cran: STAR | Projects | Ecosyste.ms: Papers

10.1002/jbm4.10071

MicroRNA‐138 Inhibits Osteogenic Differentiation and Mineralization of Human Dedifferentiated Chondrocytes by Regulating RhoC and the Actin Cytoskeleton
Cited by: 17
Author(s): Hongjun Zhang, David Ramnaraign, Britta A. Anderson, Eric Tycksen, Ryan M. Nunley, Audrey McAlinden
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms21228785

Human Thymic CD10+ PD-1+ Intraepithelial Lymphocyte Precursors Acquire Interleukin-15 Responsiveness at the CD1a– CD95+ CD28– CCR7– Developmental Stage
Cited by: 7
Author(s): Lore Billiet, Glenn Goetgeluk, Sarah Bonte, Stijn De Munter, Laurenz De Cock, Melissa Pille, Joline Ingels, Hanne Jansen, Karin Weening, Filip Van Nieuwerburgh, Tessa Kerre, Tom Taghon, Georges Leclercq, Bart Vandekerckhove
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-021-00989-3

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant
Cited by: 18
Author(s): Elise Gay, Jessica L. Soyer, Nicolas Lapalu, Juliette Linglin, Isabelle Fudal, Corinne Da Silva, Patrick Wincker, Jean‐Marc Aury, Corinne Cruaud, Anne Levrel, Jocelyne Lemoine, Régine Delourme, Thierry Rouxel, Marie‐Hélène Balesdent
Software Mentions: 1
Published: over 5 years ago

10.1172/jci.insight.141217

Liver epithelial focal adhesion kinase modulates fibrogenesis and hedgehog signaling
Cited by: 9
Author(s): Yun Weng, Tyler J Lieberthal, Vivian X. Zhou, Maya Lopez-Ichikawa, Manuel Armas-Phan, Tristan K Bond, Miya Yoshida, Won‐Tak Choi, Tzu-Ming Chang
Software Mentions: 1
Published: over 5 years ago

10.1172/jci.insight.142560

Tumor genotype, location, and malignant potential shape the immunogenicity of primary untreated gastrointestinal stromal tumors
Cited by: 10
Author(s): Daniela Gasparotto, Marta Sbaraglia, Sabrina Rossi, Davide Baldazzi, Monica Brenca, Alessia Mondello, Federica Nardi, Dominga Racanelli, Matilde Cacciatore, Angelo Paolo Dei Tos, Roberta Maestro
Software Mentions: 1
Published: over 5 years ago

10.1172/jci.insight.140627

LncRNA VINAS regulates atherosclerosis by modulating NF-κB and MAPK signaling
Cited by: 46
Author(s): Viorel Simion, Hong-Hao Zhou, Jacob B. Pierce, Dafeng Yang, Stefan Haemmig, Yevgenia Tesmenitsky, Galina K. Sukhova, Peter H. Stone, Peter Libby, Mark W. Feinberg
Software Mentions: 1
Published: over 5 years ago

10.1107/S2053229618017084

The solid-state structure of the β-blocker metoprolol: a combined experimental and <i>in silico</i> investigation
Cited by: 11
Author(s): Patrizia Rossi, Paola Paoli, L. Chelazzi, Luca Conti, Andrea Bencini
Software Mentions: 1
Published: over 7 years ago

10.1002/advs.202100805

A 3D Fiber‐Hydrogel Based Non‐Viral Gene Delivery Platform Reveals that microRNAs Promote Axon Regeneration and Enhance Functional Recovery Following Spinal Cord Injury
Cited by: 33
Author(s): Na Zhang, Junquan Lin, Vincent Po Hen Lin, Ulla Milbreta, Jiah Shin Chin, Elaine Guo Yan Chew, Michelle Mulan Lian, Jia Nee Foo, Kunyu Zhang, Wutian Wu, Sing Yian Chew
Software Mentions: 1
Published: about 5 years ago

10.1172/jci.insight.149033

Gut germinal center regeneration and enhanced antiviral immunity by mesenchymal stem/stromal cells in SIV infection
Cited by: 7
Author(s): Mariana G. Weber, C. J. Walters, Amir Kol, Clarissa Santos Rocha, Lauren A. Hirao, Abigail L Mende, Bipin Balan, Juan Arredondo, Sonny R. Elizaldi, Smita S. Iyer, Alice F. Tarantal, Satya Dandekar
Software Mentions: 1
Published: about 5 years ago

