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 5 years ago

10.7554/eLife.34985

Reduced expression of C/EBPβ-LIP extends health and lifespan in mice
Cited by: 19
Author(s): Christine Müller, Laura M Zidek, Tobias Ackermann, Tristan de Jong, Peng Liu, Verena Kliche, Mohamad Amr Zaini, Gertrud Kortman, Liesbeth Harkema, Dineke S. Verbeek, Jan Tuckermann, Julia von Maltzahn, Alain de Bruin, Victor Guryev, Zhaoqi Wang, Cornelis F. Calkhoven
Software Mentions: 1
Published: about 7 years ago

10.1093/molbev/msw139

Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats
Cited by: 13
Author(s): Arkarachai Fungtammasan, Marta Tomaszkiewicz, Rebeca Campos-Sánchez, Kristin A. Eckert, Michael DeGiorgio, Kateryna D. Makova
Software Mentions: 1
Published: about 9 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: about 5 years ago

10.1016/j.cub.2017.10.054

Stall in Canonical Autophagy-Lysosome Pathways Prompts Nucleophagy-Based Nuclear Breakdown in Neurodegeneration
Cited by: 44
Author(s): Olga Baron, Adel Boudi, Catarina Dias, Michael Schilling, Anna Nölle, Gema Vizcay‐Barrena, Ivan Rattray, Heinz Jungbluth, Wiep Scheper, Roland A. Fleck, Gillian P. Bates, Manolis Fanto
Software Mentions: 1
Published: over 7 years ago

10.1016/j.cub.2019.06.056

Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution
Cited by: 30
Author(s): Tadeusz Krassowski, Jacek Kominek, Xing‐Xing Shen, Dana A. Opulente, Xin Zhou, Antonis Rokas, Chris Todd Hittinger, Kenneth H. Wolfe
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.cub.2021.05.023

Generation of anisotropic strain dysregulates wild-type cell division at the interface between host and oncogenic tissue
Cited by: 9
Author(s): Megan E. Moruzzi, Alexander Nestor-Bergmann, Georgina K. Goddard, Nawseen Tarannum, Keith Brennan, Sarah Woolner
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.cub.2021.03.094

EPHA2-dependent outcompetition of KRASG12D mutant cells by wild-type neighbors in the adult pancreas
Cited by: 23
Author(s): William Hill, Ανδρέας Ζαραγκούλιας, Beatriz Salvador-Barbero, Geraint J. Parfitt, Markella Alatsatianos, Ana Padilha, Sean Porazinski, Thomas E. Woolley, Jennifer P. Morton, Owen J. Sansom, Catherine Hogan
Software Mentions: 1
Published: about 4 years ago

10.1016/j.cub.2020.04.041

Tissue Mechanics Regulate Mitotic Nuclear Dynamics during Epithelial Development
Cited by: 17
Author(s): Natalie J. Kirkland, Alice C. Yuen, Melda Tozluoǧlu, Ning Sze Hui, Ewa K. Paluch, Yanlan Mao
Software Mentions: 1
Published: about 5 years ago

10.1186/s13024-019-0311-y

Human Interleukin-34 facilitates microglia-like cell differentiation and persistent HIV-1 infection in humanized mice
Cited by: 46
Author(s): Saumi Mathews, Amanda Branch Woods, Ikumi Katano, Edward Makarov, Midhun Ben Thomas, Howard E. Gendelman, Larisa Y. Poluektova, Mamoru Ito, Santhi Gorantla
Software Mentions: 1
Published: over 6 years ago

10.1016/j.cub.2021.03.091

Efficiency and prioritization of inference-based credit assignment
Cited by: 2
Author(s): Rani Moran, Peter Dayan, Raymond J. Dolan
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.69951

Vaccination induces rapid protection against bacterial pneumonia via training alveolar macrophage in mice
Cited by: 17
Author(s): Hao Gu, Xi Zeng, Peng Li, Chuanying Xiang, Yangyang Zhou, Xiaomin Zhang, Jixin Zhang, Ning Wang, Gang Guo, Yan Li, Kaiyun Liu, Jiang Gu, Hao Zeng, Yuan Zhuang, Haibo Li, Jinyong Zhang, Weijun Zhang, Quanming Zou, Yun Shi
Software Mentions: 1
Published: almost 4 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 4 years ago

