Ecosyste.ms: Papers

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: almost 9 years ago

10.1186/1471-2105-9-559

WGCNA: an R package for weighted correlation network analysis
Cited by: 14,193
Author(s): Peter Langfelder, Steve Horvath
Software Mentions: 8
Published: almost 16 years ago

10.15252/msb.20188689

Defining the <scp>RNA</scp> interactome by total <scp>RNA</scp> ‐associated protein purification
Cited by: 103
Author(s): Vadim Shchepachev, Stefan Bresson, Christos Spanos, Elisabeth Petfalski, Lutz Fischer, Juri Rappsilber, David Tollervey
Software Mentions: 7
Published: over 5 years ago

10.1186/s13742-015-0077-2

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Cited by: 83
Author(s): Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Θεοδόσιος Θεοδοσίου, Anton J. Enright, Ioannis Iliopoulos
Software Mentions: 7
Published: about 9 years ago

10.18632/aging.104122

Prognostic roles of metabolic reprogramming-associated genes in patients with hepatocellular carcinoma
Cited by: 12
Author(s): Lijuan Cui, Xue Hai, Zhitong Wen, Zhihong Lu, Yunfeng Liu, Yi Zhang
Software Mentions: 7
Published: about 4 years ago

10.3758/s13428-018-1095-7

Soundgen: An open-source tool for synthesizing nonverbal vocalizations
Cited by: 48
Author(s): Andrey Anikin
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0164542

IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering
Cited by: 3
Author(s): Lingxiang Wu, Xiujie Chen, Denan Zhang, Wubing Zhang, Lei Liu, Hongzhe Ma, Jingbo Yang, Hongbo Xie, Bo Liu, Qing Jin
Software Mentions: 6
Published: about 8 years ago

10.1016/j.stem.2020.11.005

Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency
Cited by: 125
Author(s): Masaki Kinoshita, M. Barber, William Mansfield, Yingzhi Cui, Daniel Spindlow, Giuliano Giuseppe Stirparo, Sabine Dietmann, Jennifer Nichols, Austin Smith
Software Mentions: 6
Published: over 3 years ago

10.1002/2211-5463.13057

Long noncoding RNAs implicated in embryonic development in <i>Ybx1</i> knockout zebrafish
Cited by: 5
Author(s): Chen Huang, Bo Zhu, Dongliang Leng, Wei Ge, Xiaohua Douglas Zhang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0150495

Network Analysis of Metabolite GWAS Hits: Implication of CPS1 and the Urea Cycle in Weight Maintenance
Cited by: 11
Author(s): Alice Matone, Marie Pier Scott-Boyer, Jérôme Carayol, Parastoo Fazelzadeh, Grégory Lefebvre, Armand Valsesia, Céline Charon, Jacques Vervoort, Arne Astrup, Wim H. M. Saris, Melissa J. Morine, Jörg Hager
Software Mentions: 6
Published: over 8 years ago

10.1155/2021/5320445

Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental Validation
Cited by: 6
Author(s): Jiaming Yao, Junbin Yan, Jinting Wu, Jianshun Yu, Beihui He, Xi Chen
Software Mentions: 5
Published: about 3 years ago

10.1042/BSR20191547

Transcriptome profiling of digital flexor tendons after injury in a chicken model
Cited by: 1
Author(s): Wenfei Mao, Yancun Yu, Chen Chen, Ya Fang Wu
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007830

Global transcriptional regulation of innate immunity by ATF-7 in C. elegans
Cited by: 46
Author(s): Marissa Fletcher, Erik J. Tillman, Vincent Butty, Stuart S. Levine, Dennis H. Kim
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.670405

Construction of a Nine-MicroRNA-Based Signature to Predict the Overall Survival of Esophageal Cancer Patients
Cited by: 2
Author(s): Xiaobin Zhang, Yi He, Haiyong Gu, Zhichao Liu, Bin Li, Yang Yang, Jie Hao, Hua Ren
Software Mentions: 4
Published: over 3 years ago

10.1016/j.mcpro.2021.100061

Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling
Cited by: 8
Author(s): Ivan Silbern, Kuan‐Ting Pan, Maksims Fiošins, Stefan Bonn, Silvio O. Rizzoli, Eugenio F. Fornasiero, Henning Urlaub, Reinhard Jahn
Software Mentions: 4
Published: almost 4 years ago