10.1172/jci.insight.146572

The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice
Cited by: 8
Author(s): Kazunobu Matsushita, Xin Li, Yuki Nakamura, Danyue Dong, Kaori Mukai, Mindy Tsai, S Montgomery, Stephen J. Galli
Software Mentions: 1
Published: about 5 years ago

10.1172/jci.insight.146314

TNF blockade uncouples toxicity from antitumor efficacy induced with CD40 chemoimmunotherapy
Cited by: 5
Author(s): Maureen Stone, Vivian Lee, Veronica M. Herrera, Kathleen Graham, Jae Woo Lee, Austin P. Huffman, Heather Coho, Evan Tooker, Max I. Myers, Michael A. Giannone, Yan Li, Thomas H. Buckingham, Kristen B. Long, Gregory L. Beatty
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12915-020-00879-0

Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences
Cited by: 5
Author(s): Wenxia Yu, Jianan Li, Shisheng Huang, Xiangyang Li, Ping Li, Guanglei Li, Aibin Liang, Chao Tian, Xingxu Huang
Software Mentions: 1
Published: over 5 years ago

10.1172/jci.insight.148147

Type II alveolar epithelial cell–specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4
Cited by: 4
Author(s): C. Danh, Yan Zhang, Wei Tu, Xinyue Hu, Xiaojun Xiao, Jingsi Chen, Haiping Hao, Zhigang Liu, Jing Li, Shau Ku Huang, Mei Wan, Peisong Gao
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12859-019-2597-8

pblat: a multithread blat algorithm speeding up aligning sequences to genomes
Cited by: 55
Author(s): Meng Wang, Lei Kong
Software Mentions: 1
Published: over 7 years ago

10.1200/PO.18.00297

Crizotinib and Surgery for Long-Term Disease Control in Children and Adolescents With ALK-Positive Inflammatory Myofibroblastic Tumors
Cited by: 21
Author(s): Toby N. Trahair, Andrew J. Gifford, Ashleigh M. Fordham, Chelsea Mayoh, Mitali Fadia, Robyn Lukeis, Andrew C. Wood, Santosh Valvi, Rodney A. Walker, James Blackburn, Erin E. Heyer, Tim R. Mercer, Draga Barbaric, Glenn M. Marshall, Karen L. MacKenzie
Software Mentions: 1
Published: over 6 years ago

10.1200/PO.18.00105

Personalized Clinical Decision Making Through Implementation of a Molecular Tumor Board: A German Single-Center Experience
Cited by: 30
Author(s): Rouven Hoefflin, Anna-Lena Geißler, Ralph Fritsch, Rainer Claus, Julius Wehrle, Patrick Bastos Metzger, Meike Reiser, Leman Mehmed, Lisa Fauth, Dieter Henrik Heiland, Thalia Erbes, Friedrich Stock, Ágnes Csanádi, Cornelius Miething, Britta Weddeling, Frank Meiß, Dagmar von Bubnoff, Christine Dierks, Isabell Ge, Volker Brass, Steffen Heeg, Henning Schäfer, Martin Boeker, Justyna Rawluk, Elke Botzenhart, Gian Kayser, Simone Hettmer, Hauke Busch, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Laßmann, Nikolas von Bubnoff
Software Mentions: 1
Published: over 7 years ago

10.1016/j.jacc.2021.07.018

Innate Lymphoid Cells Promote Recovery of Ventricular Function After Myocardial Infarction
Cited by: 24
Author(s): Yu Lei, Stephen A. Newland, Tian Zhao, Yuning Lu, Andrew S. Sage, Yanqing Sun, Rouchelle Sriranjan, Marcella K.L., Brian Lam, Meritxell Nus, James Harrison, Simon Bond, Xiang Cheng, Jean‐Sébastien Silvestre, James H.F. Rudd, Joseph Cheriyan, Ziad Mallat
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40104-018-0288-3

