Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: Pathway

https://packages.ecosyste.ms/registries/pypi.org/packages/Pathway

Pathway is a data processing framework which takes care of streaming data updates for you.
21 versions
Latest release: 7 months ago
1 dependent package
1,787 downloads last month

Papers Mentioning Pathway 827

10.1186/gb-2011-12-8-r77
Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage
Cited by: 66
Author(s): Min Zhu, Ming Yi, Chang Hee Kim, Chu‐Xia Deng, Yang Li, Daniel Medina, Robert M. Stephens, Jeffrey E. Green
Software Mentions: 2
Published: over 13 years ago
10.1002/1878-0261.12463
Perineural invasion in pancreatic cancer: proteomic analysis and <i>in vitro</i> modelling
Cited by: 37
Author(s): Wasfi Alrawashdeh, Richard C. Jones, Laurent Dumartin, Tomasz P. Radon, Pedro R. Cutillas, Roger Feakins, Branko Dmitrović, İhsan Ekin Demir, Güralp O. Ceyhan, Tatjana Crnogorac‐Jurčević
Software Mentions: 2
Published: about 5 years ago
10.3389/fpls.2016.00842
Zinc Excess Triggered Polyamines Accumulation in Lettuce Root Metabolome, As Compared to Osmotic Stress under High Salinity
Cited by: 51
Author(s): Youssef Rouphael, Giuseppe Colla, Letizia Bernardo, David Kane, Marco Trevisan, Luigi Lucini
Software Mentions: 2
Published: almost 8 years ago
10.3389/fpls.2012.00155
An overview of existing modeling tools making use of model checking in the analysis of biochemical networks
Cited by: 26
Author(s): Miguel Carrillo, Pedro Arturo Góngora, David A. Rosenblueth
Software Mentions: 2
Published: over 12 years ago
10.1074/mcp.M115.053926
Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics*
Cited by: 45
Author(s): Harris Bell-Temin, Ashley E. Culver‐Cochran, Dale Chaput, Christina M. Carlson, Melanie N. Kuehl, Brant R. Burkhardt, Paula C. Bickford, Bin Liu, Stanley M. Stevens
Software Mentions: 2
Published: over 8 years ago
10.1186/s12943-021-01390-y
CircDIDO1 inhibits gastric cancer progression by encoding a novel DIDO1-529aa protein and regulating PRDX2 protein stability
Cited by: 57
Author(s): Yu Zhang, Jiajia Jiang, Jiayin Zhang, Han Shen, Maoye Wang, Zhen Guo, Xueyan Zang, Hui Shi, Jiayan Gao, Hui Cai, Xinjian Fang, Hui Qian, Wenrong Xu, Xu Zhang
Software Mentions: 2
Published: almost 3 years ago
10.1186/1471-2164-12-3
Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis
Cited by: 44
Author(s): Leda Mirbahai, Tim D. Williams, Huiqing Zhan, Zhiyuan Gong, J.K. Chipman
Software Mentions: 2
Published: over 13 years ago
10.3389/fphys.2016.00184
Community Structure Reveals Biologically Functional Modules in MEF2C Transcriptional Regulatory Network
Cited by: 17
Author(s): Sergio Antonio Alcalá-Corona, Tadeo Enrique Velazquez-Caldelas, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 2
Published: almost 8 years ago
10.3389/fpls.2015.00202
Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing
Cited by: 51
Author(s): Yang Xie, Shan Ye, Yan Wang, Liang Xu, Xiaoming Zhu, Juan Yang, Haiyang Feng, Rugang Yu, Benard Karanja, Yiqin Gong, Liwang Liu
Software Mentions: 2
Published: about 9 years ago
10.1186/1471-2164-13-282
NetWalker: a contextual network analysis tool for functional genomics
Cited by: 94
Author(s): Kakajan Komurov, Serkan Dursun, Serkan Erdin, Prahlad T. Ram
Software Mentions: 2
Published: over 12 years ago
10.1186/s13041-019-0498-4
Circular RNA expression profile in the spinal cord of morphine tolerated rats and screen of putative key circRNAs
Cited by: 17
Author(s): Yingqi Weng, Jing Wu, Lin Li, Jiali Shao, Zhengyiqi Li, Meiling Deng, Wangyuan Zou
Software Mentions: 2
Published: over 4 years ago
10.1002/1878-0261.12327
Loss of androgen receptor signaling in prostate cancer‐associated fibroblasts (CAFs) promotes CCL2‐ and CXCL8‐mediated cancer cell migration
Cited by: 71
Author(s): Bianca Cioni, Ekaterina Nevedomskaya, Monique Melis, Johan van Burgsteden, Suzan Stelloo, Emma Hodel, Daniele Spinozzi, Jeroen de Jong, Henk van der Poel, Jan Paul de Boer, Lodewyk Wessels, Wilbert Zwart, Andries M. Bergman
Software Mentions: 2
Published: almost 6 years ago
10.3389/fonc.2020.00267
