10.1186/s12864-019-6223-y

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process
Cited by: 23
Author(s): Rannyele Passos Ribeiro, Guillermo Ponz‐Segrelles, Christoph Bleidorn, M. Teresa Aguado
Software Mentions: 3
Published: almost 7 years ago

10.1186/s40168-021-01049-2

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field
Cited by: 41
Author(s): Selma Cadot, Hang Guan, Moritz Bigalke, Jean‐Claude Walser, Georg Jander, Matthias Erb, Marcel G. A. van der Heijden, Klaus Schlaeppi
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-2043-x

Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms
Cited by: 41
Author(s): Jing Liu, Shengqiang Wang, Tingting Qin, Na Li, Yuhui Niu, Dandan Li, Yongze Yuan, Hui Geng, Xiong Li, De Li Liu
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61857-8

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-61420-5

Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development
Cited by: 17
Author(s): Lucas F. Loffredo, Mackenzie E. Coden, Brian M. Jeong, Matthew T. Walker, Kishore R. Anekalla, Ton C. Doan, Raul I. Rodriguez, M.J. Browning, Ki-Won Nam, James J. Lee, Hiam Abdala‐Valencia, Sergejs Berdnikovs
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-58709-w

Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis
Cited by: 44
Author(s): Andrew P. Robinson, Joanne Zhongyan Zhang, Haley E. Titus, Molly Karl, Mikhail Merzliakov, Adam R. Dorfman, Stephen J. Karlik, Michael G. Stewart, Richard K. Watt, Benjin D. Facer, Jon D. Facer, Noah D. Christian, Karen S. Ho, Michael T. Hotchkin, Mark G. Mortenson, Robert H. Miller, Stephen D. Miller
Software Mentions: 3
Published: over 6 years ago

10.1186/s40168-021-01117-7

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Cited by: 23
Author(s): Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg, Gabriele Berg
Software Mentions: 3
Published: about 5 years ago

10.1111/acel.12795

Differential aging-related changes in neurophysiology and gene expression in IB4-positive and IB4-negative nociceptive neurons
Cited by: 5
Author(s): Malgorzata A. Mis, Mark F. Rogers, Aaron R. Jeffries, Anna Wilbrey, Lubin Chen, Yang Yang, Sulayman D. Dib‐Hajj, Stephen G. Waxman, Edward B. Stevens, Andrew D. Randall
Software Mentions: 3
Published: over 8 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: over 11 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-016-2572-y

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies
Cited by: 33
Author(s): Bas van Schooten, Chris D. Jiggins, Adriana D. Briscoe, Riccardo Papa
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-14-236

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Cited by: 73
Author(s): S. Ueno, Christophe Klopp, Jean‐Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Leger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-019-56790-4

Fetal androgen exposure is a determinant of adult male metabolic health
Cited by: 16
Author(s): Katarzyna Siemienowicz, Panagiotis Filis, Sophie Shaw, Alex Douglas, Jessica Thomas, Sally Mulroy, Forbes Howie, Paul A. Fowler, W. Colin Duncan, Michael T. Rae
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-017-4296-z

Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews
Cited by: 19
Author(s): Michie Kobayashi, Yukie Hiraka, Akira Abe, Hiroki Yaegashi, Satoshi Natsume, Hideko Kikuchi, Hiroki Takagi, Hiromasa Saitoh, Joe Win, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-016-2784-1

Psychoactive pharmaceuticals at environmental concentrations induce in vitro gene expression associated with neurological disorders
Cited by: 15
Author(s): Gaurav Kaushik, Yu Xia, Luobin Yang, Michael A. Thomas
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-015-0627-x

Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes
Cited by: 19
Author(s): Wei Zhang, Wei Xiang, Meng Heng-lin, Chunhua Ma, Ni-Hao Jiang, Guanghui Zhang, Shengchao Yang
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-13-484

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
Cited by: 180
Author(s): José A Robles, Sumaira Qureshi, Stuart Stephen, Susan R. Wilson, Conrad J. Burden, Jennifer Taylor
Software Mentions: 3
Published: about 14 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5984-7

An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans
Cited by: 14
Author(s): José M. C. Ribeiro, Humberto Julio Debat, Mariana Boiani, X. Ures, Sérgio Paulo Dejato da Rocha, Martı́n Breijo
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms9020452

Supernatants of Bifidobacterium longum and Lactobacillus plantarum Strains Exhibited Antioxidative Effects on A7R5 Cells
Cited by: 11
Author(s): Yusheng Wang, Zhifeng Fang, Qixiao Zhai, Shumao Cui, Jianxin Zhao, Hao Zhang, Wenwei Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-6482-7

