pypi: Pathway | Projects | Ecosyste.ms: Papers

10.3390/ijms22062822

A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research
Cited by: 6
Author(s): Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
Software Mentions: 16
Published: about 3 years ago

10.3389/fcell.2020.00790

The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer
Cited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: over 3 years ago

10.1186/s13059-021-02264-8

GeneWalk identifies relevant gene functions for a biological context using network representation learning
Cited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: over 3 years ago

10.1186/s12859-018-2486-6

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: over 5 years ago

10.1038/s42003-019-0554-8

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome
Cited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: over 4 years ago

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: over 8 years ago

10.1186/s13073-016-0384-y

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
Cited by: 131
Author(s): Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C. Knight
Software Mentions: 12
Published: over 7 years ago

10.1371/journal.pone.0131656

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data
Cited by: 1
Author(s): Ashis Saha, Minji Jeon, Aik Choon Tan, Jaewoo Kang
Software Mentions: 10
Published: almost 9 years ago

10.1186/s12859-020-03549-8

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Cited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: almost 4 years ago

10.15252/msb.20209923

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Cited by: 122
Author(s): Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian J. Theis, Dezső Módos, Tamás Korcsmáros, Julio Sáez-Rodríguez
Software Mentions: 10
Published: about 3 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: about 4 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.18236.1

BioHackathon 2015: Semantics of data for life sciences and reproducible research
Cited by: 5
Author(s): Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Seiichiro Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, K. Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández‐Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yukiko Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Toshio Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosiñach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Miguel Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
Software Mentions: 9
Published: about 4 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13045-020-00941-y

A single-cell survey of cellular hierarchy in acute myeloid leukemia
Cited by: 39
Author(s): Jinliang Wu, Yanyu Xiao, Jie Sun, Huiyu Sun, Haide Chen, Yuanyuan Zhu, Haidong Fu, Chengxuan Yu, E Weigao, Shih‐Wei Lai, Lifeng Ma, Jiaqi Li, Lijiang Fei, Mengmeng Jiang, Jingjing Wang, Fang Ye, Renying Wang, Ziyu Zhou, Guodong Zhang, Tingyue Zhang, Qiong Ding, Zou Wang, Sheng Hao, Lizhen Liu, Weiyan Zheng, Jingsong He, Weijia Huang, Yungui Wang, Jin Xie, Tiefeng Li, Tao Cheng, Xiaoping Han, He Huang, Guoji Guo
Software Mentions: 9
Published: over 3 years ago

10.1007/s00018-018-2898-5

Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-40285-3

Phenotypic and transcriptomic characterization of canine myeloid-derived suppressor cells
Cited by: 22
Author(s): Michelle R. Goulart, Sabina I. Hlavaty, Yu-Mei Chang, Gerry Polton, Anneliese Stell, James A. Perry, Ying Wu, Eshita Sharma, John Broxholme, Avery C. Lee, Balázs Szladovits, Mark Turmaine, John G. Gribben, Dong Xia, Oliver A. Garden
Software Mentions: 7
Published: about 5 years ago

10.1186/s40246-015-0050-2

A survey of computational tools for downstream analysis of proteomic and other omic datasets
Cited by: 17
Author(s): Anis Karimpour-Fard, L. Elaine Epperson, Lawrence Hunter
Software Mentions: 7
Published: over 8 years ago

10.21203/rs.3.rs-380803/v1

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Cited by: 9
Author(s): Alexandra Tsitsiklis, Beth Shoshana Zha, Ashley Byrne, Catherine DeVoe, Sophia Levan, Elze Rackaityte, Sara Sunshine, Eran Mick, Rajani Ghale, Alejandra Jauregui, Norma Neff, Aartik Sarma, Paula Hayakawa Serpa, Thomas Deiss, Amy Kistler, Sidney Carrillo, K. Mark Ansel, Aleksandra Leligdowicz, S. Christenson, Nicola L. Jones, Benjamin Wu, Spyros Darmanis, Michael A. Matthay, Susan V. Lynch, Joseph L. DeRisi, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, O. A. Rosenberg, Carolyn S. Calfee, Charles Langelier
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pcbi.1004765

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
Cited by: 29
Author(s): Yasin Şenbabaoğlu, S. Onur Sumer, Francisco Sánchez-Vega, Debra L. Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander
Software Mentions: 7
Published: about 8 years ago