RNA-seq Analysis of Wild-Type vs. FOXC2-Deficient Melanoma Cells Reveals a Role for the FOXC2 Transcription Factor in the Regulation of Multiple Oncogenic Pathways
Cited by: 4
Author(s): Kristian M. Hargadon, Corey J. Williams
Software Mentions: 2
Published: about 4 years ago
10.1038/s41380-018-0345-5
Towards precision medicine for pain: diagnostic biomarkers and repurposed drugs
Cited by: 55
Author(s): Alexander B. Niculescu, Helen Le-Niculescu, Daniel F. Levey, K. Roseberry, Katherine Soe, Jesse D. Rogers, Fuad Khan, Thaon Jones, Suzanne E. Judd, M. A. McCormick, A. R. Wessel, Amanda L. Williams, Sunil M. Kurian, Fletcher A. White
Software Mentions: 2
Published: over 5 years ago
10.3389/fonc.2020.562574
Ceramide Pathway Regulators Predict Clinical Prognostic Risk and Affect the Tumor Immune Microenvironment in Lung Adenocarcinoma
Cited by: 4
Author(s): Yuan Zhang, Jianbo Chen, Yunan Zhao, Lihong Weng, Yiquan Xu
Software Mentions: 2
Published: over 3 years ago
10.3390/ani8110188
RNA Sequencing-Based Whole-Transcriptome Analysis of Friesian Cattle Fed with Grape Pomace-Supplemented Diet
Cited by: 22
Author(s): Marco Iannaccone, Ramy Elgendy, Mery Giantin, Camillo Martino, Daniele Giansante, Andrea Ianni, Mauro Dacasto, Giuseppe Martino
Software Mentions: 2
Published: over 5 years ago
10.15252/msb.20199083
<scp>KCML</scp> : a machine‐learning framework for inference of multi‐scale gene functions from genetic perturbation screens
Cited by: 9
Author(s): Heba Sailem, Jens Rittscher, Lucas Pelkmans
Software Mentions: 2
Published: about 4 years ago
10.3389/fvets.2020.00615
Synthetic Alkaloid Treatment Influences the Intestinal Epithelium and Mesenteric Adipose Transcriptome in Holstein Steers
Cited by: 4
Author(s): Kyle J McLean, R.L. Baldwin, Congjun Li, J. L. Klotz, J. L. Edwards, K. R. McLeod
Software Mentions: 2
Published: over 3 years ago
10.3389/fnmol.2017.00307
Intermittent Ethanol during Adolescence Leads to Lasting Behavioral Changes in Adulthood and Alters Gene Expression and Histone Methylation in the PFC
Cited by: 46
Author(s): Jennifer T. Wolstenholme, Tariq Mahmood, Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 2
Published: over 6 years ago
10.3389/fnins.2019.01007
A Human Embryonic Stem Cell Model of Aβ-Dependent Chronic Progressive Neurodegeneration
Cited by: 5
Author(s): Teresa Ubina, Martha Magallanes, Saumya Srivastava, Charles Warden, Jiing‐Kuan Yee, Paul M. Salvaterra
Software Mentions: 2
Published: over 4 years ago
10.3389/fonc.2020.00307
Gene Expression Profiling of B Cell Lymphoma in Dogs Reveals Dichotomous Metabolic Signatures Distinguished by Oxidative Phosphorylation
Cited by: 4
Author(s): Ying Wu, Yu‐Mei Chang, Gerry Polton, Anneliese Stell, Balázs Szladovits, Michael Macfarlane, Laureen M. Peters, Simon L. Priestnall, Nicholas J. Bacon, Kelvin Kow, Sarah A. Stewart, Eshita Sharma, Michelle R. Goulart, John G. Gribben, Dong Xia, Oliver A. Garden
Software Mentions: 2
Published: about 4 years ago
10.1007/s00335-021-09869-1
Alternative exon splicing and differential expression in pancreatic islets reveals candidate genes and pathways implicated in early diabetes development
Cited by: 1
Author(s): Sufia Rehman, Tanja Schallschmidt, Axel Rasche, Birgit Knebel, Torben Stermann, Delsi Altenhofen, Ralf Herwig, Annette Schürmann, Alexandra Chadt, Hadi Al‐Hasani
Software Mentions: 2
Published: about 3 years ago
10.3389/fmolb.2021.715765
The Specific NLRP3 Antagonist IFM-514 Decreases Fibrosis and Inflammation in Experimental Murine Non-Alcoholic Steatohepatitis
Cited by: 12
Author(s): Sandra Torres, Maximilian Joseph Brol, Fernando Magdaleno, Robert Schierwagen, Frank Erhard Uschner, Sabine Klein, Cristina Ortiz, Olaf Tyc, Nadine Bachtler, James Stunden, Damien Bertheloot, Ana Kitanovic, Brian Sanchez, Jacob E. Schrum, William Roush, Luigi Franchi, Kate Byth, Eicke Latz, Jonel Trebicka
Software Mentions: 2
Published: almost 3 years ago
10.1186/1471-2164-14-216
CAMTA 1 regulates drought responses in Arabidopsis thaliana
Cited by: 136
Author(s): Neha Pandey, Alok Ranjan, Poonam Pant, Rajiv Kumar Tripathi, Farha Ateek, Haushilla P Pandey, Uday V Patre, Samir V. Sawant
Software Mentions: 2