Identification and characterization of long non-coding RNAs in porcine granulosa cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin
Cited by: 16
Author(s): Monika Ruszkowska, Anna Nynca, Łukasz Paukszto, Agnieszka Sadowska, Sylwia Świgońska, Karina Orlowska, Tomasz Molcan, J Jastrzebski, Renata E. Ciereszko
Software Mentions: 1
Published: over 7 years ago

10.1186/s40104-019-0331-z

Genome-wide profiling of RNA editing sites in sheep
Cited by: 10
Author(s): Yuanyuan Zhang, Deguo Han, Xianggui Dong, Jiankui Wang, Jianfei Chen, Yanzhu Yao, Hesham Y. A. Darwish, Wansheng Liu, Xuemei Deng
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-018-2203-5

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Cited by: 154
Author(s): Jens Keilwagen, Frank Hartung, Michael Paulini, Sven Twardziok, Jan Grau
Software Mentions: 1
Published: about 8 years ago

10.1186/s40104-020-00448-z

Effect of dietary supplementation with yeast cell wall extracts on performance and gut response in broiler chickens
Cited by: 19
Author(s): A. Pascual, Marianna Pauletto, Mery Giantin, Giuseppe Radaelli, Cristina Ballarin, Marco Birolo, C. Zomeño, Mauro Dacasto, Martina Bortoletti, Marta Vascellari, Gerolamo Xiccato, A. Trocino
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-019-3088-7

Exploratory analysis of transposable elements expression in the C. elegans early embryo
Cited by: 16
Author(s): Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich, Remo Sanges
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

10.1038/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/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/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

10.1038/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/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/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/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/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/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/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: 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

10.1186/s12859-019-3234-2

deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes
Cited by: 2
Author(s): Hatice Akarsu, Lisandra Aguilar-Bultet, Laurent Falquet
Software Mentions: 1
Published: over 6 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: about 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

10.1038/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/s41598-017-01165-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: about 9 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: about 9 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: about 9 years ago

10.1186/1471-2105-8-125

Detecting microsatellites within genomes: significant variation among algorithms
Cited by: 79
Author(s): Sébastien Leclercq, Éric Rivals, Philippe Jarne
Software Mentions: 1
Published: about 19 years ago

10.1177/1759091415593066

Combined HDAC1 and HDAC2 Depletion Promotes Retinal Ganglion Cell Survival After Injury Through Reduction of p53 Target Gene Expression
Cited by: 42
Author(s): Frédéric Lebrun-Julien, Ueli Suter
Software Mentions: 1
Published: about 11 years ago

10.1186/s40478-021-01170-1

Novel targetable FGFR2 and FGFR3 alterations in glioblastoma associate with aggressive phenotype and distinct gene expression programs
Cited by: 21
Author(s): Maria-Magdalena Georgescu, Mohammad Zahidul Islam, Yan Li, James Traylor, Anil Nanda
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-015-0741-7

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor
Cited by: 3
Author(s): Altan Kara, Martin Vickers, Martin Swain, David E. Whitworth, Narcís Fernández-Fuentes
Software Mentions: 1
Published: almost 11 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: about 9 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: about 9 years ago

10.1038/s41598-017-04654-0

Synergistic cellular effects including mitochondrial destabilization, autophagy and apoptosis following low-level exposure to a mixture of lipophilic persistent organic pollutants
Cited by: 18
Author(s): Nathan Earl Rainey, Ana Šarić, Alexandre Leberre, Etienne Dewailly, Christian Slomianny, Guillaume Vial, Harold I. Zeliger, Patrice X. Petit
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-7-165

Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
Cited by: 28
Author(s): Hyunsoo Kim, William Hu, Yuval Kluger
Software Mentions: 1
Published: over 20 years ago

10.1038/s41598-017-05720-3

Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder
Cited by: 36
Author(s): Efrain Ribeiro, Joseph R. Scarpa, Susanna P. Garamszegi, Andrew Kasarskis, Deborah C. Mash, Eric J. Nestler
Software Mentions: 1
Published: almost 9 years ago

10.1186/s40478-019-0783-6

Ischemic axonal injury up-regulates MARK4 in cortical neurons and primes tau phosphorylation and aggregation
Cited by: 20
Author(s): Eric Y. Hayden, Jennifer N. Putman, Stefanie Nuñez, Woo Shik Shin, Mandavi R. Oberoi, Malena Charreton, Suman Dutta, Zizheng Li, Yutaro Komuro, Mary Joy, Gal Bitan, Allan MacKenzie-Graham, Lin Jiang, Jason D Hinman
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-06914-5