10.1016/j.cub.2018.03.041

Coin Tossing Explains the Activity of Opposing Microtubule Motors on Phagosomes
Cited by: 16
Author(s): Paulomi Sanghavi, Ashwin D’Souza, Ashim Rai, Arpan Rai, Ranjith Padinhatheeri, Roop Mallik
Software Mentions: 1
Published: about 7 years ago

10.1016/j.cub.2019.11.072

Sleeping with Hippocampal Damage
Cited by: 19
Author(s): Goffredina Spanò, Frederik D. Weber, Gloria Pizzamiglio, Cornelia McCormick, Thomas D. Miller, Clive R. Rosenthal, Jamie O. Edgin, Eleanor A. Maguire
Software Mentions: 1
Published: over 5 years ago

10.1016/j.cub.2018.12.017

Reprogramming Cdr2-Dependent Geometry-Based Cell Size Control in Fission Yeast
Cited by: 62
Author(s): Giuseppe Facchetti, Benjamin D. Knapp, Ignacio Flor-Parra, Fred Chang, Martin Howard
Software Mentions: 1
Published: over 6 years ago

10.7759/cureus.694

Stereotactic Arrhythmia Radioablation (STAR) of Ventricular Tachycardia: A Treatment Planning Study
Cited by: 11
Author(s): Lei Wang, B Fahimian, Scott G. Soltys, Paul C. Zei, Anthony Lo, Edward A. Gardner, Patrick Maguire, Billy W. Loo
Software Mentions: 1
Published: about 9 years ago

10.1002/csc2.20183

Identification and characterization of high‐yielding, short‐duration rice genotypes for tropical Asia
Cited by: 7
Author(s): Phyo L.P. Won, Hongyan Liu, Niño P.M.C. Banayo, Lei Nie, Shaobing Peng, Mohammad Rafiqul Islam, Pompe Sta. Cruz, B. C. Y. Collard, Yoichiro Kato
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13054-018-2110-1

Improving glycemic control in critically ill patients: personalized care to mimic the endocrine pancreas
Cited by: 42
Author(s): J. Geoffrey Chase, Thomas Desaive, Julien Bohé, Miriam Cnop, Christophe De Block, Jan Gunst, Roman Hovorka, Pierre Kalfon, James S. Krinsley, Éric Renard, Jean‐Charles Preiser
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13054-020-03187-9

40th International Symposium on Intensive Care & Emergency Medicine 2020 – Part 2
Cited by: 0
Author(s):
Software Mentions: 1
Published: almost 5 years ago

10.1186/cc10779

Pilot trial of STAR in the medical ICU
Cited by: 0
Author(s): Liam Fisk, Aaron Le Compte, GM Shaw, Sophie Penning, Thomas Desaive, J. Geoffrey Chase
Software Mentions: 1
Published: over 13 years ago

10.1186/s13054-017-1799-6

Software-guided versus nurse-directed blood glucose control in critically ill patients: the LOGIC-2 multicenter randomized controlled clinical trial
Cited by: 44
Author(s): Jasperina Dubois, Tom Van Herpe, Roosmarijn T. van Hooijdonk, Ruben Wouters, Domien Coart, Pieter Wouters, A. Van Assche, Guy Veraghtert, Bart De Moor, Joost Wauters, Alexander Wilmer, Marcus J. Schultz, Greet Van den Berghe, Dieter Mesotten
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.csbj.2018.10.002

Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management
Cited by: 231
Author(s): Maha Elazezy, Simon A. Joosse
Software Mentions: 1
Published: over 7 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 4 years ago

10.1038/s42003-020-0815-6

A white-to-opaque-like phenotypic switch in the yeast Torulaspora microellipsoides
Cited by: 1
Author(s): Cedric A. Brimacombe, Thomas Sierocinski, Matthew S. Dahabieh
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-021-01788-w

Identification of genetic factors influencing metabolic dysregulation and retinal support for MacTel, a retinal disorder
Cited by: 25
Author(s): Roberto Bonelli, Victoria E. Jackson, Aravind Prasad, Jacob E. Munro, Samaneh Farashi, Tjebo Heeren, Nikolas Pontikos, Lea Scheppke, Martin Friedlander, Catherine Egan, Rando Allikmets, Brendan R E Ansell, Melanie Bahlo
Software Mentions: 1
Published: over 4 years ago

10.1038/s42003-020-0879-3

Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes
Cited by: 19
Author(s): Ali At, Youssef Idaghdour, Alan Hodgkinson
Software Mentions: 1
Published: over 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 4 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 4 years ago