Published: about 11 years ago
10.3389/fmed.2019.00015
Observational Study of PD-L1, TGF-β, and Immune Cell Infiltrates in Hepatocellular Carcinoma
Cited by: 20
Author(s): Christian Ihling, Bartholomew J. Naughton, Yue Zhang, Alex Rolfe, Eveline Frick-Krieger, Luigi Terracciano, Isabelle Dussault
Software Mentions: 2
Published: over 5 years ago
10.1016/S2542-5196(18)30240-7
Implications for workability and survivability in populations exposed to extreme heat under climate change: a modelling study
Cited by: 63
Author(s): Oliver Andrews, Corinne Le Quéré, Tord Kjellström, Bruno Lemke, Andy Haines
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-015-1364-0
Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency
Cited by: 51
Author(s): Nan Zhou, William R. Lee, Behnam Abasht
Software Mentions: 2
Published: about 9 years ago
10.3389/fimmu.2021.667690
Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis
Cited by: 39
Author(s): Wenxing Su, Ying Zhao, Yuqian Wei, Xiaoyan Zhang, Ji Jiang, Shun Fa Yang
Software Mentions: 2
Published: almost 3 years ago
10.3389/fonc.2020.584683
Multiple Myeloma Cells Alter Adipogenesis, Increase Senescence-Related and Inflammatory Gene Transcript Expression, and Alter Metabolism in Preadipocytes
Cited by: 19
Author(s): Heather Fairfield, Samantha Costa, Carolyne Falank, Mariah Farrell, Connor Murphy, Anastasia D’Amico, Heather Driscoll, Michaela R. Reagan
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-016-1119-5
DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases
Cited by: 227
Author(s): Symen Ligthart, Carola Marzi, Stella Aslibekyan, Michael Mendelson, Karen N. Conneely, Toshiko Tanaka, Elena Colicino, Lindsay L. Waite, Roby Joehanes, Weihua Guan, Jennifer A. Brody, Cathy E. Elks, Riccardo E. Marioni, Min A. Jhun, Golareh Agha, Jan Bressler, Cavin Ward‐Caviness, Brian H. Chen, Tianxiao Huan, Kelly M. Bakulski, Elias Salfati, Giovanni Fiorito, Simone Wahl, Katharina Schramm, Sha Jiang, Dena G. Hernandez, Allan C. Just, Jennifer A. Smith, Nona Sotoodehnia, Luke C. Pilling, James S. Pankow, Philip S. Tsao, Chunyu Liu, Wei Zhao, Simonetta Guarrera, Vasiliki Michopoulos, Alicia K. Smith, Marjolein J. Peters, David Melzer, Pantel Vokonas, Myriam Fornage, Holger Prokisch, Joshua C. Bis, Audrey Y. Chu, Christian Herder, Harald Grallert, Chen Yao, Sonia Shah, Allan F. McRae, Honghuang Lin, Steve Horvath, Danièle Fallin, Albert Hofman, Nicholas J. Wareham, Kerri L. Wiggins, Andrew P. Feinberg, John M. Starr, Peter M. Visscher, Joanne M. Murabito, Sharon L.R. Kardia, Devin Absher, Elisabeth B. Binder, Andrew B. Singleton, Stefania Bandinelli, Annette Peters, Mélanie Waldenberger, Giuseppe Matullo, Joel Schwartz, Ellen W. Demerath, André G. Uitterlinden, Joyce B. J. van Meurs, Oscar H. Franco, Yii‐Der Ida Chen, Daniel Levy, Stephen T. Turner, Ian J. Deary, Kerry J. Ressler, Josée Dupuis, Luigi Ferrucci, Ken K. Ong, Themistocles L. Assimes, Eric Boerwinkle, Wolfgang Köenig, Donna K. Arnett, Andrea A. Baccarelli, Emelia J. Benjamin, Abbas Dehghan
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-13694-5
Modeling cadmium-induced endothelial toxicity using human pluripotent stem cell-derived endothelial cells
Cited by: 22
Author(s): Ling Tang, Jun Su, Ping Liang
Software Mentions: 2
Published: over 6 years ago
10.1002/cam4.1301
Biological signaling pathways and potential mathematical network representations: biological discovery through optimization
Cited by: 4
Author(s): Clara E. Isaza, Juan Miguel Pérez Rosas, Enery Lorenzo, Arlette Marrero, Cristina Ortiz, Michael Ortiz, Lynn Perez, Mauricio Cabrera‐Ríos
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2021.716163
Transcriptome and Metabolome Analyses of the Flowers and Leaves of Chrysanthemum dichrum
Cited by: 5
Author(s): Hua Liu, Xiaoxi Chen, Hạixia Chen, Jie Lu, Dongliang Chen, Chao Luo, Xi Cheng, Jing Yin, Conglin Huang
Software Mentions: 2
Published: over 2 years ago
10.1186/2041-1480-4-S1-S5
Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data
Cited by: 19
Author(s): Leyla Jael Castro, Casey McLaughlin, Alexander García
Software Mentions: 2
Published: over 11 years ago