10.7150/jca.51173

Identification of a Prognostic Signature Model with Tumor Microenvironment for predicting Disease-free Survival after Radical Prostatectomy
Cited by: 6
Author(s): Hao Zhao, Xuening Zhang, Zhan Shi, Bingxin Guo, Wenli Zhang, Kun He, Xueqi Hu, Songhe Shi
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2229-14-97

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks
Cited by: 35
Author(s): Ricardo A. Chávez Montes, Gerardo Coello, Karla L. González-Aguilera, Nayelli Marsch-Martínez, Stefan de Folter, Elena Álvarez-Buylla
Software Mentions: 4
Published: over 10 years ago

10.3389/fonc.2021.665080

Bioinformatics, Molecular Docking and Experiments In Vitro Analyze the Prognostic Value of CXC Chemokines in Breast Cancer
Cited by: 14
Author(s): Fei Wang, Chong Yuan, Wu H, Bo Liu, Yong Yang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-019-1686-3

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Cited by: 71
Author(s): Lin Zeng, Xiaolong Tu, He Dai, Fengming Han, LU Bing-she, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiaolong Li, Lili Ji, David M. Irwin, Zhou Hong, Min Liu, Hongkun Zheng, Ali Esmailizadeh, Dong‐Dong Wu
Software Mentions: 4
Published: over 5 years ago

10.3390/s140203001

Low-Cost 3D Systems: Suitable Tools for Plant Phenotyping
Cited by: 201
Author(s): Stefan Paulus, Jan Behmann, Anne-Katrin Mahlein, Lutz Plümer, Heiner Kuhlmann
Software Mentions: 4
Published: almost 11 years ago

10.3390/ani11030627

Comparative Transcriptome Profile between Iberian Pig Varieties Provides New Insights into Their Distinct Fat Deposition and Fatty Acids Content
Cited by: 6
Author(s): Ana Villaplana-Velasco, J. L. Noguera, Ramona N. Pena, María Ballester, Lourdes Gaitán Muñoz, Elena González, J.F. Tejeda, Noelia Ibáñez‐Escriche
Software Mentions: 4
Published: over 3 years ago

10.18632/aging.102766

Screening and identification of genes associated with cell proliferation in cholangiocarcinoma
Cited by: 1
Author(s): Li Guo, Yaodong Zhang, Zibo Yin, Yaya Ji, Guowei Yang, Bowen Qian, Sunjing Li, Jun Wang, Tingming Liang, Changxian Li, Xiangcheng Li
Software Mentions: 4
Published: almost 5 years ago

10.1042/BSR20193349

Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma
Cited by: 5
Author(s): Yu Jin, Xing Qin
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0179901

Microarray analyses of otospheres derived from the cochlea in the inner ear identify putative transcription factors that regulate the characteristics of otospheres
Cited by: 2
Author(s): Takehiro Iki, Michihiro Tanaka, Shin‐ichiro Kitajiri, Tomoko Kita, Yoshihisa Kawasaki, Akifumi Mizukoshi, Wataru Fujibuchi, Takayuki Nakagawa, Tatsutoshi Nakahata, Juichi Ito, Koichi Omori, Megumu K. Saito
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.684281

A Robust Seven-Gene Signature Associated With Tumor Microenvironment to Predict Survival Outcomes of Patients With Stage III–IV Lung Adenocarcinoma
Cited by: 3
Author(s): Hao Zhao, Xuening Zhang, Liting Guo, Songhe Shi, Ciyong Lu
Software Mentions: 4
Published: about 3 years ago

10.3390/cells9051272

Secretome of Mesenchymal Stromal Cells Prevents Myofibroblasts Differentiation by Transferring Fibrosis-Associated microRNAs within Extracellular Vesicles
Cited by: 40
Author(s): Nataliya Basalova, Georgy Sagaradze, Mikhail Arbatskiy, Evgeniy G. Evtushenko, Konstantin Kulebyakin, Olga Grigorieva, Zhanna Akopyan, Kalinina Ni, Anastasia Efimenko
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21031078