10.1186/s13045-017-0406-2

Analyses of caspase-1-regulated transcriptomes in various tissues lead to identification of novel IL-1β-, IL-18- and sirtuin-1-independent pathways
Cited by: 43
Author(s): Yafeng Li, Gayani Nanayakkara, Yu Sun, Xinyuan Li, Luqiao Wang, Ramón Cueto, Ying Shao, Hangfei Fu, Candice Johnson, Jiali Cheng, Xiongwen Chen, Wenhui Hu, Jun Yu, Eric T. Choi, Hong Wang, Xiaofeng Yang
Software Mentions: 7
Published: over 7 years ago

10.1155/2014/649453

Computational Approaches for Microalgal Biofuel Optimization: A Review
Cited by: 21
Author(s): Joseph Koussa, Amphun Chaiboonchoe, Kourosh Salehi‐Ashtiani
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-020-69905-z

A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype
Cited by: 20
Author(s): Alberto Cedro‐Tanda, Magdalena Ríos-Romero, Sandra Romero-Córdoba, Mireya Cisneros-Villanueva, Rosa Rebollar-Vega, Luis Alfaro-Ruiz, Silvia Jiménez-Morales, Carlos Alberto Domínguez-Reyes, Felipe Villegas-Carlos, Alberto Tenorio-Torres, Verónica Bautista-Piña, Fredy Omar Beltrán-Anaya, Alfredo Hidalgo‐Miranda
Software Mentions: 6
Published: almost 4 years ago

10.1242/dmm.049012

Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol
Cited by: 16
Author(s): Karen E. Boschen, Travis Ptacek, Matthew E. Berginski, Jeremy M. Simon, Scott E. Parnell
Software Mentions: 6
Published: almost 3 years ago

10.3389/fgene.2019.01203

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling
Cited by: 67
Author(s): Sarah Mubeen, Charles Tapley Hoyt, André Gemünd, Martin Hofmann‐Apitius, Holger Fröhlich, Daniel Domingo‐Fernándéz
Software Mentions: 6
Published: over 4 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1005053

Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53
Cited by: 47
Author(s): Kristina Kirschner, Shamith A. Samarajiwa, Jonathan Cairns, Suraj Menon, Pedro A. Pérez–Mancera, Kosuke Tomimatsu, Camino Bermejo‐Rodríguez, Yoko Itō, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimurâ, Tetsuya Ohbayashi, Simon Tavaré
Software Mentions: 6
Published: about 9 years ago

10.1038/sdata.2017.35

A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Cited by: 6
Author(s): Aria S. Hahn, Tomer Altman, Kishori M. Konwar, Niels W. Hanson, Dongjae Kim, David A. Relman, David L. Dill, Steven J. Hallam
Software Mentions: 6
Published: about 7 years ago

10.1186/s13326-020-00228-8

Identifying disease trajectories with predicate information from a knowledge graph
Cited by: 4
Author(s): Wytze J. Vlietstra, Rein Vos, Marjan van den Akker, Erik M. van Mulligen, Jan A. Kors
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0116095

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes
Cited by: 9
Author(s): Yuanshuai Zhou, Yongjing Liu, Kening Li, Rui Zhang, Fujun Qiu, Ning Zhao, Yan Xu
Software Mentions: 6
Published: about 9 years ago

10.1186/s12864-021-07437-0

Transcriptomics analysis of Toxoplasma gondii-infected mouse macrophages reveals coding and noncoding signatures in the presence and absence of MyD88
Cited by: 7
Author(s): Kayla L. Menard, Lijing Bu, Eric Denkers
Software Mentions: 6
Published: about 3 years ago

10.1186/s12864-019-5797-8

Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows
Cited by: 13
Author(s): S.G. Moore, Aaron C. Ericsson, Susanta K. Behura, W. R. Lamberson, Timothy J. Evans, Matthew S. McCabe, S.E. Poock, M.C. Lucy
Software Mentions: 6
Published: almost 5 years ago

10.3390/cancers11122023

Identification of a Subtype of Hepatocellular Carcinoma with Poor Prognosis Based on Expression of Genes within the Glucose Metabolic Pathway
Cited by: 11
Author(s): Xiaoli Zhang, Jin Li, Kalpana Ghoshal, Soledad Fernández, Lang Li
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0111661

How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?
Cited by: 18
Author(s): Djordje Djordjevic, Andrian Yang, Armella Zadoorian, Kevin Rungrugeecharoen, Joshua W. K. Ho
Software Mentions: 6
Published: over 9 years ago