10.3389/fgene.2020.590924
Characteristics of Genetic Variations Associated With Lennox-Gastaut Syndrome in Korean Families
Cited by: 1
Author(s): Jin Yang, Min Hyuk Choi, Ji‐Yong Yoon, Jeong-Ju Lee, Sang Ook Nam, Soo Young Jun, Hyeok Hee Kwon, Sohyun Yun, Sang-Woon Jeon, Iksu Byeon, Debasish Halder, Jai-Yul Kong, Byung-Wook Lee, Jeehun Lee, Joon‐Won Kang, Nam-Soon Kim
Software Mentions: 2
Published: over 3 years ago
10.3389/fendo.2018.00815
Acylated Ghrelin Supports the Ovarian Transcriptome and Follicles in the Mouse: Implications for Fertility
Cited by: 14
Author(s): Luba Sominsky, Jéferson Ferraz Goularte, Zane B. Andrews, Sarah J. Spencer
Software Mentions: 2
Published: over 5 years ago
10.3390/jcm10112446
Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study
Cited by: 1
Author(s): Marianne Koch, Pavel Lyatoshinsky, Goran Mitulović, Barbara Bodner‐Adler, Sören Lange, Engelbert Hanzal, Wolfgang Umek
Software Mentions: 2
Published: almost 3 years ago
10.7717/peerj.3698
Genomic and functional analysis of<i>Romboutsia ilealis</i>CRIB<sup>T</sup>reveals adaptation to the small intestine
Cited by: 74
Author(s): J. Gerritsen, Bastian Hornung, Bernadet Renckens, Sacha A. F. T. van Hijum, Vítor A. P. Martins dos Santos, Ger T. Rijkers, Peter J. Schaap, Willem M. de Vos, Hauke Smidt
Software Mentions: 2
Published: over 6 years ago
10.3389/fgene.2020.01034
Identification and Characterization of lncRNAs Related to the Muscle Growth and Development of Japanese Flounder (Paralichthys olivaceus)
Cited by: 11
Author(s): Shuangyan Wu, Jingru Zhang, Binghua Liu, Yajuan Huang, Siping Li, Haishen Wen, Meizhao Zhang, Jifang Li, Yun Li, Feng He
Software Mentions: 2
Published: over 3 years ago
10.1186/s13058-018-0938-6
Increased circulating resistin levels in early-onset breast cancer patients of normal body mass index correlate with lymph node negative involvement and longer disease free survival: a multi-center POSH cohort serum proteomics study
Cited by: 15
Author(s): Bashar Zeidan, Antigoni Manousopoulou, Diana J. Garay‐Baquero, Cory H. White, Samantha Larkin, Kathleen Potter, Theodoros I. Roumeliotis, Evangelia K. Papachristou, Ellen Copson, Ramsey I. Cutress, Stephen A. Beers, Diana Eccles, Paul A. Townsend, Spiros D. Garbis
Software Mentions: 2
Published: about 6 years ago
10.3389/fcell.2019.00380
Deciphering the Association of Cytokines, Chemokines, and Growth Factors in Chondrogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells Using an ex vivo Osteochondral Culture System
Cited by: 17
Author(s): Mohammad Alam Jafri, Kalamegam Gauthaman, Mohammed Abbas, Mohammed Alkaff, Farid Ahmed, Sherin Bakhashab, Mahmood Rasool, Muhammad Imran Naseer, Vasan Sinnadurai, Peter Natesan Pushparaj
Software Mentions: 2
Published: over 4 years ago
10.1186/1477-7827-8-65
Impact of methoxyacetic acid on mouse Leydig cell gene expression
Cited by: 15
Author(s): Gargi Bagchi, Yijing Zhang, David J. Waxman
Software Mentions: 2
Published: almost 14 years ago
10.1186/s12864-017-3641-6
Tissue and time specific expression pattern of interferon regulated genes in the chicken
Cited by: 17
Author(s): Susanne Röll, Stefan Härtle, Thomas Lütteke, Bernd Kaspers, Sonja Härtle
Software Mentions: 2
Published: about 7 years ago
10.1111/acel.12380
Chronic <scp>mTOR</scp> inhibition in mice with rapamycin alters <scp>T</scp>,<scp> B</scp>, myeloid, and innate lymphoid cells and gut flora and prolongs life of immune‐deficient mice
Cited by: 89
Author(s): Vincent Hurez, Vinh Dao, Aijie Liu, Srilakshmi Pandeswara, Jonathan Gelfond, Liangdan Sun, Molly A. Bergman, Carlos J. Orihuela, Verónica Galván, Álvaro Padrón, Justin Drerup, Yang Liu, Paul Hasty, Zelton Dave Sharp, Tyler J. Curiel
Software Mentions: 2
Published: over 8 years ago
10.1186/s12920-016-0229-y
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia
Cited by: 31
Author(s): Sheng-An Lee, Kuo-Chuan Huang
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pbio.1002597
Narciclasine attenuates diet-induced obesity by promoting oxidative metabolism in skeletal muscle
Cited by: 34