10.1186/s13024-021-00468-x

SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer’s disease
Cited by: 3
Author(s): Maria Bichmann, Nuria Prat Oriol, Ebru Ercan-Herbst, David C. Schöndorf, Borja Gomez Ramos, Vera Schwärzler, Marie A. Neu, Annabelle Schlüter, Xue Wang, Lina Jin, Chenqi Hu, Yu Tian, Janina S. Ried, Per Haberkant, Laura Gasparini, Dagmar E. Ehrnhoefer
Software Mentions: 1
Published: about 4 years ago

10.1038/s42003-020-0904-6

Prostaglandin EP2 receptor downstream of Notch signaling inhibits differentiation of human skeletal muscle progenitors in differentiation conditions
Cited by: 7
Author(s): Fusako Sakai‐Takemura, Kenichiro Nogami, Ahmed Elhussieny, Kota Kawabata, Yusuke Maruyama, Naohiro Hashimoto, Shin’ichi Takeda, Yuko Miyagoe‐Suzuki
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-019-0321-x

A large CRISPR-induced bystander mutation causes immune dysregulation
Cited by: 18
Author(s): Dimitre R. Simeonov, Alexander Brandt, Alice Chan, Jessica T Cortez, Zhongmei Li, Jonathan M. Woo, Youjin Lee, Claudia M.B. Carvalho, A Indart, Theodore L. Roth, James Zou, Andrew P. May, James R. Lupski, Mark S. Anderson, F. William Buaas, Daniel S. Rokhsar, Alexander Marson
Software Mentions: 1
Published: over 6 years ago

10.1038/s42003-019-0720-z

Attenuation of NAD[P]H:quinone oxidoreductase 1 aggravates prostate cancer and tumor cell plasticity through enhanced TGFβ signaling
Cited by: 10
Author(s): Dinesh Thapa, Shih‐Bo Huang, Amanda R. Muñoz, Xiaoyu Yang, Roble Bedolla, Chia Nung Hung, Chun-Liang Chen, Tim H.M. Huang, Michael A. Liss, Robert L. Reddick, Hiroshi Miyamoto, Addanki P. Kumar, Rita Ghosh
Software Mentions: 1
Published: over 5 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 6 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 6 years ago

10.1038/s42003-020-0928-y

BMPR2 promotes fatty acid oxidation and protects white adipocytes from cell death in mice
Cited by: 13
Author(s): Shuwen Qian, Jiabao Pan, Yan Su, Yan Tang, Yina Wang, Ying Zou, Yi Zhao, Hong Ma, Youyou Zhang, Yang Liu, Liang Guo, Qi‐Qun Tang
Software Mentions: 1
Published: about 5 years ago

10.1093/gbe/evaa195

Comprehensive Transcriptome of the Maize Stalk Borer,<i>Busseola fusca</i>, from Multiple Tissue Types, Developmental Stages, and Parasitoid Wasp Exposures
Cited by: 1
Author(s):
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 4 years ago

10.1093/gbe/evab178

The Genome of the Haptophyte <i>Diacronema lutheri</i> (<i>Pavlova lutheri</i>, 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 4 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 10 years ago

10.1007/s12035-019-01822-3

Endothelial Cell-Specific Transcriptome Reveals Signature of Chronic Stress Related to Worse Outcome After Mild Transient Brain Ischemia in Mice
Cited by: 4
Author(s): Stephanie Wegner, Ria Uhlemann, Valérie Boujon, Burcu Ersoy, Matthias Endres, Golo Kronenberg, Karen Gertz
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-020-01573-1

The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
Cited by: 8
Author(s): Linda Kvastad, Konstantin Carlberg, Ludvig Larsson, Eva Gracia Villacampa, Alexander Stuckey, Linnea Stenbeck, Annelie Mollbrink, Margherita Zamboni, Jens P Magnusson, Elisa Basmaci, Alia Shamikh, Gabriela Prochazka, A Schaupp, Åke Borg, Lars Fugger, Monica Nistér, Joakim Lundeberg
Software Mentions: 1
Published: over 4 years ago

10.1093/molbev/msaa250

Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome
Cited by: 11
Author(s): Jae Hak Son, Richard P. Meisel
Software Mentions: 1
Published: almost 5 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: about 7 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: over 6 years ago