10.1186/1743-422X-11-126

Reactive astrogliosis in response to hemorrhagic fever virus: microarray profile of Junin virus-infected human astrocytes
Cited by: 8
Author(s): Olga A. Kolokoltsova, Nadezhda E. Yun, Slobodan Paessler
Software Mentions: 6
Published: almost 10 years ago

10.1186/1471-2164-14-14

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity
Cited by: 26
Author(s): Katie S Viljoen, Jonathan M. Blackburn
Software Mentions: 6
Published: over 11 years ago

10.1093/gbe/evu149

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities
Cited by: 33
Author(s): Diego Santos-García, Amparo Latorre, Andrés Moya, George Gibbs, Viktor Hartung, Konrad Dettner, Stefan Martin Kuechler, Francisco J. Silva
Software Mentions: 6
Published: almost 10 years ago

10.18632/oncotarget.25329

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma
Cited by: 13
Author(s): Toshima Z. Parris, Elisabeth Werner Rönnerman, Hanna Engqvist, Jana Biermann, Katarina Truvé, Szilárd Nemes, Eva Forssell-Aronsson, Giovanni Solinas, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-66377-z

Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation
Cited by: 10
Author(s): Marine Barthez, Mathilde Poplineau, Marwa Elrefaey, Nathalie Caruso, Yacine Graba, Andrew J. Saurin
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.30862

Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation
Cited by: 54
Author(s): Angela Halstead, Chiraag D Kapadia, Jennifer K. Bolzenius, Clarence E Chu, Andrew E. Schriefer, Lukas D. Wartman, Gregory R. Bowman, Vivek Arora
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.02200

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms
Cited by: 206
Author(s): Mary A. Allen, Zdeněk Andrysík, Veronica L. Dengler, Hestia Mellert, Anna L. Guarnieri, John H. Freeman, Kelly D. Sullivan, Matthew D. Galbraith, Xin Luo, W. Lee Kraus, Robin D. Dowell, Joaquín M. Espinosa
Software Mentions: 5
Published: almost 10 years ago

10.3390/ijms22010382

Exosomal miRNAs as Potential Biomarkers to Monitor Phosphodiesterase 5 Inhibitor Induced Anti-Fibrotic Effects on CCl4 Treated Rats
Cited by: 9
Author(s): Andre Broermann, RM Schmid, Ogsen Gabrielyan, Marlene Sakowski, Claudia Eisele, Sascha Keller, Michael Wolff, Patrick Baum, Birgit Stierstorfer, J. Huber, Bernhard K. Krämer, Berthold Hocher, Ruediger Streicher, Denis Delić
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-021-01052-7

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome
Cited by: 54
Author(s): Jordi Mayneris‐Perxachs, Marina Cardellini, Lesley Hoyles, Jéssica Latorre, Francesca Davato, José María Moreno-Navarrete, María Arnoriaga-Rodríguez, Matteo Sérino, James Abbott, Richard H. Barton, Josep Puig, Xavier Fernández-Real, Wifredo Ricart, Christopher Tomlinson, Mark Woodbridge, Paolo Gentileschi, Sarah Butcher, Elaine Holmes, Jeremy K. Nicholson, Vicente Pérez‐Brocal, Andrés Moya, Donald Mc Clain, Rémy Burcelin, Marc Dumas, Massimo Federici, José‐Manuel Fernández‐Real
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.00675

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
Cited by: 344
Author(s): Katherine Noelani Chang, Shan Zhong, Matthew T. Weirauch, Gary C. Hon, Mattia Pelizzola, Hai Li, S. Huang, Robert J. Schmitz, Mark A. Urich, Dwight Kuo, Joseph R. Nery, Hong Qiao, Ally Yang, Abdullah Jamali, Huaming Chen, Trey Ideker, Bing Ren, Ziv Bar‐Joseph, Timothy R. Hughes, Joseph R. Ecker
Software Mentions: 5
Published: almost 11 years ago

10.7554/eLife.61968

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species
Cited by: 36
Author(s): Arnaud Belcour, Clémence Frioux, Méziane Aïte, Anthony Bretaudeau, Falk Hildebrand, Anne Siegel
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0055635

Functional-Network-Based Gene Set Analysis Using Gene-Ontology
Cited by: 6
Author(s): Billy Chang, Rafal Kustra, Weidong Tian
Software Mentions: 5
Published: about 11 years ago