Author(s): Sylvain Julien, Sun-Yee Kim, Reinhard Brunmeir, Joanna R. Sinnakannu, Xiaojia Ge, Hongyu Li, Wei Ma, Jadegoud Yaligar, Bhanu Prakash Kn, S. Sendhil Velan, Pia V. Röder, Qiongyi Zhang, Choon Kiat Sim, Jingyi Wu, Marta Garcia-Miralles, Mahmoud A. Pouladi, Wei Xie, Craig McFarlane, Weiping Han, Feng Xu
Software Mentions: 2
Published: over 7 years ago
10.3389/fcvm.2020.616920
Iron-Deficiency Anemia Results in Transcriptional and Metabolic Remodeling in the Heart Toward a Glycolytic Phenotype
Cited by: 10
Author(s): Yong Chung, Pawel Swietach, M. Kate Curtis, Vicky Ball, Peter A. Robbins, Samira Lakhal‐Littleton
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2021.745637
Thrombospondin-4 Is a Soluble Dermal Inflammatory Signal That Selectively Promotes Fibroblast Migration and Keratinocyte Proliferation for Skin Regeneration and Wound Healing
Cited by: 12
Author(s): Mariliis Klaas, Kristina Mäemets-Allas, Elizabeth Heinmäe, Heli Lagus, Claudia Griselda Cárdenas-León, Terje Arak, Mart Eller, Külli Kingo, Esko Kankuri, Viljar Jaks
Software Mentions: 2
Published: over 2 years ago
10.3389/fnhum.2020.585664
Increased Amygdala-Paracentral Lobule/Precuneus Functional Connectivity Associated With Patients With Mood Disorder and Suicidal Behavior
Cited by: 14
Author(s): Ran Zhang, Luheng Zhang, Shengnan Wei, Pengshuo Wang, Xiaowei Jiang, Yanqing Tang, Fei Wang
Software Mentions: 2
Published: over 3 years ago
10.18632/aging.203230
Integrated analysis of m6A mRNA methylation in rats with monocrotaline-induced pulmonary arterial hypertension
Cited by: 15
Author(s): Yiwei Zeng, Ting Huang, Wanyun Zuo, Dan Wang, Yonghui Xie, Xun Wang, Xiao Zhou, Zhi Chen, Qiming Liu, Na Liu, Yunbin Xiao
Software Mentions: 2
Published: almost 3 years ago
10.1186/1756-8935-8-7
STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer
Cited by: 33
Author(s): Joseph D. Fleming, Paul G. Giresi, Marianne Lindahl-Allen, Elizabeth A. Krall, Jason D. Lieb, Kevin Struhl
Software Mentions: 2
Published: over 9 years ago
10.1155/2013/293010
A Two-Level Model for the Analysis of Syndrome of Acute Ischemic Stroke: From Diagnostic Model to Molecular Mechanism
Cited by: 5
Author(s): Wen Dai, Liu Xi, Zhichen Zhang, Jianxin Chen, R. S. Guo, Hong Zheng, Xin Jin, Shengfang Wen, Yibo Gao, Tiangang Li, Peng Lu, Yunling Zhang
Software Mentions: 2
Published: over 11 years ago
10.1186/s12864-017-3984-z
Proteomic and transcriptomic studies of HBV-associated liver fibrosis of an AAV-HBV-infected mouse model
Cited by: 19
Author(s): Fangming Kan, Lei Ye, Tao Yan, Jiaqi Cao, Jianhua Zheng, Wuping Li
Software Mentions: 2
Published: over 6 years ago
10.15252/embr.201948961
EVL regulates VEGF receptor‐2 internalization and signaling in developmental angiogenesis
Cited by: 13
Author(s): Joana Zink, Maike Frye, Timo Frömel, Claudia Carlantoni, David John, Danny Schreier, Andreas Weigert, Hebatullah Laban, Gabriela Salinas, Heike Stingl, Lea Günther, Rüdiger Popp, Jiong Hu, Benoît Vanhollebeke, Hannes Schmidt, Amparo Acker‐Palmer, Thomas Renné, Ingrid Fleming, P. Benz
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-13-68
Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis
Cited by: 38
Author(s): Yang Wang, Chong Liu, Yīng Fāng, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen, Qigai He
Software Mentions: 2
Published: over 12 years ago
10.1289/ehp.10861
Drinking-Water Arsenic Exposure Modulates Gene Expression in Human Lymphocytes from a U.S. Population
Cited by: 128
Author(s): Angeline S. Andrew, Dianne V. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, Margaret R. Karagas
Software Mentions: 2
Published: about 16 years ago
10.1186/1471-2164-15-327
Transcriptome profiling of liver of non-genetic low birth weight and long term health consequences
Cited by: 4
Author(s): Alberto Miranda, Angela Patricia López‐Cardona, Ricardo Laguna‐Barraza, Alexandra Calle, Irene López‐Vidriero, Belén Pintado, Alfonso Gutiérrez‐Adán
Software Mentions: 2
Published: over 10 years ago
10.1093/database/bau126
Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
Cited by: 86
Author(s): Saikat Chowdhury, Ram Rup Sarkar
Software Mentions: 2
Published: over 9 years ago
10.1016/j.csbj.2015.11.006