RNA sequencing reveals resistance of TLR4 ligand-activated microglial cells to inflammation mediated by the selective jumonji H3K27 demethylase inhibitor
Cited by: 28
Author(s): Amitabh Das, Sarder Arifuzzaman, Tae-Ho Yoon, Sun Hwa Kim, Jin Choul Chai, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 1
Published: almost 9 years ago

10.1186/s40478-020-01061-x

Bexarotene normalizes chemotherapy-induced myelin decompaction and reverses cognitive and sensorimotor deficits in mice
Cited by: 15
Author(s): Angie C.A. Chiang, Alexandre V. Seua, Pooja Singhmar, Luis D. Arroyo, Rajasekaran Mahalingam, Jian Hu, Annemieke Kavelaars, Cobi J. Heijnen
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-8-382

XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Cited by: 139
Author(s): Aaron M. Newman, J. B. Cooper
Software Mentions: 1
Published: over 18 years ago

10.3390/ijms22094504

HERV-Derived Ervpb1 Is Conserved in Simiiformes, Exhibiting Expression in Hematopoietic Cell Lineages Including Macrophages
Cited by: 1
Author(s): Ayumi Matsuzawa, Jiyoung Lee, So Nakagawa, Johbu Itoh, Mahoko Takahashi Ueda, Satomi Mitsuhashi, Yuta Kochi, Tomoko Kaneko-Ishino, Fumitoshi Ishino
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-08320-3

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems
Cited by: 19
Author(s): Kathy Ushakov, Tal Koffler-Brill, Aviv Rom, Kobi Perl, Igor Ulitsky, Karen B. Avraham
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-10044-3

Establishment and genomic characterization of the new chordoma cell line Chor-IN-1
Cited by: 14
Author(s): Roberta Bosotti, Paola Magnaghi, Sebastiano Di Bella, Liviana Cozzi, Carlo Cusi, Fabio Bozzi, Nicola Beltrami, Giovanni Carapezza, Dario Ballinari, Nadia Amboldi, Rosita Lupi, Alessio Somaschini, Laura Raddrizzani, Barbara Salom, Arturo Galvani, Silvia Stacchiotti, Elena Tamborini, Antonella Isacchi
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-09517-2

Hypertension Susceptibility Loci are Associated with Anthracycline-related Cardiotoxicity in Long-term Childhood Cancer Survivors
Cited by: 20
Author(s): Michelle A.T. Hildebrandt, Monica E. Reyes, Xifeng Wu, Xia Pu, Kara Thompson, Jianchao Ma, Andrew P. Landstrom, Alanna C. Morrison, Joann L. Ater
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-015-0654-5

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
Cited by: 122
Author(s): Hani Z. Girgis
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-018-2436-3

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Cited by: 25
Author(s): Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22094750

Targeting Mitochondrial Metabolism in Clear Cell Carcinoma of the Ovaries
Cited by: 7
Author(s): Xiaonan Zhang, Mihir Shetty, Valentino Clemente, Stig Linder, Martina Bazzaro
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-017-12179-9

RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken
Cited by: 29
Author(s): Zhuo Zhu, Susan J. Lamont, Behnam Abasht
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-13835-w

HIV-1 viral protein R (Vpr) induces fatty liver in mice via LXRα and PPARα dysregulation: implications for HIV-specific pathogenesis of NAFLD
Cited by: 27
Author(s): Neeti Agarwal, Dinakar Iyer, Chiara Gabbi, Pradip Kumar Saha, Sanjeet G. Patel, Qianxing Mo, Benny Hung-Junn Chang, Biman Goswami, Ulrich S. Schubert, Jeffrey B. Kopp, Dorothy E. Lewis, Ashok Balasubramanyam
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-020-03593-4

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Cited by: 5
Author(s): Stefan Niebler, André C. Müller, Thomas Hankeln, Bertil Schmidt
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-020-03869-9

TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification
Cited by: 12
Author(s): Yuchen Tang, Yu Wang, Hua Wang, Miao Li, Linmin Peng, Guochao Wei, Yixing Zhang, Li Jin, Zhibo Gao
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-14264-5

A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies
Cited by: 50
Author(s): María Galli de Amorim, Renan Valieris, Rodrigo Duarte Drummond, Melissa Pool Pizzi, Vanessa M. Freitas, Rita Sinigaglia‐Coimbra, George A. Calin, Renata Pasqualini, Wadih Arap, Israel Tojal da Silva, Emmanuel Dias‐Neto, Diana Noronha Nunes
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms22094791

Identification of Novel Fusion Transcripts in High Grade Serous Ovarian Cancer
Cited by: 3
Author(s): A.M. Newtson, Henry Reyes Pineda, Eric J. Devor, Michael J. Goodheart, Jesús González Bosquet
Software Mentions: 1
Published: about 5 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

10.1038/s41598-017-16892-3

Decreased miRNA expression in Klinefelter syndrome
Cited by: 16
Author(s): Laura Cimino, Michele Salemi, Rossella Cannarella, Rosita A. Condorelli, Giorgio Giurato, Giovanna Marchese, Sandro La Vignera, Aldo E. Calogero
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-17475-y

The Human Blood-Nerve Barrier Transcriptome
Cited by: 30
Author(s): Steven P. Palladino, E. Scott Helton, Preti Jain, Chaoling Dong, Michael R. Crowley, David K. Crossman, Eroboghene E. Ubogu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-17665-8

A Novel Cell Line Based Orthotopic Xenograft Mouse Model That Recapitulates Human Hepatoblastoma
Cited by: 25
Author(s): Sarah E. Woodfield, Yan Shi, Roma H. Patel, Jingling Jin, Angela Major, Stephen F. Sarabia, Zbigniew Starosolski, Barry Zorman, Siddharth Gupta, Zhenghu Chen, Aryana M. Ibarra, Karl Dimiter Bissig, Ketan B. Ghaghada, Pavel Sumazin, Dolores López‐Terrada, Sanjeev A. Vasudevan
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-017-18397-5

Primed primary metabolism in systemic leaves: a functional systems analysis
Cited by: 55
Author(s): Jens Schwachtje, Axel Fischer, Alexander Erban, Joachim Kopka
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-019-2786-5

Ryūtō: network-flow based transcriptome reconstruction
Cited by: 20
Author(s): Thomas Gatter, Peter F. Stadler
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms22105290

Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta
Cited by: 6
Author(s): Pierre Moffatt, Iris Boraschi-Diaz, Juliana Marulanda, Ghalib Bardai, Frank Rauch
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-19173-9

NIPBL+/− haploinsufficiency reveals a constellation of transcriptome disruptions in the pluripotent and cardiac states
Cited by: 24
Author(s): Jason A. Mills, Pamela S. Herrera, Maninder Kaur, Lanfranco Leo, Deborah McEldrew, Jesus A Tintos-Hernández, Ramakrishnan Rajagopalan, Alyssa Gagne, Zhe Zhang, Xilma R. Ortiz-González, Ian D. Krantz
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19581-x

The microRNA regulatory landscape of MSC-derived exosomes: a systems view
Cited by: 248
Author(s): Scott Ferguson, Jinli Wang, Christine J Lee, Maixian Liu, Sriram Neelamegham, John M. Canty, Juliane Nguyen
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19855-4

Biologically active constituents of the secretome of human W8B2+ cardiac stem cells
Cited by: 15
Author(s): Shuai Nie, Xin Wang, Priyadharshini Sivakumaran, Mark M.W. Chong, Xin Liu, Tara Karnezis, Nadeeka Bandara, Kaloyan Takov, Cameron J. Nowell, Stephen Wilcox, Mitch Shambrook, Andrew Hill, Nicole C. Harris, Andrew Newcomb, Pádraig Strappe, Ramin Shayan, Damián Hernández, J. E. M. Clarke, Eric Hanssen, Sean M. Davidson, Gregory J. Dusting, Alice Pébay, Joshua W. K. Ho, Nicholas A. Williamson, Shiang Y. Lim
Software Mentions: 1
Published: over 8 years ago