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma
Cited by: 21
Author(s): Paola Ostano, Maurizia Mello-Grand, Debora Sesia, Ilaria Gregnanin, Caterina Peraldo-Neia, Francesca Guana, Elena Jachetti, Antonella Farsetti, Giovanna Chiorino
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.202738

Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan
Cited by: 3
Author(s): Arman Ali Shah, Binghua Liu, Zhihuai Tang, Wang Wang, Wenjie Yang, Quanjun Hu, Yan Liu, Nianhui Zhang, Ke Liu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0193067

Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues
Cited by: 13
Author(s): Lee A. Newberg, Xiaowei Chen, Chinnappa D. Kodira, Maria I. Zavodszky
Software Mentions: 3
Published: over 6 years ago

10.1111/cpr.13090

Continuous expression of reprogramming factors induces and maintains mouse pluripotency without specific growth factors and signaling inhibitors
Cited by: 0
Author(s): Yihuan Mao, Yunlong Wang, Bei Zhong, Ning Yang, Zhikun Li, Tongtong Cui, Guihai Feng, Wei Li, Ying Zhang, Qi Zhou
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0184155

Engineering human cell spheroids to model embryonic tissue fusion in vitro
Cited by: 15
Author(s): David G. Belair, Cynthia J. Wolf, Carmen R. Wood, Hongzu Ren, Rachel D. Grindstaff, William T. Padgett, Adam Swank, Denise K. MacMillan, Anna Fisher, Witold Winnik, Barbara D. Abbott
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: about 11 years ago

10.3390/cancers12102766

Targeted Inhibition of the NUP98-NSD1 Fusion Oncogene in Acute Myeloid Leukemia
Cited by: 27
Author(s): Sagarajit Mohanty, Nidhi Jyotsana, Amit Sharma, Arnold Kloos, Razif Gabdoulline, Basem Othman, Courteney K. Lai, Renate Schottmann, Madhvi Mandhania, Johannes Schmoellerl, Florian Grebien, Euan Ramsay, Anitha Thomas, Hans‐Peter Vornlocher, Arnold Ganser, Felicitas Thol, Michael Heuser
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0232542

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs
Cited by: 10
Author(s): Mayla Regina Souza, A. M. G. Ibelli, Igor Ricardo Savoldi, Mauricio Egídio Cantão, J. de O. Peixoto, M. A. Z. Morés, Jader Silva Lopes, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0119448

Analyzing Large Gene Expression and Methylation Data Profiles Using StatBicRM: Statistical Biclustering-Based Rule Mining
Cited by: 28
Author(s): Ujjwal Maulik, Saurav Mallik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-47405-z

Uncovering missed indels by leveraging unmapped reads
Cited by: 8
Author(s): Mohammad Shabbir Hasan, Xiaowei Wu, Liqing Zhang
Software Mentions: 3
Published: over 5 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-8-455

Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells
Cited by: 49
Author(s): Yan Xu, Machiko Ikegami, Yanhua Wang, Yasushi Matsuzaki, Jeffrey A. Whitsett
Software Mentions: 3
Published: almost 18 years ago

10.1038/srep32346

Physiological basis for low-temperature survival and storage of quiescent larvae of the fruit fly Drosophila melanogaster
Cited by: 32
Author(s): Vladimı́r Košťál, Jaroslava Korbelová, Tomáš Štětina, Rodolphe Poupardin, Hervé Colinet, Helena Zahradníčková, Iva Opekarová, Martin Moos, Petr Šimek
Software Mentions: 3
Published: about 8 years ago

10.1098/rsos.180983

Vertebral morphometrics and lung structure in non-avian dinosaurs
Cited by: 15
Author(s): Robert J. Brocklehurst, Emma R. Schachner, William I. Sellers
Software Mentions: 3
Published: about 6 years ago

10.1186/s12953-015-0063-8

Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway
Cited by: 8
Author(s): Gry H. Dihazi, G. Muêller, Abdul R. Asif, Marwa Eltoweissy, Johannes T. Wessels, Hassan Dihazi
Software Mentions: 3
Published: almost 10 years ago