Disease, Models, Variants and Altered Pathways—Journeying RGD Through the Magnifying Glass
Cited by: 3
Author(s): Victoria Petri, G. Thomas Hayman, Marek Tutaj, Jennifer Smith, Stan Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R. Dwinell
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2407-10-192
Interference with Activator Protein-2 transcription factors leads to induction of apoptosis and an increase in chemo- and radiation-sensitivity in breast cancer cells
Cited by: 19
Author(s): Verena Thewes, Francesca Orso, Richard Jäger, Dawid Eckert, Sabine Schäfer, Gregor Kirfel, Stephan Garbe, Daniela Taverna, Hubert Schorle
Software Mentions: 2
Published: about 14 years ago
10.1093/database/baaa113
Large-scale regulatory and signaling network assembly through linked open data
Cited by: 1
Author(s): Marie Lefebvre, Alban Gaignard, Maxime Folschette, Jérémie Bourdon, Carito Guziołowski
Software Mentions: 2
Published: over 3 years ago
10.1242/bio.058593
Oviductal fluid counterbalances the negative effect of high temperature on sperm in an ectotherm model
Cited by: 5
Author(s): Nicola De Rossi, Guadalupe López Juri, Margarita Chiaraviglio, Gabriela Cardozo
Software Mentions: 2
Published: about 3 years ago
10.1093/bioinformatics/btaa987
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data
Cited by: 9
Author(s): Andrew E. Teschendorff, Alok Kumar Maity, Hao Xue, Weiyan Chen, Matthias Lechner
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-9-478
Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma
Cited by: 19
Author(s): Mary H. Estler, Goran Bošković, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles
Software Mentions: 2
Published: over 15 years ago
10.1093/bioinformatics/bty188
SPV: a JavaScript Signaling Pathway Visualizer
Cited by: 9
Author(s): Alberto Calderone, Gianni Cesareni
Software Mentions: 2
Published: about 6 years ago
10.1111/acel.13092
Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver
Cited by: 20
Author(s): Andrew Price, Mohan C. Manjegowda, Jessica Kain, Swetha Anandh, Irina M. Bochkis
Software Mentions: 2
Published: over 4 years ago
10.5936/csbj.201304004
A NETWORK VIEW ON PARKINSON'S DISEASE
Cited by: 43
Author(s): S. Chandrasekaran, Danail Bonchev
Software Mentions: 2
Published: about 11 years ago
10.1093/database/baw009
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework
Cited by: 28
Author(s): Yi‐An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
Software Mentions: 2
Published: over 8 years ago
10.12688/f1000research.3818.2
Systems analysis of the prostate tumor suppressor NKX3.1 supports roles in DNA repair and luminal cell differentiation
Cited by: 5
Author(s): Changjun Yang, Alicia S. Chung, Chia‐Yu Ku, Laurence M. Brill, Roy Williams, David E. Wolf
Software Mentions: 2
Published: over 9 years ago
10.3389/fimmu.2017.00541
Hypoxia Modulates the Response of Mast Cells to Staphylococcus aureus Infection
Cited by: 21
Author(s): Helene Möllerherm, Katja Branitzki‐Heinemann, Graham Brogden, Ayssar A. Elamin, Wulf Oehlmann, Herbert Fuhrmann, Mahavir Singh, Hassan Y. Naim, Maren von Köckritz‐Blickwede
Software Mentions: 2
Published: about 7 years ago
10.1186/s13040-021-00279-2
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation
Cited by: 6
Author(s): Mila Glavaški, Lazar Velicki
Software Mentions: 2
Published: over 2 years ago
10.1186/s12864-017-3546-4
Transcriptome analysis of coding and long non-coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs
Cited by: 23
Author(s): Fu Wang, Yang Li, Xiaoshan Wu, Min Yang, Cong Wang, Zhipeng Fan, Jinsong Wang, Chunmei Zhang, Jie Du, Songlin Wang
Software Mentions: 2
Published: over 7 years ago
10.1186/1752-0509-7-1
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
Cited by: 62
Author(s): Michael Weber, Sebastian Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J. van Zoelen, Dominik Driesch
Software Mentions: 2
Published: over 11 years ago
10.1111/acel.12676
Age‐associated dysregulation of protein metabolism in the mammalian oocyte
Cited by: 80
Author(s): Francesca E. Duncan, Susmita Jasti, Ariel Paulson, John M. Kelsh, Barbara Fegley, Jennifer L. Gerton