10.1186/s40478-020-00951-4

Fusions involving BCOR and CREBBP are rare events in infiltrating glioma
Cited by: 11
Author(s): David Pisapia, Kentaro Ohara, Rohan Bareja, David Wilkes, Erika Hissong, Jaclyn A. Croyle, Joon‐Hyung Kim, Jad Saab, Theresa Y. MacDonald, Shaham Beg, Catherine O’Reilly, Sarah Kudman, Mark A. Rubin, Olivier Elemento, Andrea Sboner, Jeffrey P. Greenfield, Juan Miguel Mosquera
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-21104-7

Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription
Cited by: 40
Author(s): Young Ho Kim, Gregory R. Grant, Anita S. Bowman, Naqi Haider, Harini V. Gudiseva, Venkata R M Chavali
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-21190-7

Characterization of viral RNA splicing using whole-transcriptome datasets from host species
Cited by: 11
Author(s): Chengran Zhou, Shanlin Liu, Wenhui Song, Shiqi Luo, Guanliang Meng, Chentao Yang, Hua Yang, Jinmin Ma, Liang Wang, Shan Gao, Jian Wang, Huanming Yang, Yun Zhao, Hui Wang, Xin Zhou
Software Mentions: 1
Published: over 8 years ago

10.1186/s40478-021-01238-y

Supratentorial non-RELA, ZFTA-fused ependymomas: a comprehensive phenotype genotype correlation highlighting the number of zinc fingers in ZFTA-NCOA1/2 fusions
Cited by: 16
Author(s): Arnault Tauziède‐Espariat, Aurore Siegfried, Yvan Nicaise, Thomas Kergrohen, Philipp Sievers, Alexandre Vasiljevic, Alexandre Roux, Edouard Dezamis, Chiara Benevello, Marie‐Christine Machet, Sophie Michalak, Chloé Puiseux, Francisco Llamas-Gutierrez, Pierre Leblond, Franck Bourdeaut, Jacques Grill, Christelle Dufour, Léa Guerrini-Rousseau, Samuel Abbou, Volodia Dangouloff-Ros, Nathalie Boddaert, Raphaël Saffroy, Lauren Hasty, Ellen Wahler, Mélanie Pagès, Felipe Andreiuolo, Emmanuèle Lechapt‐Zalcman, Fabrice Chrétien, Thomas Blauwblomme, Kévin Beccaria, Johan Pallud, Stéphanie Puget, Emmanuelle Uro‐Coste, Pascale Varlet
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms22115741

Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Fusarium oxysporum Infection in Tomato Based on Transcriptome Profiling
Cited by: 7
Author(s): Marina P. Slezina, Е. А. Истомина, Tatyana V. Korostyleva, Alexey S. Kovtun, Artem S. Kasianov, Alexey A. Konopkin, Л. А. Щербакова
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-23749-w

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution
Cited by: 34
Author(s): Simon Blanchoud, Kim Rutherford, Lisa Zondag, Neil J. Gemmell, Megan J. Wilson
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24298-y

Accurate identification of RNA editing sites from primitive sequence with deep neural networks
Cited by: 12
Author(s): Zhangyi Ouyang, Feng Liu, Chenghui Zhao, Chao Ren, Gaole An, Chuan Mei, Xiaochen Bo, Wenjie Shu
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms22126478

Differential Regulation of Gonadotropins as Revealed by Transcriptomes of Distinct LH and FSH Cells of Fish Pituitary
Cited by: 15
Author(s): Lian Hollander-Cohen, Matan Golan, Berta Levavi‐Sivan
Software Mentions: 1
Published: about 5 years ago

10.5713/ajas.19.0097

Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross
Cited by: 3
Author(s): Byeongyong Ahn, Mi Hyun Choi, Joori Yum, In-Cheol Cho, Jin‐Hoi Kim, Chankyu Park
Software Mentions: 1
Published: over 6 years ago