10.1007/s12035-019-01681-y

Age and Sex Influence the Hippocampal Response and Recovery Following Sepsis
Cited by: 29
Author(s): Jolie Barter, Ashok Kumar, Julie A. Stortz, McKenzie K. Hollen, Dina C. Nacionales, Philip A. Efron, Lyle L. Moldawer, Thomas C. Foster
Software Mentions: 1
Published: about 6 years ago

10.1038/s42003-020-01246-z

Omental macrophages secrete chemokine ligands that promote ovarian cancer colonization of the omentum via CCR1
Cited by: 47
Author(s): Venkatesh Krishnan, Supreeti Tallapragada, Bruce T. Schaar, Kalika Kamat, Anita M. Chanana, Yue Zhang, Sonia A. Patel, Vinita Parkash, Carrie W. Rinker‐Schaeffer, Ann K. Folkins, Erinn B. Rankin, Oliver Dorigo
Software Mentions: 1
Published: almost 5 years ago

10.1038/s42003-019-0685-y

Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures
Cited by: 22
Author(s): Luca Bargelloni, Massimiliano Babbucci, Serena Ferraresso, Chiara Papetti, Nicola Vitulo, R. Carraro, Marianna Pauletto, Gianfranco Santovito, Magnus Lucassen, Felix Christopher Mark, Lorenzo Zane, Tomaso Patarnello
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 5 years ago

10.1002/cti2.1314

RNA sequencing identifies global transcriptional changes in peripheral CD4⁺ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis
Cited by: 0
Author(s): Melanie A. Ruffner, Zhe Zhang, Kelly Maurer, Amanda B. Muir, Antonella Cianferoni, Kathleen E. Sullivan, Jonathan M. Spergel
Software Mentions: 1
Published: over 4 years ago

10.1007/s00062-017-0639-z

Iatrogenic Vessel Dissection in Endovascular Treatment of Acute Ischemic Stroke
Cited by: 34
Author(s): Barbara Goeggel Simonetti, Justine Hulliger, Etienne Mathier, Simon Jung, Urs Fischer, Hakan Sarıkaya, Johannes Slotboom, Gerhard Schroth, Pasquale Mordasini, Jan Gralla, Marcel Arnold
Software Mentions: 1
Published: over 7 years ago

10.1186/s13148-015-0087-z

Epigenetic reprogramming of melanoma cells by vitamin C treatment
Cited by: 69
Author(s): Christopher B. Gustafson, Chao Yang, Kevin M. Dickson, Hongwei Shao, Derek Van Booven, J. William Harbour, Zhao Jun Liu, Gaofeng Wang
Software Mentions: 1
Published: about 10 years ago

10.1186/s13148-021-01023-7

BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer
Cited by: 11
Author(s): Katherine A. Giles, Cathryn M. Gould, Joanna Achinger-Kawecka, Scott G. Page, Georgia R. Kafer, Samuel Rogers, Phuc-Loi Luu, Anthony J. Cesare, Susan J. Clark, Phillippa C. Taberlay
Software Mentions: 1
Published: over 4 years ago

10.1186/s13148-018-0598-5

Histone deacetylase inhibitors exert anti-tumor effects on human adherent and stem-like glioma cells
Cited by: 45
Author(s): Halina Waś, Sylwia Król, Dante Rotili, Antonello Mai, Bartosz Wojtaś, Bożena Kamińska, Marta Maleszewska
Software Mentions: 1
Published: over 6 years ago

10.1111/cen.14109

Primary adrenal insufficiency: New genetic causes and their long‐term consequences
Cited by: 45
Author(s): Federica Buonocore, John C. Achermann
Software Mentions: 1
Published: over 5 years ago

10.1007/s10577-021-09658-1

Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization
Cited by: 13
Author(s): Jessica L. Soyer, Colin Clairet, Nicolas Lapalu, Thierry Rouxel, Eva H. Stukenbrock, Isabelle Fudal
Software Mentions: 1
Published: about 4 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 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 6 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 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 9 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 4 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 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 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 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 7 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 7 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 8 years ago

10.1093/molbev/msw079

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
Cited by: 574
Author(s): Erfan Sayyari, Siavash Mirarab
Software Mentions: 1
Published: over 9 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 8 years ago