Software Mentions: 2
Published: over 6 years ago
10.1186/1752-0509-3-99
An editor for pathway drawing and data visualization in the Biopathways Workbench
Cited by: 24
Author(s): Robert W. Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David R. Nadeau, Shankar Subramaniam
Software Mentions: 2
Published: over 14 years ago
10.3390/cells10092380
Mitochondrial Disruption by Amyloid Beta 42 Identified by Proteomics and Pathway Mapping
Cited by: 11
Author(s): Patricia Sinclair, Ancha Baranova, Nadine Kabbani
Software Mentions: 2
Published: over 2 years ago
10.1007/s12094-021-02621-w
Aberrantly low STAT3 and STAT5 responses are associated with poor outcome and an inflammatory gene expression signature in pediatric acute myeloid leukemia
Cited by: 5
Author(s): Priya Narayanan, Tsz-Kwong Man, Robert B. Gerbing, Rhonda E. Ries, Alexandra M. Stevens, Y.-C. Wang, Xin Long, Alan S. Gamis, Todd M. Cooper, Soheil Meshinchi, Todd A. Alonzo, Michele S. Redell
Software Mentions: 2
Published: about 3 years ago
10.1186/1752-0509-4-156
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
Cited by: 102
Author(s): Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F. Urchueguı́a, Kiran Raosaheb Patil
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0227928
miRNA expression in advanced Algerian breast cancer tissues
Cited by: 8
Author(s): Mohamad Ali Tfaily, Farah Nassar, Leila-Sarah Sellam, Zine-Charaf Amir-Tidadini, F. Asselah, Mehdi Bourouba, Rihab Nasr
Software Mentions: 2
Published: over 4 years ago
10.1186/s12964-019-0504-6
miR-544 promotes maturity and antioxidation of stem cell-derived endothelial like cells by regulating the YY1/TET2 signalling axis
Cited by: 8
Author(s): Jianming Guo, Xiang Qiu, Xin Yao-jie, Yongyi Huang, Gang Zou, Te Liu
Software Mentions: 2
Published: about 4 years ago
10.3390/cancers13143520
Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers
Cited by: 6
Author(s): Geeng-Fu Jang, John S. Crabb, Bo Hu, Belinda Willard, Helen Kalirai, Arun D. Singh, Sarah E. Coupland, John W. Crabb
Software Mentions: 2
Published: almost 3 years ago
10.1371/journal.pone.0012222
Hybrid Models Identified a 12-Gene Signature for Lung Cancer Prognosis and Chemoresponse Prediction
Cited by: 45
Author(s): Ying-Wooi Wan, Ebrahim Sabbagh, Rebecca Raese, Yong Qian, Dajie Luo, James Denvir, Val Vallyathan, Vincent Castranova, Nancy Lan Guo
Software Mentions: 2
Published: almost 14 years ago
10.1186/1471-2105-12-19
Context-dependent transcriptional regulations between signal transduction pathways
Cited by: 6
Author(s): Shin Hwang, Sangwoo Kim, Heon‐Cheol Shin, Doheon Lee
Software Mentions: 2
Published: over 13 years ago
10.1186/1747-1028-4-20
Proteomics, pathway array and signaling network-based medicine in cancer
Cited by: 56
Author(s): David Y. Zhang, Fei Ye, Ling Gao, Xiaoliang Liu, Xin Zhao, Yufang Che, Hongxia Wang, Libo Wang, Josephine W. Wu, Dong Eun Song, Wei Liu, Hong Xu, Bo Jiang, Weijia Zhang, Jinhua Wang, Peng Lee
Software Mentions: 2
Published: over 15 years ago
10.3390/cancers13163972
Plasma Based Protein Signatures Associated with Small Cell Lung Cancer
Cited by: 2
Author(s): Johannes F. Fahrmann, Hiroyuki Katayama, Ehsan Irajizad, Ashish Chakraborty, Toshiro Kato, Xiangying Mao, Soyoung Park, Eunice Murage, Leona Rusling, Chuan Yu, Yinging Cai, Fu Chung Hsiao, Jennifer B. Dennison, Hai T. Tran, Edwin J. Ostrin, David O. Wilson, Jian Min Yuan, Jody Vykoukal, Samir Hanash
Software Mentions: 2
Published: almost 3 years ago
10.3390/cancers13143613
Canopy Homolog 2 as a Novel Molecular Target in Hepatocarcinogenesis
Cited by: 3
Author(s): Anna Kakehashi, Shugo Suzuki, Masayuki Shiota, Nina Raymo, Min Gi, Taro Tachibana, В. Е. Стефанов, Hideki Wanibuchi
Software Mentions: 2
Published: almost 3 years ago
10.3390/cancers11081151
SLMP53-2 Restores Wild-Type-Like Function to Mutant p53 through Hsp70: Promising Activity in Hepatocellular Carcinoma
Cited by: 19
Author(s): Sara Gomes, Bartolomeo Bosco, Joana B. Loureiro, Helena Ramos, Liliana Raimundo, Joana Soares, Naïr Nazareth, Valentina Barcherini, Lucı́lia Domingues, Carla Cristina Marques de Oliveira, Alessandra Bisio, Silvano Piazza, Matthias R. Bauer, João Brás, Maria Inês Almeida, Célia Gomes, Flávio Reis, Alan R. Fersht, Alberto Inga, Maria M. M. Santos, Lucı́lia Saraiva