10.1186/s40478-021-01148-z

TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6
Cited by: 10
Author(s): Erik M. Lehmkuhl, Suvithanandhini Loganathan, Eric Alsop, Alexander D. Blythe, Tina Kovalik, Nicholas P. Mortimore, Dianne Barrameda, Chuol Kueth, Randall J. Eck, Bhavani Bagevalu Siddegowda, Archi Joardar, Hannah E. Ball, Maria E. Macias, Robert Bowser, Kendall Van Keuren‐Jensen, Daniela C. Zarnescu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02511-3

Identification of small RNAs during cold acclimation in Arabidopsis thaliana
Cited by: 21
Author(s): Bhavika Tiwari, Kristin Habermann, Muhammad Arif, Heinrich Lukas Weil, Antoni García-Molina, Tatjana Kleine, Timo Mühlhaus, Wolfgang Frank
Software Mentions: 3
Published: over 4 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: over 3 years ago

10.7150/thno.57237

The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity
Cited by: 14
Author(s): Petra I. Lorenzo, Eugenia Martin Vázquez, Livia López-Noriega, Esther Fuente-Martín, José Manuel Mellado-Gil, Jaime M. Franco, Nadia Cobo-Vuilleumier, José A. Guerrero-Martínez, Silvana Y. Romero-Zerbo, Jesús A Perez-Cabello, Sabrina Rivero, Antonio Campos‐Caro, Christian Claude Lachaud, Alejandra Crespo Barreda, Manuel Aguilar‐Diosdado, Esther Fuentes, Aléjandro Martín-Montalvo, Manuel Álvarez‐Dolado, Franz Martı́n, Gemma Rojo‐Martínez, David Pozo, Francisco Javier Bermúdez‐Silva, Valentine Comaills, José Carlos Castañeda Reyes, Benoît Gauthier
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13058-021-01455-2

Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland
Cited by: 5
Author(s): Manish Ranjan, Oukseub Lee, Gannon Cottone, Elnaz Mirzaei Mehrabad, Benjamin T. Spike, Zexian Zeng, Shivangi Yadav, Robert T. Chatterton, Julie Kim, Susan E. Clare, Seema A. Khan
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2017.01992

Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells
Cited by: 39
Author(s): Tanya Sezin, Artem Vorobyev, Christian D. Sadik, Detlef Zillikens, Yask Gupta, Ralf J. Ludwig
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13041-015-0104-3

Brain transcriptome profiles in mouse model simulating features of post-traumatic stress disorder
Cited by: 41
Author(s): Seid Muhie, Aarti Gautam, James L. Meyerhoff, Nabarun Chakraborty, Rasha Hammamieh, Marti Jett
Software Mentions: 3
Published: over 9 years ago

10.3389/fnagi.2019.00101

Transcriptional Dysregulation Study Reveals a Core Network Involving the Progression of Alzheimer's Disease
Cited by: 22
Author(s): Guofeng Meng, Hongkang Mei
Software Mentions: 3
Published: over 5 years ago

10.1016/j.exger.2018.10.003

Identification of key pathways and metabolic fingerprints of longevity in C. elegans
Cited by: 45
Author(s): Arwen W. Gao, Reuben L. Smith, Michel van Weeghel, Rashmi Kamble, Georges E. Janssens, Riekelt H. Houtkooper
Software Mentions: 3
Published: about 6 years ago

10.15252/embj.2018100788

The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment
Cited by: 41
Author(s): Thomas Burgold, M. Barber, Susan L. Kloet, Julie Cramard, Sarah Gharbi, Robin Floyd, Masaki Kinoshita, Markus Ralser, Michiel Vermeulen, Nicola Reynolds, Sabine Dietmann, Brian Hendrich
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-80868-z

Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy
Cited by: 8
Author(s): Kristina Sonnenschein, Jan Fiedler, David de Gonzalo-Calvo, Xiaoyan Ke, Angelika Pfanne, Annette Just, Carolin Zwadlo, Samira Soltani, Udo Bavendiek, Theresia Kraft, Cristobal dos Remedios, Serghei Cebotari, Johann Bauersachs, Thomas Thum
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12886-020-1333-5

Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: a transcriptomic approach
Cited by: 12
Author(s): Deborah A. Lipski, Vincent Foucart, Rémi Dewispelaere, Laure Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
Software Mentions: 2
Published: over 4 years ago