10.1186/gm500

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
Cited by: 105
Author(s): Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope M. Sheehan, Yun Dai, Richard Saffery, Lex W. Doyle, Jeffrey M Craig
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0249994

Modeling impacts of faster productivity growth to inform the CGIAR initiative on Crops to End Hunger
Cited by: 15
Author(s): Keith Wiebe, Timothy B. Sulser, Shahnila Dunston, Mark W. Rosegrant, Keith O. Fuglie, Dirk Willenbockel, Gerald C. Nelson
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-019-57110-6

Single-cell transcriptional profiles in human skeletal muscle
Cited by: 160
Author(s): Aliza Rubenstein, Gregory R. Smith, Ulrika Raue, Gwénaëlle Begue, Kiril Minchev, Frederique Ruf-Zamojski, Venugopalan D. Nair, Xingyu Wang, Lan Zhou, Elena Zaslavsky, Todd A. Trappe, Scott Trappe, Stuart C. Sealfon
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: over 9 years ago

10.12688/f1000research.5499.1

Visualisation of BioPAX Networks using BioLayout Express3D
Cited by: 16
Author(s): Derek W. Wright, Tim Angus, Anton J. Enright, Tom C. Freeman
Software Mentions: 5
Published: over 9 years ago

10.1186/s12881-020-01108-9

Deep vein thrombosis inhibitor may play a therapeutic role in post-stroke patients
Cited by: 1
Author(s): Xiao Xiang, Di Yuan, Peiyan Kong, Ting Chen, Han Yao, Shijia Lin, Xi Zhang, Hongbao Cao
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-1072

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column
Cited by: 18
Author(s): Satadal Chatterjee, V. Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 5
Published: over 9 years ago

10.1186/s12881-020-01099-7

Understanding the molecular association between hyperkalemia and lung squamous cell carcinomas
Cited by: 2
Author(s): Xianping Meng, Huiqi Lu, Xia Jiang, Bin Huang, Song Wu, Guiping Yu, Hongbao Cao
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-017-1462-x

Comparative network stratification analysis for identifying functional interpretable network biomarkers
Cited by: 5
Author(s): Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.8390

Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis
Cited by: 46
Author(s): Weisong Cai, Haohuan Li, Yubiao Zhang, Guoge Han
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-020-3465-2

PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data
Cited by: 33
Author(s): Amina Lemsara, Salima Ouadfel, Holger Fröhlich
Software Mentions: 4
Published: about 4 years ago

10.3389/fcell.2021.671806

Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching
Cited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: almost 3 years ago

10.3389/fgene.2020.557188

Bioinformatics Identification of the Expression and Clinical Significance of E2F Family in Endometrial Cancer
Cited by: 8
Author(s): YunZheng Zhang, Zihao Wang, Jian Ma, Jianing Huo, Yibing Li, YuShan Wang, Hao Chen, LuHe Shan, Xiaoxin Ma
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ebiom.2018.09.024

Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism
Cited by: 10
Author(s): Meltem Weger, Benjamin D. Weger, Benjamin Görling, Gernot Poschet, Melek Yıldız, Rüdiger Hell, Burkhard Luy, Teoman Akçay, Tülay Güran, Thomas Dickmeis, Ferenc Müller, Nils Krone
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-13-S17-S24

TranSeqAnnotator: large-scale analysis of transcriptomic data
Cited by: 6
Author(s): Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan
Software Mentions: 4
Published: over 11 years ago

10.1042/BSR20194459

GPNMB contributes to a vicious circle for chronic obstructive pulmonary disease
Cited by: 1
Author(s): Xijuan Zhang, Zhong‐hua Cui, Yan Dong, Xiuwen Liang, Yanxin Zhao, Ancha Baranova, Hongbao Cao, Ling Wang
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-14-475

Variable promoter methylation contributes to differential expression of key genes in human placenta-derived venous and arterial endothelial cells
Cited by: 30
Author(s): Jihoon E. Joo, Ursula Hiden, Luciana Lassance, Lavinia Gordon, David Martino, Gernot Desoyé, Richard Saffery
Software Mentions: 4
Published: almost 11 years ago

10.4056/sigs.5279417

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
Cited by: 21
Author(s): Dagmar Waltemath, Frank Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolás Rodríguez, Falk Schreiber, Lucian P. Smith, Fengkai Zhang, Eric Bonnet
Software Mentions: 4
Published: about 10 years ago