10.1186/s13075-018-1631-y

Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue
Cited by: 82
Author(s): Laura T. Donlin, Deepak A. Rao, Kevin Wei, Kamil Slowikowski, Mandy J. McGeachy, Jason D. Turner, Nida Meednu, Fumitaka Mizoguchi, María Gutiérrez‐Arcelus, David Lieb, Joshua Keegan, Kaylin Muskat, Joshua Hillman, Cristina Rozo, Edd Ricker, Thomas Eisenhaure, Shuqiang Li, Edward P. Browne, Adam Chicoine, Danielle Sutherby, Akiko Noma, Accelerating Medicines Partnership, Chad Nusbaum, Stephen Kelly, Alessandra B. Pernis, Lionel B. Ivashkiv, Susan M. Goodman, William H. Robinson, Paul J. Utz, James A. Lederer, Ellen M. Gravallese, Brendan F. Boyce, Nir Hacohen, Costantino Pitzalis, Peter K. Gregersen, Gary S. Firestein, Soumya Raychaudhuri, Larry W. Moreland, V. Michael Holers, Vivian P. Bykerk, Andrew Filer, David L. Boyle, Michael B. Brenner, Jennifer H. Anolik
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-88628-3

Arginyltransferase (Ate1) regulates the RGS7 protein level and the sensitivity of light-evoked ON-bipolar responses
Cited by: 5
Author(s): Marie E. Fina, Junling Wang, Sergei Nikonov, Stephanie Sterling, Noga Vardi, Anna Kashina, Dawei Dong
Software Mentions: 1
Published: about 5 years ago

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: about 5 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: about 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: about 5 years ago

10.1161/ATVBAHA.118.312190

Intussusceptive Vascular Remodeling Precedes Pathological Neovascularization
Cited by: 19
Author(s): Zaheer Ali, Anthony Mukwaya, Antje Biesemeier, Maria Ntzouni, Daniel Ramsköld, Sarantis Giatrellis, Parviz Mammadzada, Renhai Cao, Anton Lennikov, Michele Marass, Claudia Gerri, Camilla Hildesjö, Michael R. Taylor, Qiaolin Deng, Beatrice Bourghardt Peebo, Luis del Peso, Anders Kvanta, Rickard Sandberg, Ulrich Schraermeyer, Helder André, John F. Steffensen, Neil Lagali, Yihai Cao, Julianna Kele, Lasse D. Jensen
Software Mentions: 1
Published: about 7 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: about 5 years ago

10.1523/ENEURO.0276-17.2018

Translatome Regulation in Neuronal Injury and Axon Regrowth
Cited by: 25
Author(s): Meir Rozenbaum, Marek Rajman, Ida Rishal, Indrek Koppel, Sandip Koley, Katalin F. Medzihradszky, Juan Oses-Prieto, Riki Kawaguchi, Paul S. Amieux, Alma L. Burlingame, Giovanni Coppola, Mike Fainzilber
Software Mentions: 1
Published: over 8 years ago

10.1007/s00705-021-05138-3

Two novel bornaviruses identified in colubrid and viperid snakes
Cited by: 7
Author(s): Florian Pfaff, Dennis Rubbenstroth
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22136872

Sympathetic Denervation Alters the Inflammatory Response of Resident Muscularis Macrophages upon Surgical Trauma and Ameliorates Postoperative Ileus in Mice
Cited by: 9
Author(s): Shilpashree Mallesh, Reiner Schneider, Bianca Schneiker, Mariola Lysson, Patrik Efferz, Eaton Lin, Wouter J. de Jonge, Sven Wehner
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22137002

Sex-Based Differences in Cardiac Gene Expression and Function in BDNF Val66Met Mice
Cited by: 1
Author(s): Marcus Negron, Jeffrey Kristensen, Van Thuan Nguyen, Lauren E Gansereit, F Raucci, Julia L Chariker, Aaron Heck, Imamulhaq Brula, Gabrielle Kitchen, Cassandra P. Awgulewitsch, Lin Zhong, Eric C. Rouchka, Simran Banga, Cristi L. Galindo
Software Mentions: 1
Published: about 5 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: about 5 years ago

10.3390/nu10121829

Nobiletin Enhances Chemosensitivity to Adriamycin through Modulation of the Akt/GSK3β/β–Catenin/MYCN/MRP1 Signaling Pathway in A549 Human Non-Small-Cell Lung Cancer Cells
Cited by: 30
Author(s): Jeong Yong Moon, Le Van Hung, Tatsuya Unno, Somi Kim Cho
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: about 5 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759