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2105-12-176
Web-based metabolic network visualization with a zooming user interface
Cited by: 31
Author(s): Mario Latendresse, Peter D. Karp
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0082435
Fyn-Dependent Gene Networks in Acute Ethanol Sensitivity
Cited by: 23
Author(s): Sean P. Farris, Michael F. Miles
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0028254
Filaggrin Genotype Determines Functional and Molecular Alterations in Skin of Patients with Atopic Dermatitis and Ichthyosis Vulgaris
Cited by: 60
Author(s): M Winge, Torborg Hoppe, Berit Berne, Anders Vahlquist, Magnus Nordenskjöld, J. F. N. Bradley, Hans Törmä
Software Mentions: 2
Published: over 12 years ago
10.1186/s12919-021-00213-8
Abstracts from the 4th Annual Student Medical Summit
Cited by: 1
Author(s):
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0208993
SLC3A2 is a novel endoplasmic reticulum stress-related signaling protein that regulates the unfolded protein response and apoptosis
Cited by: 17
Author(s): Chunlei Liu, Xin Li, Chen Li, Zeyu Zhang, Xiaojian Gao, Zhilong Jia, Haixu Chen, Qian Jia, Xiaojing Zhao, Jixuan Liu, Bohan Liu, Zhihong Xu, Yaping Tian, Kunlun He
Software Mentions: 2
Published: over 5 years ago
10.1186/1756-0500-4-356
CastorDB: a comprehensive knowledge base for Ricinus communis
Cited by: 6
Author(s): Shalabh Thakur, Sanjay Jha, Bharat B. Chattoo
Software Mentions: 2
Published: over 12 years ago
10.3390/cancers5020491
Metabolomic Dynamic Analysis of Hypoxia in MDA-MB-231 and the Comparison with Inferred Metabolites from Transcriptomics Data
Cited by: 15
Author(s): I‐Lin Tsai, Tien-Chueh Kuo, Tsung Jung Ho, Yeu-Chern Harn, San-Yuan Wang, Wen‐Mei Fu, Ching‐Hua Kuo, Yufeng J. Tseng
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0020623
Evaluation of Cell Cycle Arrest in Estrogen Responsive MCF-7 Breast Cancer Cells: Pitfalls of the MTS Assay
Cited by: 64
Author(s): Eileen McGowan, Nikki Alling, Elise Jackson, Daniel Yagoub, Nikolas K. Haass, John D. Allen, Rosetta Martinello-Wilks
Software Mentions: 2
Published: almost 13 years ago
10.1186/s12864-017-4035-5
Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ
Cited by: 39
Author(s): Christopher Resnyk, Wilfrid Carré, X. Wang, Tom E. Porter, Jean Simon, Elisabeth Le Bihan‐Duval, M. J. Duclos, Samuel E. Aggrey, Larry A. Cogburn
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0127630
Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
Cited by: 74
Author(s): Tomas Persson, Kai Battenberg, Irina V. Demina, Theoden Vigil-Stenman, Brian Vanden Heuvel, Petar Pujic, Marc T. Facciotti, Elizabeth G. Wilbanks, Anna O'Brien, Pascale Fournier, Maria Antonia Cruz Hernandez, Alberto Herrera, Claudine Médigue, Philippe Normand, Katharina Pawlowski, Alison M. Berry
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0217592
Understanding climate change from a global analysis of city analogues
Cited by: 67
Author(s): Jean François Bastin, Emily Clark, T. R. Elliott, Simon P. Hart, Johan van den Hoogen, Iris Hordijk, Haozhi Ma, Sabiha Majumder, Gabriele Manoli, Julia Maschler, Lidong Mo, Devin Routh, Kailiang Yu, Constantin M. Zohner, Thomas W. Crowther
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0221446
An in silico approach towards identification of novel drug targets in pathogenic species of Leptospira
Cited by: 13
Author(s): Reena Gupta, Rashi Verma, Dibyabhaba Pradhan, Arun K. Jain, Amineni Umamaheswari, C. S.
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0013017
Defining Hypo-Methylated Regions of Stem Cell-Specific Promoters in Human iPS Cells Derived from Extra-Embryonic Amnions and Lung Fibroblasts
Cited by: 51
Author(s): Koichiro Nishino, Masashi Toyoda, Mayu Yamazaki-Inoue, Hidenari Makino, Yoshihiro Fukawatase, Emi Chikazawa, Yoriko Takahashi, Yoshitaka Miyagawa, Hajime Okita, Nobutaka Kiyokawa, Hidenori Akutsu, Akihiro Umezawa
Software Mentions: 2
Published: over 13 years ago