pypi: Pathway | Projects | Ecosyste.ms: Papers

10.3390/cancers12061629

Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection
Cited by: 19
Author(s): Victoria El-Khoury, Anna Schritz, Sang Yoon Kim, Antoine Lesur, Katriina Sertamo, François Bernardin, Konstantinos Pétritis, Patrick Pirrotte, Cheryl Selinsky, Jeffrey R. Whiteaker, Haizhen Zhang, Jacob J. Kennedy, Chenwei Lin, Lik Wee Lee, Ping Yan, Nhan L. Tran, Landon J. Inge, Khaled Chalabi, G. Anton Decker, Rolf Bjerkvig, Amanda G. Paulovich, Guy Berchem, Yeoun Jin Kim
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12862-018-1199-9

The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish
Cited by: 28
Author(s): Masato Yoshizawa, Alexander Settle, Meredith C. Hermosura, Lillian J. Tuttle, Nicolas Cetraro, Courtney N. Passow, Suzanne E. McGaugh
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers12051090

Integrative Transcriptome Analyses of the Human Fallopian Tube: Fimbria and Ampulla—Site of Origin of Serous Carcinoma of the Ovary
Cited by: 12
Author(s): Ramlogan Sowamber, Omar L. Nelson, Leah V. Dodds, Victoria Decastro, Iru Paudel, Anca Milea, Michael Considine, Leslie Cope, André Pinto, Matthew Schlumbrecht, Brian M. Slomovitz, Patricia Shaw, Sophia George
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-75657-7

Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation
Cited by: 12
Author(s): Hye‐Yeong Jo, Youngsun Lee, Hongryul Ahn, Heon-Seok Han, Ara Kwon, Boyoung Kim, Hye-Yeong Ha, Sang Cheol Kim, Jung-Hyun Kim, Yong-Ou Kim, Sun Kim, Soo Kyung Koo, Mi-Hyun Park
Software Mentions: 3
Published: over 3 years ago

10.3390/jpm11020111

Clinical Utility of microRNAs in Exhaled Breath Condensate as Biomarkers for Lung Cancer
Cited by: 12
Author(s): C. Pérez-Sánchez, Nuria Barbarroja, Lucas Carminatti Pantaleão, Laura M. López‐Sánchez, Susan E. Ozanne, Bernabé Jurado-Gámez, Enrique Aranda, Chary López‐Pedrera, Antonio Rodríguez‐Ariza
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0033542

Gene Expression Profile of Adult Human Olfactory Bulb and Embryonic Neural Stem Cell Suggests Distinct Signaling Pathways and Epigenetic Control
Cited by: 36
Author(s): Hany E. Marei, Ahmed Abd‐Elmaksoud, Fabrizio Michetti, Mario Pescatori, Roberto Pallini, Patricia Casalbore, Carlo Cenciarelli, Mohamed Elhadidy
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0210675

Murine trophoblast-derived and pregnancy-associated exosome-enriched extracellular vesicle microRNAs: Implications for placenta driven effects on maternal physiology
Cited by: 27
Author(s): Adrianne L. Stefanski, Nadine Martinez, Lisa K. Peterson, Tiffany J. Callahan, Eileen P. Treacy, Marisa E. Luck, Samantha F. Friend, Amy Hermesch, Emin Maltepe, Tzu L. Phang, Leonard L. Dragone, Virginia D. Winn
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.19557

cFLIP critically modulates apoptotic resistance in epithelial-to-mesenchymal transition
Cited by: 6
Author(s): Chandrasekhar Padmanabhan, Eric J. Rellinger, Jing Zhu, Hanbing An, Luke Woodbury, Dai H. Chung, Alex G. Waterson, Craig W. Lindsley, Anna L. Means, R. Daniel Beauchamp
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.50135

Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model
Cited by: 127
Author(s): Magdalena Kasendra, Raymond Luc, Jianyi Yin, Dimitris V. Manatakis, Gauri Kulkarni, Carolina Lucchesi, Josiah Sliz, Αθανασία Αποστόλου, Laxmi Sunuwar, Jenifer Obrigewitch, Kyung Jin Jang, Mark Donowitz, Katia Karalis
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.14295