10.3390/cancers12030620

RNA Immune Signatures from Pan-Cancer Analysis Are Prognostic for High-Grade Serous Ovarian Cancer and Other Female Cancers
Cited by: 12
Author(s): Wendell Jones, Chad M. Michener, Charles V. Biscotti, Elena Ioana Braicu, Jalid Sehouli, Mahrukh K. Ganapathi, Ram Ganapathi
Software Mentions: 1
Published: over 5 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 9 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 9 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: about 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 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: almost 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: almost 9 years ago

10.7554/eLife.26464

Loss of adult skeletal muscle stem cells drives age-related neuromuscular junction degeneration
Cited by: 96
Author(s): Wenxuan Liu, Alanna Klose, Sophie Forman, Nicole D. Paris, Lan Wei-LaPierre, Mariela Cortés-López, Aidi Tan, Morgan Flaherty, Pedro Miura, Robert T. Dirksen, Joe V. Chakkalakal
Software Mentions: 1
Published: about 8 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 8 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 8 years ago

10.3390/cancers13092250

IGF2 Mediates Resistance to Isoform-Selective-Inhibitors of the PI3K in HPV Positive Head and Neck Cancer
Cited by: 6
Author(s): Mai Badarni, Manu Prasad, Artemiy Golden, Baisali Bhattacharya, Liron Levin, Ksenia M. Yegodayev, Orr Dimitstein, Ben‐Zion Joshua, Limor Cohen, Ekaterina Khrameeva, Dexin Kong, Angel Porgador, Alex Braiman, Jennifer R. Grandis, Barak Rotblat, Moshe Elkabets
Software Mentions: 1
Published: about 4 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 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 8 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 8 years ago

10.3390/cancers12071719

Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes
Cited by: 5
Author(s): Timothy J. Lavelle, Tine Norman Alver, Karen‐Marie Heintz, Patrik Wernhoff, Vegard Nygaard, Sigve Nakken, Geir Frode Øy, Sigurd Leinæs Bøe, Alfonso Urbanucci, Eivind Hovig
Software Mentions: 1
Published: about 5 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 8 years ago

10.3390/molecules24183217

Moringin Pretreatment Inhibits the Expression of Genes Involved in Mitophagy in the Stem Cell of the Human Periodontal Ligament
Cited by: 16
Author(s): Luigi Chiricosta, Agnese Gugliandolo, Francesca Diomede, Jacopo Pizzicannella, Oriana Trubiani, Renato Iori, Giuseppe Tardiolo, Simone Guarnieri, Placido Bramantı, Emanuela Mazzon
Software Mentions: 1
Published: almost 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: over 8 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 8 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 8 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 8 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 8 years ago

10.7554/eLife.45920

Exercise-induced enhancement of synaptic function triggered by the inverse BAR protein, Mtss1L
Cited by: 25
Author(s): Christina Chatzi, Yingyu Zhang, William D. Hendricks, Yang Chen, Eric Schnell, Richard H. Goodman, Gary L. Westbrook
Software Mentions: 1
Published: about 6 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 8 years ago

10.3390/cancers13071546

Pulsed-Focused Ultrasound Slows B16 Melanoma and 4T1 Breast Tumor Growth through Differential Tumor Microenvironmental Changes
Cited by: 5
Author(s): Gadi Cohen, Parwathy Chandran, Rebecca M. Lorsung, Ömer Aydın, Lauren E. Tomlinson, Robert Rosenblatt, Scott R. Burks, Joseph A. Frank
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules26092677

Cocrystal of Apixaban–Quercetin: Improving Solubility and Bioavailability of Drug Combination of Two Poorly Soluble Drugs
Cited by: 21
Author(s): Li Zhang, Dewen Kong, Hongjuan Wang, Lingtai Jiao, Xiaoyue Zhao, Junke Song, Dezhi Yang, Haiguang Yang, Shumei Yang, Guanhua Du, Yang Lű
Software Mentions: 1
Published: about 4 years ago

10.3390/molecules25122928

Antifungal Agent 4-AN Changes the Genome-Wide Expression Profile, Downregulates Virulence-Associated Genes and Induces Necrosis in Candida albicans Cells
Cited by: 3
Author(s): Aleksandra Martyna, Maciej Masłyk, Monika Janeczko, Elżbieta Kochanowicz, Bartłomiej Gielniewski, Aleksandra Świercz, Oleg M. Demchuk, Konrad Kubiński
Software Mentions: 1
Published: about 5 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 8 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 8 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 8 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: about 8 years ago