10.1186/s12862-015-0466-2

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus
Cited by: 36
Author(s): Praveen Baskaran, Christian Rödelsperger, Neel Prabh, Vahan Serobyan, Gabriel V. Markov, Antje Hirsekorn, Christoph Dieterich
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-018-5039-5

Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model
Cited by: 46
Author(s): Lyudmila V. Dergunova, Ivan B. Filippenkov, Vasily V. Stavchansky, Alina E. Denisova, Vadim V. Yuzhakov, С. А. Мозеров, Leonid V. Gubsky, Svetlana A. Limborska
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-020-07074-z

Differentially expressed genes in cotyledon of ewes fed mycotoxins
Cited by: 1
Author(s): Jessica Britt, Rooksana E. Noorai, S. K. Duckett
Software Mentions: 2
Published: about 4 years ago

10.1186/s12920-021-00932-z

MicroRNA related prognosis biomarkers from high throughput sequencing data of kidney renal clear cell carcinoma
Cited by: 12
Author(s): Mengxi Huang, Ti Zhang, Zhen Yao, Chaoqung Xing, Qin Wu, Yuanwu Liu, Xiao-Liang Xing
Software Mentions: 2
Published: over 3 years ago

10.1186/1752-0509-5-46

Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells
Cited by: 8
Author(s): Francisco Azuaje, Haiying Wang, Huiru Zheng, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux, Daniel R. Wagner
Software Mentions: 2
Published: over 13 years ago

10.1155/2020/5973082

A Novel Three-miRNA Signature Identified Using Bioinformatics Predicts Survival in Esophageal Carcinoma
Cited by: 8
Author(s): Kun-Zhe Wu, Chun‐Dong Zhang, Dong‐Qiu Dai
Software Mentions: 2
Published: almost 5 years ago

10.1155/2021/5533946

Uncovering the Mechanisms and Molecular Targets of Weibing Formula 1 against Gastritis: Coupling Network Pharmacology with GEO Database
Cited by: 4
Author(s): Ke Chen, Luojian Zhang, Qu Zhou, Feng Wan, Jia Li, Yongqiang Yang, Hui Yan, Shile Huang
Software Mentions: 2
Published: over 3 years ago

10.1042/BSR20203699

Insight into molecular profile changes after skeletal muscle contusion using microarray and bioinformatics analyses
Cited by: 6
Author(s): Na Li, Rufeng Bai, Chun Li, Li-hong Dang, Qiu-xiang Du, Qianqian Jin, Jie Cao, Ying-Yuan Wang, Jun-hong Sun
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41380-019-0370-z

Towards precision medicine for stress disorders: diagnostic biomarkers and targeted drugs
Cited by: 37
Author(s): Helen Le-Niculescu, K. Roseberry, Daniel F. Levey, Jesse D. Rogers, K. Kosary, Srishti Prabha, Thaon Jones, Suzanne E. Judd, M. A. McCormick, A. R. Wessel, Amanda L. Williams, Peter Phalen, Firoza Mamdani, Adolfo Sequeira, Sunil M. Kurian, Alexander B. Niculescu
Software Mentions: 2
Published: over 5 years ago

10.20411/pai.v5i1.376

The Effects of Anti-retroviral Therapy on Epigenetic Age Acceleration Observed in HIV-1-infected Adults
Cited by: 20
Author(s): Mary E. Sehl, Tammy M. Rickabaugh, Roger Shih, Otoniel Martı́nez-Maza, Steve Horvath, Christina M. Ramirez, Beth D. Jamieson
Software Mentions: 2
Published: about 4 years ago

10.1111/pce.13811

Natural variation of photosynthetic efficiency in<i><scp>Arabidopsis thaliana</scp></i>accessions under low temperature conditions
Cited by: 15
Author(s): Aina E. Prinzenberg, Lucia Campos-Domínguez, Willem Kruijer, Jeremy Harbinson, Mark G. M. Aarts
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1005706

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation
Cited by: 78
Author(s): Wenjun Deng, I. Ramesh Babu, Dan Su, Shanye Yin, Thomas J. Begley, Peter C. Dedon
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0037046