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation
Cited by: 125
Author(s): Ryuta Ishimura, Gábor Nagy, Iván Dotú, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.9030

GCGene: a gene resource for gastric cancer with literature evidence
Cited by: 1
Author(s): Min Zhao, Luming Chen, Yining Liu, Hong Qu
Software Mentions: 3
Published: about 8 years ago

10.1042/BSR20200350

Uterine fibroids may play a protecting role against endometrial carcinoma in Chinese women with gynecological diseases
Cited by: 4
Author(s): Qiao Li, Lili Xia, Yan Dong, Yajuan Cheng, Hongbao Cao
Software Mentions: 3
Published: almost 4 years ago

10.1186/1751-0473-6-5

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format
Cited by: 6
Author(s): Ryan L Webb, Avi Ma’ayan
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0138210

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma
Cited by: 9
Author(s): Brian J. Capaldo, Devin G. Roller, Mark J. Axelrod, Alexander F. Koeppel, Emanuel F. Petricoin, Craig L. Slingluff, Michael J. Weber, Aaron J. Mackey, Daniel Gioeli, Stefan Bekiranov
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0031858

Functional Complexity of the Axonal Growth Cone: A Proteomic Analysis
Cited by: 38
Author(s): Adriana Estrada-Bernal, Staci D. Sanford, Lucas J. Sosa, Glenn C. Simon, Kirk C. Hansen, Karl H. Pfenninger
Software Mentions: 3
Published: about 12 years ago

10.1186/s13058-020-01275-w

In utero estrogenic endocrine disruption alters the stroma to increase extracellular matrix density and mammary gland stiffness
Cited by: 14
Author(s): Clarissa Wormsbaecher, Andrea R. Hindman, Alex Avendano, Marcos Cortes-Medina, Caitlin E. Jones, Andrew R. Bushman, Lotanna Onua, Claire E Kovalchin, Alina R. Murphy, Hannah L. Helber, Ali Shapiro, Kyle Voytovitch, Xingyan Kuang, Renán Aguilar-Valenzuela, Jennifer L. Leight, Jonathan W. Song, Craig J. Burd
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-020-6697-7

iMarmot: an integrative platform for comparative and functional genomics of marmots
Cited by: 3
Author(s): Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Zhao Song, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan, Enqi Liu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-64326-4

Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans
Cited by: 7
Author(s): Pascal Gottmann, Meriem Ouni, Lisa Zellner, Markus Jähnert, Kilian Rittig, Dirk Walther, Annette Schürmann
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-019-56878-x

Delineation of hypoxia-induced proteome shifts in osteosarcoma cells with different metastatic propensities
Cited by: 16
Author(s): Zifeng Song, Martin C. Pearce, Yuan Jiang, Liping Yang, Cheri P. Goodall, Cristobal L. Miranda, Milan Milovancev, Shay Bracha, Siva Kumar Kolluri, Claudia S. Maier
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-56656-9

Identification of a key gene module associated with glucocorticoid- induced derangement in bone mineral density in patients with asthma
Cited by: 5
Author(s): Suh Young Lee, Ha Kyeong Won, Byung-Keun Kim, Sae Hoon Kim, Yoon Seok Chang, Sang Heon Cho, H. William Kelly, Kelan G. Tantisira, Heung-Woo Park
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0137908

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View
Cited by: 8
Author(s): Edoardo Saccenti, David F. Nieuwenhuijse, Jasper J. Koehorst, Vítor A. P. Martins dos Santos, Peter J. Schaap
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-020-62130-8

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
Cited by: 14
Author(s): Dinka Mandaković, Ángela Cintolesi, Jonathan Maldonado, Sebastián N. Mendoza, Méziane Aïte, Alexis Gaete, Francisco Saitua, Miguel L. Allende, Verónica Cambiazo, Anne Siegel, Alejandro Maass, Maurício González, Mauricio Latorre
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-10-405