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression
Cited by: 15
Author(s): Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou, Shuisheng Hou
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41389-018-0083-1

The FAK inhibitor BI 853520 exerts anti-tumor effects in breast cancer
Cited by: 49
Author(s): Stefanie Tiede, Nathalie Meyer-Schaller, Ravi Kiran Reddy Kalathur, Robert Ivánek, Ernesta Fagiani, Philip Schmassmann, Patrick Stillhard, Simon Häfliger, Norbert Kraut, Norbert Schweifer, Irene C. Waizenegger, Ruben Bill, Gerhard Christofori
Software Mentions: 3
Published: about 8 years ago

10.1186/s12870-019-1952-2

Genome-wide transcriptional adaptation to salt stress in Populus
Cited by: 28
Author(s): Jin-Gui Liu, Xiao Han, Tianbo Yang, Wenhui Cui, Aimin Wu, Chunxiang Fu, Baichen Wang, Lijun Liu
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-55132-8

Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury
Cited by: 7
Author(s): Yasuhiro Shiga, Akina Shiga, Pinar Mesci, HyoJun Kwon, Coralie Brifault, Jung Hyun Kim, Jacob Jeziorski, Chanond A. Nasamran, Seiji Ohtori, Alysson R. Muotri, Steven L. Gonias, W. Marie Campana
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12870-020-02459-4

Reducing the nicotine content of tobacco by grafting with eggplant
Cited by: 5
Author(s): Mengjuan Ren, Mengyue Zhang, Huijuan Yang, Hongzhi Shi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-020-07099-4

Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed
Cited by: 3
Author(s): Xi Liu, Frédéric Herault, Christian Diot, Erwan Corre
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.104004

Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21113870

Time-course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air
Cited by: 5
Author(s): Habibu Aliyu, Teresa Mohr, Don A. Cowan, Pieter De Maayer, Anke Neumann
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-54180-4

A framework for identification of on- and off-target transcriptional responses to drug treatment
Cited by: 23
Author(s): Yi Huang, Masaaki Furuno, Takahiro Arakawa, Satoshi Takizawa, Michiel de Hoon, Harukazu Suzuki, Erik Arner
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms7040096

Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii
Cited by: 27
Author(s): Senjie Lin, Liying Yu, Huan Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms8020244

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
Cited by: 5
Author(s): Ohana Y.A. Costa, Marcelo M. Zerillo, Daniela Zühlke, Anna M. Kielak, Agata Pijl, Katharina Riedel, Eiko E. Kuramae
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8040609

Incidental Prophylactic Appendectomy Is Associated with a Profound Microbial Dysbiosis in the Long-Term
Cited by: 13
Author(s): Lidia Sánchez-Alcoholado, José Carlos Fernández‐García, Carolina Gutiérrez-Repiso, María Rosa Bernal-López, Luis Ocaña-Wilhelmi, Eduardo Garcı́a-Fuentes, Isabel Moreno-Indias, Francisco J. Tinahones
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-954

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Cited by: 33
Author(s): Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xinwei Sun, Yan Meng, Paul Stothard, Graham Plastow, Christopher K. Tuggle, James M. Reecy, Eric R. Fritz-Waters, Samuel M. Abrams, Joan K. Lunney, Leluo Guan
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 10 years ago

10.1186/s13195-021-00810-x

Comorbidity between Alzheimer’s disease and major depression: a behavioural and transcriptomic characterization study in mice
Cited by: 15
Author(s): Ana Martín‐Sánchez, Janet Piñero, Lara Nonell, Magdalena Arnal, Elena M. Ribé, Alejo J. Nevado‐Holgado, Simon Lovestone, Ferrán Sanz, Laura I. Furlong, Olga Valverde
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1254-5

Global transcriptomic profiling demonstrates induction of oxidative stress and of compensatory cellular stress responses in brown trout exposed to glyphosate and Roundup
Cited by: 85
Author(s): Tamsyn M. Uren Webster, Eduarda M. Santos
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-017-3973-2

Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars
Cited by: 37
Author(s): Rugang Yu, Dan Li, Xiaodong Du, Shenglan Xia, Caifeng Liu, Gangrong Shi
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-52559-x

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Cited by: 35
Author(s): Xia Tang, Delong Feng, Min Li, Jinxue Zhou, Xiaoyuan Li, Dachun Zhao, Bingtao Hao, Dewei Li, Keyue Ding
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-52375-3

A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle
Cited by: 4
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms8071012

Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores
Cited by: 7
Author(s): Ilaria Bassani, Corinne Rancurel, Sophie Pagnotta, François Orange, Nicolas Pons, Kévin Lebrigand, Franck Panabières, Laurent Counillon, Xavier Noblin, Eric Galiana
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-50718-8

The role of extracellular matrix in mouse and human corneal neovascularization
Cited by: 19
Author(s): Marco Barbariga, F. Vallone, Ettore Mosca, Fabio Bignami, Cinzia Magagnotti, Phillippe Fonteyne, Federica Chiappori, Luciano Milanesi, Paolo Rama, Annapaola Andolfo, Giulio Ferrari
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-50310-0

Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component
Cited by: 9
Author(s): Dylan Sheerin, Daniel O’Connor, Christina Dold, Elizabeth A. Clutterbuck, Moustafa Attar, Christine S. Rollier, Manish Sadarangani, Andrew J. Pollard
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-50229-6

Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
Cited by: 8
Author(s): Yan Xu, Li Xing, Jessica Su, Xuekui Zhang, Weiliang Qiu
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-3433-4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: almost 10 years ago

10.3390/microorganisms8122007

Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair
Cited by: 7
Author(s): Eleftherios Kontizas, Spyros Tastsoglou, Timokratis Karamitros, Yiannis Karayiannis, Panagoula Κollia, Artemis G. Hatzigeorgiou, Dionyssios N. Sgouras
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms9020370

Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model
Cited by: 12
Author(s): Hyunjoon Park, Soyoung Yeo, Seok‐Won Kang, Chul Sung Huh
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-49647-3

Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle
Cited by: 7
Author(s): Sampurna Mukhopadhyay, Yupu Liang, Hong Hur, G. Villegas, Giulia Calenda, Alexandra Reis, Lily Millen, Patrick Barnable, Lisa Mamkina, Narender Kumar, Tamara Kalir, Rhoda Sperling, Natalia Teleshova
Software Mentions: 3
Published: about 7 years ago

10.3390/microorganisms8111793

Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Cited by: 10
Author(s): Jinxin Zhao, Yan Zhu, Ji-Ru Han, Yu Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-49440-2

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice
Cited by: 23
Author(s): Carlos Díaz-Castillo, Raquel Chamorro-García, Toshihiro Shioda, Bruce Blumberg
Software Mentions: 3
Published: about 7 years ago

10.1186/s12866-021-02110-8

HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium
Cited by: 1
Author(s): Selwan Hamed, Riham M. Shawky, Mohamed Emara, James M. Slauch, Christopher V. Rao
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-48741-w

SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages
Cited by: 24
Author(s): Wayne A. Schroder, Thiago Dominguez Crespo Hirata, Thuy T. Le, Joy Gardner, Glen M. Boyle, Jonathan Ellis, Eri Nakayama, Dilan Pathirana, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-47389-w

Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model
Cited by: 30
Author(s): Karla Mychellyne Costa Oliveira, John H. Barker, Eugène Berezikov, Lukas Pindur, S Kynigopoulos, Maria Eischen-Loges, Zhongchao Han, Mit Balvantray Bhavsar, Dirk Henrich, Liudmila Leppik
Software Mentions: 3
Published: about 7 years ago

10.1186/s13229-019-0285-1

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation
Cited by: 13
Author(s): Ayden Saffari, Matt Arno, Eric Nasser, Angelica Ronald, Chloe Wong, Leonard C Schalkwyk, Jonathan Mill, Frank Dudbridge, Emma L. Meaburn
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07959-7

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens
Cited by: 7
Author(s): Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd, Robert Söderlund
Software Mentions: 3
Published: about 5 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.1186/s13229-018-0219-3

Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders
Cited by: 57
Author(s): Lam Son Nguyen, Julien Fregeac, Christine Bôle‐Feysot, Nicolas Cagnard, Anand M. Iyer, Jasper J. Anink, Eleonora Aronica, Olivier Alibeu, Patrick Nitschké, Laurence Colleaux
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/6827057

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database
Cited by: 11
Author(s): Wenqing Zhou, Yongkui Pang, Yunmin Yao, Huiying Qiao
Software Mentions: 3
Published: about 6 years ago

10.1186/s13229-020-0318-9

Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy
Cited by: 19
Author(s): Cui-Xia Fan, Yue Gao, Guanmei Liang, Lang Huang, Jing Wang, Xiaoxue Yang, Yi‐Wu Shi, Ursula C. Dräger, Ming Zhong, Tianming Gao, Xinping Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13229-019-0311-3

TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling
Cited by: 27
Author(s): Pauline Martín, Vilas Wagh, Surya A. Reis, Serkan Erdin, Roberta L. Beauchamp, Ghalib Shaikh, Michael E. Talkowski, Elizabeth A. Thiele, Steven D. Sheridan, Stephen J. Haggarty, Vijaya Ramesh
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btv209

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Cited by: 39
Author(s): Emmanuel Dimont, Jiantao Shi, Rory Kirchner, Winston Hide
Software Mentions: 3
Published: over 11 years ago

10.1093/bib/bbx149

Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
Cited by: 20
Author(s): Francesca Vitali, Haiquan Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, Yves A. Lussier
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-46473-5

Differential expression of individual transcript variants of PD-1 and PD-L2 genes on Th-1/Th-2 status is guaranteed for prognosis prediction in PCNSL
Cited by: 22
Author(s): Yasuo Takashima, Atsushı Kawaguchi, Ryuichi Sato, Kenichi Yoshida, Azusa Hayano, Jumpei Homma, Junya Fukai, Yasuo Iwadate, Koji Kajiwara, Shin Ishizawa, Hiroaki Hondoh, Masakazu Nakano, Seishi Ogawa, Kei Tashiro
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.101578

High expression of the breast cancer susceptibility gene BRCA1 in long-lived termite kings
Cited by: 9
Author(s): Eisuke Tasaki, Yuki Mitaka, Tomonari Nozaki, Keiko Kobayashi, Kenji Matsuura, Yoshihito Iuchi
Software Mentions: 3
Published: about 8 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-019-45821-9

Skeletal muscle in MuRF1 null mice is not spared in low-gravity conditions, indicating atrophy proceeds by unique mechanisms in space
Cited by: 39
Author(s): Samuel M. Cadena, Yunyu Zhang, Jian Fang, Sophie Brachat, Pia Kuss, E. Giorgetti, Louis S. Stodieck, Michaela Kneissel, David J. Glass
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-45528-x

Loss of MafA and MafB expression promotes islet inflammation
Cited by: 13
Author(s): Tania Singh, Jesper K. Colberg, Luis Sarmiento, Patrícia Chaves, Lars Bolvig Hansen, Sara Bsharat, Luis Rodrigo Cataldo, Monika Dudenhöffer-Pfeifer, Malin Fex, David Bryder, Dan Holmberg, Ewa Sitnicka, Corrado Cilio, Rashmi B. Prasad, Isabella Artner
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45665-3

Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep
Cited by: 32
Author(s): Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi, Ali A. Alamouti, Rostam Abdollahi-Arpanahi, Seyed Alireza Salami
Software Mentions: 3
Published: over 7 years ago

10.1093/molbev/msy217

Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes
Cited by: 24
Author(s): Darren J. Parker, Jens Bast, Kirsten M. Jalvingh, Zoé Dumas, Marc Robinson‐Rechavi, Tanja Schwander
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-44600-w

Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development
Cited by: 27
Author(s): Ablat Sulayman, Kechuan Tian, Xixia Huang, Yuezhen Tian, Xinming Xu, Xuefeng Fu, Bi Zhao, Weiwei Wu, Dan Wang, Aynur Yasin, Hanikezi Tulafu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-2897-6

Detection of high variability in gene expression from single-cell RNA-seq profiling
Cited by: 35
Author(s): Hung I Harry Chen, Yufang Jin, Yufei Huang, Yidong Chen
Software Mentions: 3
Published: over 10 years ago

10.1038/s41389-020-0204-5

Transglutaminase-2 facilitates extracellular vesicle-mediated establishment of the metastatic niche
Cited by: 79
Author(s): Aparna Shinde, Juan Sebastian Paez, Sarah Libring, Kelsey Hopkins, Luis Solorio, Michael K. Wendt
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-44924-7

Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites
Cited by: 23
Author(s): Tuan M. Tran, Else M. Bijker, Mariëlle C. Haks, Tom H. M. Ottenhoff, Leo G. Visser, Remko Schats, Pratap Venepally, Hernán Lorenzi, Peter D. Crompton, Robert W. Sauerwein
Software Mentions: 3
Published: over 7 years ago

10.1186/s13041-020-00702-5

Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq
Cited by: 17
Author(s): Lisa C. Lyons, Snehajyoti Chatterjee, Yann Vanrobaeys, Marie E. Gaine, Ted Abel
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-015-0643-x

Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions
Cited by: 29
Author(s): Shamila Abeynayake, Stephen Byrne, Istvàn Nagy, Kristina Jonavičienė, Thomas Etzerodt, Birte Boelt, Torben Asp
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-019-44944-3

Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis
Cited by: 35
Author(s): Morteza Kouhsar, Sadegh Azimzadeh Jamalkandi, Ali Moeini, Ali Masoudi‐Nejad
Software Mentions: 3
Published: over 7 years ago

10.3390/ani9060313

Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
Cited by: 11
Author(s): Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Yan Hua, Fuping Zhao, Longchao Zhang, Lixian Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43935-8

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data
Cited by: 105
Author(s): Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic
Software Mentions: 3
Published: over 7 years ago

10.1038/s41389-021-00338-7

USP29-mediated HIF1α stabilization is associated with Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis
Cited by: 29
Author(s): Ruize Gao, David Buechel, Ravi Kiran Reddy Kalathur, Marco Morini, Mairene Coto‐Llerena, Caner Ercan, Salvatore Piscuoglio, Qian Chen, Tanja Blumer, Xueya Wang, Eva Dazert, Markus H. Heim, Michael N. Hall, Fengyuan Tang, Gerhard Christofori
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.9701

A prognostic long non-coding RNA-associated competing endogenous RNA network in head and neck squamous cell carcinoma
Cited by: 13
Author(s): Chengyao Zhang, Wei Cao, Jiawu Wang, Jiannan Liu, Jialiang Li, Hao Wu, Siyi Li, Chenping Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12870-021-03124-0

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots
Cited by: 17
Author(s): Yanting Wang, Hernando G. Suárez Duran, Jan C. van Haarst, Elio Schijlen, Carolien Ruyter-Spira, Marnix H. Medema, Lemeng Dong, Harro J. Bouwmeester
Software Mentions: 3
Published: over 5 years ago

10.1515/jib-2020-0031

Differentially methylated CpG sites associated with the high-risk group of prostate cancer
Cited by: 2
Author(s): Anastasiya A. Kobelyatskaya, Elena A. Pudova, Maria Fedorova, K. M. Nyushko, B. Ya. Alekseev, А. Д. Каприн, Д. Ю. Трофимов, Г. Т. Сухих, Anastasiya V. Snezhkina, George S. Krasnov, S. V. Razin, Anna V. Kudryavtseva
Software Mentions: 3
Published: almost 6 years ago

10.3390/ani10111944

Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Cited by: 12
Author(s): Shijun Li, Sayed Haidar Abbas Raza, Chunping Zhao, Gong Chen, Zan Liu
Software Mentions: 3
Published: about 6 years ago

10.1155/2019/9107806

Circ_MDM2_000139, Circ_ATF2_001418, Circ_CDC25C_002079, and Circ_BIRC6_001271 Are Involved in the Functions of XAV939 in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Haixiang Yu, Liping Xu, Zhengjia Liu, Bo Guo, Zhifeng Han, Xin Hua
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.3773

Canopy soil bacterial communities altered by severing host tree limbs
Cited by: 9
Author(s): Cody R. Dangerfield, Nalini M. Nadkarni, William J. Brazelton
Software Mentions: 3
Published: about 9 years ago

10.1038/srep40049

The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features
Cited by: 41
Author(s): José Manuel Latorre-Estivalis, Hugh M. Robertson, Kimberly K. O. Walden, Jerônimo C. Ruiz, Leilane Oliveira Gonçalves, Alessandra A. Guarneri, Marcelo G. Lorenzo
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep37536

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Cited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12870-020-02634-7

The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development
Cited by: 12
Author(s): Dandan Wang, Zhaodong Hao, Xiaofei Long, Zhanjun Wang, Xianrui Zheng, Daiquan Ye, Peng Ye, Weihuang Wu, Xiangyang Hu, Guibin Wang, Renhua Zheng, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: almost 6 years ago

10.3390/ph14010041

Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients
Cited by: 4
Author(s): Hana Votavová, Zuzana Urbanová, David Kundrát, Michaela Dostálová Merkerová, Martin Vostrý, Monika Hruba, Jaroslav Čermák, Monika Beličková
Software Mentions: 3
Published: almost 6 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 8 years ago

10.1016/j.ccell.2018.08.015

The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation
Cited by: 75
Author(s): N Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasińska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Dan Coleman, Sirintra Nakjang, Salam A. Assi, Victoria J. Forster, Mojgan Reza, Edward Law, Philip Berry, Dorothée Mueller, Cameron S. Osborne, Alex Elder, Simon Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, Olaf Heidenreich
Software Mentions: 3
Published: about 8 years ago

10.1152/physiolgenomics.00123.2014

Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout
Cited by: 14
Author(s): Tamsyn M. Uren Webster, Janice A. Shears, Karen Moore, Eduarda M. Santos
Software Mentions: 3
Published: about 11 years ago