Transcriptional Programs Controlling Perinatal Lung Maturation
Cited by: 65
Author(s): Yan Xu, Yanhua Wang, Valérie Besnard, Machiko Ikegami, Susan E. Wert, Caleb Heffner, Stephen A. Murray, Leah Rae Donahue, Jeffrey A. Whitsett
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0018215

Systems-Scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine
Cited by: 22
Author(s): Lijie Sun, Hong Mei Li, Manfredo J. Seufferheld, Kent R. Walters, Venu M. Margam, Amber Jannasch, Naomi Diaz, Catherine P. Riley, Weilin Sun, Yueh Feng Li, William M. Muir, Jun Xie, Jing Wu, Fan Zhang, Jake Y. Chen, Eric L. Barker, Jiřı́ Adamec, Barry R. Pittendrigh
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0252450

A proteomic-informed view of the changes induced by loss of cellular adherence: The example of mouse macrophages
Cited by: 2
Author(s): Sacnite Ramirez Rios, Anaëlle Torres, Hélène Diemer, Véronique Collin-Faure, Sarah Cianférani, Laurence Lafanéchère, Thierry Rabilloud
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0004802

Human and Murine Kidneys Show Gender- and Species-Specific Gene Expression Differences in Response to Injury
Cited by: 61
Author(s): Han Si, Ramandeep S. Banga, Pinelopi P. Kapitsinou, Manjunath Ramaiah, Janis Lawrence, Ganesh Kambhampati, Antje Gruenwald, Erwin P. Böttinger, Daniel Glicklich, Vivian A. Tellis, Stuart Greenstein, David B. Thomas, James Pullman, Melissa Fazzari, Katalin Suszták
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0166312

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities
Cited by: 42
Author(s): Richa Rai, Sudhir Kumar Chauhan, Vikas Vikram Singh, Madhukar Rai, Geeta Rai
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0184880

Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines
Cited by: 7
Author(s): Chao Huang, Yang Yang, Xuetong Chen, Chao Wang, Yan Li, Chunli Zheng, Yonghua Wang
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0244394

Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for clear cell renal cell carcinoma using integrated bioinformatics analysis
Cited by: 7
Author(s): Miaoru Han, Haifeng Yan, Kang Yang, Boya Fan, Panying Liu, Hongtao Yang
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.ebiom.2018.12.003

HDAC inhibitor valproic acid protects heart function through Foxm1 pathway after acute myocardial infarction
Cited by: 45
Author(s): Shuo Tian, Ienglam Lei, Wenbin Gao, Liu Liu, Yijing Guo, Jeffery Creech, Todd J. Herron, Shaoxiang Xian, X. Peter, Y. Eugene Chen, Yongqing Li, Hasan B. Alam, Zhong Wang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13072-020-00376-2

Genome-wide occupancy reveals the localization of H1T2 (H1fnt) to repeat regions and a subset of transcriptionally active chromatin domains in rat spermatids
Cited by: 4
Author(s): Vasantha Shalini, Utsa Bhaduri, Anjhana C Ravikkumar, Anusha Rengarajan, R. Satyanarayana
Software Mentions: 2
Published: almost 4 years ago

10.1002/2211-5463.13167

Identification of crucial noncoding RNAs and mRNAs in hypertrophic scars via RNA sequencing
Cited by: 6
Author(s): Xiaodong Li, Zeliang He, Julei Zhang, Yan Han
Software Mentions: 2
Published: over 3 years ago

10.3389/fchem.2021.607139

Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery
Cited by: 2
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Antônio Mauro Rezende
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.690053

Immune-Related Gene Expression Analysis Revealed Three lncRNAs as Prognostic Factors for Colon Cancer
Cited by: 7
Author(s): Xiao-Liang Xing, Ti Zhang, Zhen Yao, Chaoqun Xing, Chunxiao Wang, Yuanwu Liu, Mengxi Huang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.636550

Bovine Pre-adipocyte Adipogenesis Is Regulated by bta-miR-150 Through mTOR Signaling
Cited by: 6
Author(s): Xingyi Chen, Sayed Haidar Abbas Raza, Xinhao Ma, Jiangfang Wang, Xiaohui Wang, Chengcheng Liang, Xinran Yang, Chugang Mei, Syed Muhammad Suhail, Zan Liu
Software Mentions: 2
Published: almost 4 years ago