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients
Cited by: 151
Author(s): Christiaan G J Saris, Steve Horvath, Paul W.J. van Vught, Michael A. van Es, Hylke M. Blauw, Tova Fuller, Peter Langfelder, Joseph DeYoung, John H. J. Wokke, Jan H. Veldink, Leonard H van den Berg, Roel A. Ophoff
Software Mentions: 3
Published: over 14 years ago

10.1128/mSystems.00061-19

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
Cited by: 36
Author(s): Taniya Roy Chowdhury, Joon‐Yong Lee, Eric Bottos, Colin Brislawn, Richard Allen White, Lisa Bramer, Joseph Brown, Jeremy Zucker, Young Mo Kim, Ari Jumpponen, Charles W. Rice, Sarah Fansler, Thomas O. Metz, Lee Ann McCue, Stephen Callister, Hyun‐Seob Song, Janet K. Jansson
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-021-04040-8

A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications
Cited by: 6
Author(s): Umesh Kathad, Aditya Kulkarni, Joseph McDermott, Jordan Wegner, Peter Carr, Neha Biyani, Rama Modali, Jaepyeong Cha, Panna Sharma, Kishor Bhatia
Software Mentions: 3
Published: about 3 years ago

10.1038/srep33262

Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
Cited by: 13
Author(s): Chenchen Feng, Jian Zhang, Xuecang Li, Bo Ai, Junwei Han, Qiuyu Wang, Taiming Wei, Yong Xu, Meng Li, Shang Li, Chao Song, Chunquan Li
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-18528-y

Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival
Cited by: 30
Author(s): Ulrich von Both, Maurice Berk, Paul‐Michael Agapow, J. D. Wright, Anna Git, Melissa Shea Hamilton, Gregory M. Goldgof, Nazneen Siddiqui, Evangelos Bellos, Victoria Wright, Lachlan Coin, Sandra M. Newton, Michael Levin
Software Mentions: 3
Published: over 6 years ago

10.1038/srep13099

Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
Cited by: 48
Author(s): Otto Kauko, Teemu D. Laajala, Mikael Jumppanen, Petteri Hintsanen, Veronika Suni, Pekka Haapaniemi, Garry L. Corthals, Tero Aittokallio, Jukka Westermarck, Susumu Y. Imanishi
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12885-019-5715-0

A novel long non-coding RNA from the HOXA6-HOXA5 locus facilitates colon cancer cell growth
Cited by: 6
Author(s): Saki Saijo, Yuki Kuwano, Shoichiro Tange, Kazuhito Rokutan, Kensei Nishida
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-21172-9

Future global productivity will be affected by plant trait response to climate
Cited by: 82
Author(s): Nima Madani, John S. Kimball, Ashley P. Ballantyne, David L. R. Affleck, Peter M. van Bodegom, Peter B. Reich, Jens Kattge, Anna Sala, Mona Nazeri, Matthew O. Jones, Maosheng Zhao, Steven W. Running
Software Mentions: 3
Published: over 6 years ago

10.1111/jcmm.15183

PTBP1 modulates osteosarcoma chemoresistance to cisplatin by regulating the expression of the copper transporter SLC31A1
Cited by: 33
Author(s): Cheng Cheng, Qiuyue Ding, Zhicai Zhang, Shangyu Wang, Botao Zhong, Xin Huang
Software Mentions: 3
Published: about 4 years ago

10.21203/rs.3.rs-513461/v1

SARS-CoV-2 Infection Causes Dopaminergic Neuron Senescence
Cited by: 17
Author(s): Shuibing Chen, Yanxiao Han, Liuliu Yang, Tae Il Kim, Manoj S. Nair, Oliver Harschnitz, Pengfei Wang, Jiajun Zhu, So Yeon Koo, Xiaoxue Tang, Lauretta A. Lacko, Vasuretha Chandar, Yaron Bram, Tuo Zhang, Wei Zhang, Feng He, James Caicedo, Yaoxing Huang, Todd Evans, Paul van der Valk, Maarten J. Titulaer, Jochem K. H. Spoor, Robert L. Furler, Peter Canoll, James E. Goldman, Serge Przedborski, Robert E. Schwartz, David D. Ho, Lorenz Studer
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pntd.0009081

