
Author(s): Manuel Razo-Mejia, Stephanie L. Barnes, Nathan M. Belliveau, Griffin Chure, Tal Einav, Mitchell Lewis, Rob Phillips
Software Mentions: 1
Published: over 8 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759