10.3389/fnmol.2018.00290

Salivary MicroRNAs: Diagnostic Markers of Mild Traumatic Brain Injury in Contact-Sport
Cited by: 68
Author(s): Valentina Di Pietro, Edoardo Porto, Marco Ragusa, Cristina Barbagallo, David Davies, Mario Forcione, Ann Logan, Cinzia Di Pietro, Michele Purrello, Michael J. Grey, Douglas Hammond, Vijay Sawlani, Aron K. Barbey, Antonio Belli
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2019.00381

HypoxamiRs Profiling Identify miR-765 as a Regulator of the Early Stages of Vasculogenic Mimicry in SKOV3 Ovarian Cancer Cells
Cited by: 22
Author(s): Yarely M. Salinas‐Vera, Dolores Gallardo‐Rincón, Raúl García‐Vázquez, Olga N. Hernández-de la Cruz, Laurence A. Marchat, Juan Antonio González-Barrios, Erika Ruíz‐García, Carlos Vázquez‐Calzada, Estefanía Contreras-Sanzón, Martha Resendiz-Hernández, Horacio Astudillo‐de la Vega, José L. Cruz-Colín, Alma D. Campos‐Parra, César López-Camarillo
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.656657

Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana
Cited by: 10
Author(s): Bhavika Tiwari, Kristin Habermann, Muhammad Arif, Oguz Top, Wolfgang Frank
Software Mentions: 2
Published: over 3 years ago

10.3390/genes11060600

Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels
Cited by: 9
Author(s): Katarzyna Ropka‐Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, M. Tyra, Natalia Derebecka, Joanna Wesoły, Tomasz Szmatoła, Katarzyna Piórkowska
Software Mentions: 2
Published: over 4 years ago

10.3390/genes12020216

The Genetics of Sudden Infant Death Syndrome—Towards a Gene Reference Resource
Cited by: 5
Author(s): Emma B Johannsen, Linda B. Baughn, Neeraj Sharma, Nicolina Zjacic, Mehdi Pirooznia, Eran Elhaik
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13073-015-0183-x

Restoration of mesenchymal retinal pigmented epithelial cells by TGFβ pathway inhibitors: implications for age-related macular degeneration
Cited by: 87
Author(s): Monte J. Radeke, Carolyn M. Radeke, Ying-Hsuan Shih, Jane Hu, Dean Bok, Lincoln V. Johnson, Peter Coffey
Software Mentions: 2
Published: over 9 years ago

10.3390/jcm9082457

Danon Disease-Associated LAMP-2 Deficiency Drives Metabolic Signature Indicative of Mitochondrial Aging and Fibrosis in Cardiac Tissue and hiPSC-Derived Cardiomyocytes
Cited by: 11
Author(s): Giorgia Del Favero, Alois Bonifacio, Teisha J. Rowland, Shanshan Gao, Kunhua Song, Valter Sergo, Eric Adler, Luisa Mestroni, Orfeo Sbaizero, Matthew R.G. Taylor
Software Mentions: 2
Published: over 4 years ago

10.1007/s13238-017-0450-2

Single-cell transcriptomics reveals gene signatures and alterations associated with aging in distinct neural stem/progenitor cell subpopulations
Cited by: 29
Author(s): Zhanping Shi, Yanan Geng, Jiping Liu, Huina Zhang, Libing Zhou, Qing Lin, Juehua Yu, Kunshan Zhang, Jie Liu, Xinpei Gao, Chunxue Zhang, Yinan Yao, Chong Zhang, Yi Sun
Software Mentions: 2
Published: over 7 years ago

10.1038/srep35680

Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells
Cited by: 36
Author(s): Ryo Ohta, Akira Niwa, Yukimasa Taniguchi, Naoya Suzuki, Junko Toga, Emiko Yagi, Norikazu Saiki, Yoko Nishinaka‐Arai, Chihiro Okada, Akira Watanabe, Tatsutoshi Nakahata, Kiyotoshi Sekiguchi, Megumu K. Saito
Software Mentions: 2
Published: about 8 years ago