Potential impacts of climate change on geographical distribution of three primary vectors of African Trypanosomiasis in Tanzania’s Maasai Steppe: G. m. morsitans, G. pallidipes and G. swynnertoni
Cited by: 12
Author(s): Happiness J. Nnko, Paul Gwakisa, Anibariki Ngonyoka, Calvin Sindato, Anna B. Estes
Software Mentions: 3
Published: over 3 years ago

10.1186/s12931-020-01364-6

Increased mortality of acute respiratory distress syndrome was associated with high levels of plasma phenylalanine
Cited by: 17
Author(s): Jing Xu, Tingting Pan, Xiaoling Qi, Ruoming Tan, Xiaoli Wang, Zhaojun Liu, Zheying Tao, Yi Zhang, Hong Chen, Yihui Wang, Jingjing Zhang, Jie Wang, Jialin Liu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-21506-7

CXCL12/CXCR4-Mediated Procollagen Secretion Is Coupled To Cullin-RING Ubiquitin Ligase Activation
Cited by: 13
Author(s): Susan Patalano, Jose Antonio Rodriguez-Nieves, Cory Colaneri, Justin Cotellessa, Diego Almanza, Alisa Zhilin-Roth, Todd Riley, Jill A. Macoska
Software Mentions: 3
Published: about 6 years ago

10.3390/genes12020129

Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis
Cited by: 11
Author(s): DeAnna Baker Frost, Willian A. da Silveira, E. Starr Hazard, Ilia Atanelishvili, Robert Wilson, Jonathan Flume, Kayleigh L. Day, Jim C. Oates, Galina S. Bogatkevich, Carol Feghali‐Bostwick, Gary Hardiman, Paula S. Ramos
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006122

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations
Cited by: 35
Author(s): Han Zhang, William Wheeler, Paula L. Hyland, Yifan Yang, Jianxin Shi, Nilanjan Chatterjee, Kai Yu
Software Mentions: 3
Published: almost 8 years ago

10.18632/genesandcancer.101

FGF19 functions as autocrine growth factor for hepatoblastoma
Cited by: 18
Author(s): David J. Elzi, Meihua Song, Barron Blackman, Susan T. Weintraub, Dolores López‐Terrada, Yidong Chen, Gail E. Tomlinson, Yuzuru Shiio
Software Mentions: 3
Published: about 8 years ago

10.1186/s12918-014-0115-1

A computational platform to maintain and migrate manual functional annotations for BioCyc databases
Cited by: 4
Author(s): Jesse R. Walsh, Taner Z. Sen, Julie A. Dickerson
Software Mentions: 3
Published: over 9 years ago

10.3389/fphys.2018.01755

The Use of Targeted Next Generation Sequencing to Explore Candidate Regulators of TGF-β1’s Impact on Kidney Cells
Cited by: 7
Author(s): Bo Wang, Guanyu Ji, Haroon Naeem, Junwen Wang, Phillip Kantharidis, David Powell, Sharon D. Ricardo
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1003367

A Novel Role for the RNA–Binding Protein FXR1P in Myoblasts Cell-Cycle Progression by Modulating p21/Cdkn1a/Cip1/Waf1 mRNA Stability
Cited by: 64
Author(s): Laetitia Davidovic, Nelly Durand, Olfa Khalfallah, Ricardo Tabet, Pascal Barbry, Bernard Mari, Sabrina Sacconi, Hervé Moine, Barbara Bardoni
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-019-5673-6

Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids
Cited by: 19
Author(s): Mark Lammers, Ken Kraaijeveld, Janine Mariën, Jacintha Ellers
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2021.542063

Construction of Gene Modules and Analysis of Prognostic Biomarkers for Cervical Cancer by Weighted Gene Co-Expression Network Analysis
Cited by: 7
Author(s): Jiamei Liu, Shengye Liu, Xianghong Yang
Software Mentions: 3
Published: about 3 years ago

10.1186/1752-0509-8-79

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database
Cited by: 42
Author(s): Daniel Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen, Peter D. Karp
Software Mentions: 3
Published: over 10 years ago

10.3389/fmolb.2016.00002

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks
Cited by: 6
Author(s): Benjamin Merlet, Nils Paulhe, Florence Vinson, Clément Frainay, Maxime Chazalviel, Nathalie Poupin, Yoann Gloaguen, Franck Giacomoni, Fabien Jourdan
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2018.00621

Identification and Characterization of als Genes Involved in D-Allose Metabolism in Lineage II Strain of Listeria monocytogenes
Cited by: 7
Author(s): Lu Zhang, Yan Wang, Dongxin Liu, Lijuan Luo, Yi Wang, Changyun Ye
Software Mentions: 3
Published: about 6 years ago

10.3389/fnmol.2018.00192

Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling
Cited by: 18
Author(s): Anna A. Igolkina, Chris Armoskus, Jeremy R.B. Newman, Oleg V. Evgrafov, Lauren McIntyre, Sergey V. Nuzhdin, Maria Samsonova
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1007652

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network
Cited by: 2
Author(s): Andreï Zinovyev, Urszula Czerwińska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0007764

Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction
Cited by: 20
Author(s): Rosane M. B. Teles, Jing Lü, Maria Tió-Coma, Isabela M. B. Goulart, Sayera Banu, Deanna A. Hagge, Kidist Bobosha, Tom H. M. Ottenhoff, Matteo Pellegrini, Annemieke Geluk, Robert L. Modlin
Software Mentions: 3
Published: over 4 years ago

10.3389/fphys.2020.00653

Rehabilitative Impact of Exercise Training on Human Skeletal Muscle Transcriptional Programs in Parkinson’s Disease
Cited by: 13
Author(s): Kaleen M. Lavin, Yongchao Ge, Stuart C. Sealfon, Venugopalan D. Nair, Katarzyna Wilk, Jeremy McAdam, Samuel T. Windham, Preeti Lakshman Kumar, Merry-Lynn McDonald, Marcas M. Bamman
Software Mentions: 3
Published: almost 4 years ago

10.1186/gb-2013-14-10-r115

DNA methylation age of human tissues and cell types
Cited by: 4,174
Author(s): Steve Horvath
Software Mentions: 3
Published: over 11 years ago

10.7717/peerj.2834

Transcriptome analysis of the oriental melon (<i>Cucumis melo</i>L. var.<i>makuwa</i>) during fruit development
Cited by: 26
Author(s): Ah-Young Shin, Yongmin Kim, Namjin Koo, Su‐Min Lee, Seok-Hyeon Nahm, Suk‐Yoon Kwon
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2019.00851

Consensus-Expressed CXCL8 and MMP9 Identified by Meta-Analyzed Perineural Invasion Gene Signature in Gastric Cancer Microarray Data
Cited by: 16
Author(s): Xiuzhi Jia, Minjia Lu, Rui Chen, Ying Xiao
Software Mentions: 3
Published: over 4 years ago

10.1186/s12917-021-02785-1

Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus
Cited by: 12
Author(s): Qian Dong, Joan K. Lunney, Kyu-Sang Lim, Yet Nguyen, Andrew S. Hess, Hamid Beiki, Raymond R. R. Rowland, Kristen Walker, James M. Reecy, Christopher K. Tuggle, Jack C. M. Dekkers
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1000115

An Integrated Approach for the Analysis of Biological Pathways using Mixed Models
Cited by: 59
Author(s): Lily Wang, Bing Zhang, Russell D. Wolfinger, Xi Chen
Software Mentions: 3
Published: almost 16 years ago

10.3389/fgene.2016.00172

Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains
Cited by: 12
Author(s): Aharon Nachshon, Hanifa J. Abu‐Toamih Atamni, Yael Steuerman, Roa'a Sheikh-Hamed, Alexandra Dorman, Richard Mott, Juliane C. Dohm, Hans Lehrach, Marc Sultan, Ron Shamir, Sascha Sauer, Heinz Himmelbauer, Fuad A. Iraqi, Irit Gat‐Viks
Software Mentions: 3
Published: over 7 years ago