10.1038/srep42809

Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering
Cited by: 12
Author(s): Sushmita Paul, Petra Lakatos, Arndt Hartmann, Regine Schneider‐Stock, Julio Vera
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-07922-1

Specific calpain inhibition protects kidney against inflammaging
Cited by: 11
Author(s): Guillaume Hanouna, Michel Laurent, Sophie Vandermeersch, Joëlle Perez, Sandrine Placier, Jean‐Philippe Haymann, Fabien Campagne, Julien Moroch, Aurélien Bataille, Laurent Baud, Emmanuel Letavernier
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-29086-2

Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases
Cited by: 41
Author(s): Kun Wang, Di Wu, Haoyue Zhang, Arabinda Das, Mahashweta Basu, Justin Malin, Kan Cao, Sridhar Hannenhalli
Software Mentions: 2
Published: over 6 years ago

10.1186/s13046-018-0982-1

TNF-alpha and metalloproteases as key players in melanoma cells aggressiveness
Cited by: 62
Author(s): Stefania Rossi, Martina Cordella, Claudio Tabolacci, Giovanni Nassa, Daniela D’Arcangelo, Cinzia Senatore, Paolo Pagnotto, Roberta Magliozzi, Annamaria Salvati, Alessandro Weisz, Antonio Facchiano, Francesco Facchiano
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms18071440

Semi-Quantitative Mass Spectrometry in AML Cells Identifies New Non-Genomic Targets of the EZH2 Methyltransferase
Cited by: 6
Author(s): Yordan Sbirkov, Colin Kwok, Amandeep Bhamra, Andrew J. Thompson, Veronica Gil, Arthur Zelent, Kevin Petrie
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms19041208

Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data
Cited by: 18
Author(s): Katarzyna Ropka‐Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Katarzyna Piórkowska, G. Żak, Artur Gurgul, Natalia Derebecka, Joanna Wesoły
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20143468

Interleukin (IL)-22 from IL-20 Subfamily of Cytokines Induces Colonic Epithelial Cell Proliferation Predominantly through ERK1/2 Pathway
Cited by: 26
Author(s): Md. Moniruzzaman, Ran Wang, Varinder Jeet, Michael A. McGuckin, Sumaira Z. Hasnain
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21155567

Cell Sheets from Adipose Tissue MSC Induce Healing of Pressure Ulcer and Prevent Fibrosis via Trigger Effects on Granulation Tissue Growth and Vascularization
Cited by: 15
Author(s): Natalya Alexandrushkina, Peter Nimiritsky, Roman Eremichev, В. С. Попов, Mikhail Arbatskiy, Н В Данилова, П.Г. Мальков, Zhanna Akopyan, В. А. Ткачук
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22094715

Detecting the Mechanism behind the Transition from Fixed Two-Dimensional Patterned Sika Deer (Cervus nippon) Dermal Papilla Cells to Three-Dimensional Pattern
Cited by: 2
Author(s): Guanning Wei, Huiling Sun, Hou Wei, Tao Qin, Yumei Yang, Xiaohong Xu, Shuping Zhao
Software Mentions: 2
Published: over 3 years ago

10.1186/s12974-017-0915-5

MHC class II expression and potential antigen-presenting cells in the retina during experimental autoimmune uveitis
Cited by: 42
Author(s): Deborah A. Lipski, Rémi Dewispelaere, Vincent Foucart, Laure Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.13650

Association of a cytarabine chemosensitivity related gene expression signature with survival in cytogenetically normal acute myeloid leukemia
Cited by: 10
Author(s): Han Yan, Lijun Wen, Dan Tan, Ping Xie, Feng-Mei Pang, Hong‐Hao Zhou, Wei Zhang, Zhao‐Qian Liu, Jie Tang, Xi Li, Xiaoping Chen
Software Mentions: 2
Published: almost 8 years ago

10.18632/oncotarget.23148

Identification of human age-associated gene co-expressions in functional modules using liquid association
Cited by: 5
Author(s): Jialiang Yang, Yufang Qin, Tiantian Zhang, Fayou Wang, Lihong Peng, Lijuan Zhu, Dawei Yuan, Pan Gao, Jujuan Zhuang, Zhongyang Zhang, Jun Wang, Yun Fang
Software Mentions: 2
Published: almost 7 years ago