10.1186/s12969-018-0265-6

Proceedings of the 25th European Paediatric Rheumatology Congress (PReS 2018)
Cited by: 27
Author(s):
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-6507-2

Transcriptomic profiles of Dunaliella salina in response to hypersaline stress
Cited by: 18
Author(s): Qinghua He, Yaqiu Lin, Hong Kee Tan, Yu Zhou, Yan Wen, Jiajia Gan, Ruiwen Li, Qinglian Zhang
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.650213

Predicting the Key Genes Involved in Aortic Valve Calcification Through Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Dinghui Wang, Tianhua Xiong, Wenlong Yu, Bin Liu, Jing Wang, Kaihu Xiao, Sheng Qiang
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2019.01019

IRF1 Maintains Optimal Constitutive Expression of Antiviral Genes and Regulates the Early Antiviral Response
Cited by: 67
Author(s): Debasis Panda, Erisa Gjinaj, Mahesh Bachu, Erica Squire, Hilary Novatt, Keiko Ozato, Ronald L. Rabin
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.133393

Histone deacetylases 1 and 2 restrain CD4+ cytotoxic T lymphocyte differentiation
Cited by: 20
Author(s): Teresa Preglej, Patricia Hamminger, Maik Luu, Tanja Bulat, Liisa Andersen, Lisa Göschl, Valentina Stolz, Ramona Rica, Lisa Sandner, Darina Waltenberger, Roland Tschismarov, Thomas Faux, Thorina Boenke, Asta Laiho, Laura L. Elo, Shoji Sakaguchi, Günter Steiner, Thomas Decker, Barbara Bohle, Alexander Visekruna, Christoph Bock, Birgit Strobl, Christian Seiser, Nicole Boucheron, Wilfried Ellmeier
Software Mentions: 3
Published: about 4 years ago

10.3390/v11090793

Comparison of Transcriptome Differences in Soybean Response to Soybean Mosaic Virus under Normal Light and in the Shade
Cited by: 19
Author(s): Lei Zhang, Jing Shang, Wenming Wang, Junbo Du, Kai Li, Xiaoling Wu, Yu Liu, Chunyan Liu, Muhammad Ibrahim Khaskheli, Wenyu Yang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12989-019-0332-2

Hepatotoxicity and the role of the gut-liver axis in rats after oral administration of titanium dioxide nanoparticles
Cited by: 71
Author(s): Zhangjian Chen, Di Zhou, Shuo Han, Shiyong Zhou
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.659659

SAMD9 Is Relating With M2 Macrophage and Remarkable Malignancy Characters in Low-Grade Glioma
Cited by: 16
Author(s): Wenping Ma, Kenan Zhang, Zhaoshi Bao, Tao Jiang, Ying Zhang
Software Mentions: 3
Published: about 3 years ago

10.3389/fcell.2021.663130

Androgen Activity Is Associated With PD-L1 Downregulation in Thyroid Cancer
Cited by: 10
Author(s): Timmy O’Connell, Sina Dadafarin, Melanie Jones, Tomás Rodríguez, Anvita Gupta, Edward J. Shin, Augustine Moscatello, Codrin Iacob, Humayun Islam, Raj K. Tiwari, Jan Geliebter
Software Mentions: 3
Published: almost 3 years ago

10.3389/fcell.2020.00842

Epitranscriptomic N4-Acetylcytidine Profiling in CD4+ T Cells of Systemic Lupus Erythematosus
Cited by: 18
Author(s): Gangqiang Guo, Xinyu Shi, Huijing Wang, Lele Ye, Xinya Tong, Kejing Yan, Ning Ding, Chaosheng Chen, Huidi Zhang, Xiangyang Xue
Software Mentions: 3
Published: over 3 years ago

10.3389/fbioe.2019.00048

Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior With Prior Knowledge of Biological Networks
Cited by: 15
Author(s): Hooman Sedghamiz, Matthew M. Morris, Travis J. A. Craddock, Darrell Whitley, Gordon Broderick
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2020.583434

Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells
Cited by: 9
Author(s): Elizabeth Weber, Yung-Chih Lai, Mingxing Lei, Ting‐Xin Jiang, Cheng‐Ming Chuong
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9020382

Bacillus amyloliquefaciens TL Downregulates the Ileal Expression of Genes Involved in Immune Responses in Broiler Chickens to Improve Growth Performance
Cited by: 7
Author(s): Yuxuan Hong, Cheng Yang, Leluo Guan, Zutao Zhou, Xiaowen Li, Deshi Shi, Yufei Xiao
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-017-0357-4

Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota
Cited by: 61
Author(s): Richard Wu, Pekka Määttänen, Scott Napper, Erin Scruten, Bo Li, Yuhki Koike, Kathene C. Johnson‐Henry, Agostino Pierro, Laura Rossi, Steven R. Botts, Michael G. Surette, Philip M. Sherman
Software Mentions: 3
Published: over 6 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

10.1093/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

10.1016/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

10.1093/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

10.1186/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

10.1186/1471-2164-10-570

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
Cited by: 54
Author(s): Lejla Pašić, Beltran Rodriguez-Mueller, Ana-Belén Martín-Cuadrado, Álex Mira, Forest Rohwer, Francisco Rodrı́guez-Valera
Software Mentions: 2
Published: over 14 years ago

10.1186/s12920-021-00894-2

Integrated analysis of differentially expressed genes and construction of a competing endogenous RNA network in human Huntington neural progenitor cells
Cited by: 3
Author(s): Xiaoping Tan, Yang Liu, Taiming Zhang, Shuyan Cong
Software Mentions: 2
Published: over 3 years ago

10.1186/s12920-015-0094-0

The cis and trans effects of the risk variants of coronary artery disease in the Chr9p21 region
Cited by: 18
Author(s): Wei Zhao, Jennifer A. Smith, Guangmei Mao, Myriam Fornage, Patricia A. Peyser, Yan V. Sun, Stephen T. Turner, Sharon L.R. Kardia
Software Mentions: 2
Published: about 9 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

10.1007/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

10.1186/1471-2105-16-S10-S2

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013
Cited by: 52
Author(s): Sampo Pyysalo, Tomoko Ohta, Rafał Rak, Andrew Rowley, Hong Woo Chun, Sung Jae Jung, Sung Pil Choi, Jun’ichi Tsujii, Sophia Ananiadou
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-019-6401-y

Transcriptomic analyses of Pinus koraiensis under different cold stresses
Cited by: 24
Author(s): Fang Wang, Song Chen, Dan Liang, Guanzheng Qu, Su Chen, Xiyang Zhao
Software Mentions: 2
Published: over 4 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

10.1186/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/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

10.1186/s12864-015-2139-3

Deep sequencing of the uterine immune response to bacteria during the equine oestrous cycle
Cited by: 22
Author(s): C Marth, Neil D. Young, Lisa Y. Glenton, Drew M. Noden, Glenn F. Browning, Natali Krekeler
Software Mentions: 2
Published: over 8 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

10.3390/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/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

10.3390/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

10.1186/1471-2164-12-3

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

10.3390/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

10.1186/1471-2164-13-282

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

10.1371/journal.pone.0082634

RNA-Seq Transcriptome Profiling of Upland Cotton (Gossypium hirsutum L.) Root Tissue under Water-Deficit Stress
Cited by: 56
Author(s): Megan J. Bowman, Wonkeun Park, Philip J. Bauer, Joshua A. Udall, Justin T. Page, Joshua A. Raney, Brian E. Scheffler, Don C. Jones, B. Todd Campbell
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0142693

Transcriptomic Analysis of Induced Pluripotent Stem Cells Derived from Patients with Bipolar Disorder from an Old Order Amish Pedigree
Cited by: 32
Author(s): Kwi Hye Kim, Jiangang Liu, Rachelle J. Sells Galvin, Jeffrey L. Dage, Janice A. Egeland, Rosamund C. Smith, Kalpana Merchant, Steven M. Paul
Software Mentions: 2
Published: over 8 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

10.1371/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.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

Projects: pypi: Pathway

Papers Mentioning Pathway 827