10.1186/s13578-018-0227-1

Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages
Cited by: 9
Author(s): Xinyu Feng, Jia-Tong Wu, Shui-Sen Zhou, Jingwen Wang, Wei Hu
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2407-14-739

MicroRNA expression as risk biomarker of breast cancer metastasis: a pilot retrospective case-cohort study
Cited by: 42
Author(s): Augusto L F Marino, Adriane Feijó Evangelista, René Aloísio da Costa Vieira, Taciane Macedo, Lígia Maria Kerr, Lucas Faria Abrahão-Machado, Adhemar Longatto‐Filho, Henrique C. S. Silveira, Márcia Maria Chiquitelli Marques
Software Mentions: 4
Published: over 9 years ago

10.1038/s41398-021-01309-7

Gut microbial taxa elevated by dietary sugar disrupt memory function
Cited by: 42
Author(s): Emily E. Noble, C. Anders Olson, Elizabeth A. Davis, Linda Tsan, Yen‐Wei Chen, Ruth Schade, Clarissa Liu, Andrea N. Suarez, Roshonda B. Jones, Claire de La Serre, Xia Yang, Elaine Y. Hsiao, Scott E. Kanoski
Software Mentions: 4
Published: about 3 years ago

10.1038/srep17901

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: over 8 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: about 8 years ago

10.1038/s41438-020-0338-9

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
Cited by: 43
Author(s): Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei, Yongsheng Liu, Yi Zheng
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-12-497

Partition decoupling for multi-gene analysis of gene expression profiling data
Cited by: 10
Author(s): Rosemary Braun, Gregory Leibon, Scott D. Pauls, Daniel N. Rockmore
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0240841

Risk screening methods for extreme heat: Implications for equity-oriented adaptation
Cited by: 3
Author(s): Lynée L. Turek-Hankins, Miyuki Hino, Katharine J. Mach
Software Mentions: 4
Published: over 3 years ago

10.1098/rsos.202265

The impacts of past, present and future ocean chemistry on predatory planktonic snails
Cited by: 4
Author(s): Deborah Wall-Palmer, Lisette Mekkes, Paula Ramos-Silva, Linda K. Dämmer, Erica Goetze, Karel Bakker, Elza Duijm, Katja T. C. A. Peijnenburg
Software Mentions: 4
Published: almost 3 years ago

10.1038/srep26846

Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB
Cited by: 48
Author(s): Daniel Haustead, Andrew Stevenson, Vishal Saxena, Fiona Marriage, Martin J Firth, Robyn C Silla, Lisa W. Martin, Katharine F. Adcroft, Suzanne Rea, Philip J. Day, Phillip E. Melton, Fiona Wood, Mark W. Fear
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0015147

Analysis of Ultra Low Genome Conservation in Clostridium difficile
Cited by: 58
Author(s): Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
Software Mentions: 4
Published: over 13 years ago

10.3389/fphar.2019.00415

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches
Cited by: 7
Author(s): Pantelis Natsiavas, Andigoni Malousi, Cédric Bousquet, Marie-Christine Jaulent, Vassilis Koutkias
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.120.401183

Resistance Mechanisms ofSaccharomyces cerevisiaeto Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure
Cited by: 8
Author(s): Apoorva Ravishankar, Amaury Pupo, Jennifer E. Gallagher
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0032453

Astrocyte-Specific Expression Patterns Associated with the PDGF-Induced Glioma Microenvironment
Cited by: 66
Author(s): Amanda Katz, Nduka Amankulor, Kenneth L. Pitter, Karim Y. Helmy, Massimo Squatrito, Eric C. Holland
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pntd.0008230

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota
Cited by: 12
Author(s): Sivaranjani Namasivayam, Bassirou Diarra, Seydou Diabaté, Yeya dit Sadio Sarro, A. Koné, Bourahima Kone, Mohamed Tolofoudié, Bocar Baya, M L Diakité, Ousmane Kodio, Keira A. Cohen, Jane L. Holl, Chad Achenbach, S. Chatterjee, Robert L. Murphy, William R. Bishai, Souleymane Diallo, Alan Sher, Mamoudou Maiga
Software Mentions: 4
Published: almost 4 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: almost 3 years ago

10.18632/genesandcancer.133

Genetically transforming human osteoblasts to sarcoma: development of an osteosarcoma model
Cited by: 21
Author(s): Yi Yuan Yang, Rui Yang, Michael Roth, Sajida Piperdi, Wendong Zhang, Howard D. Dorfman, Pulivarthi H. Rao, Amy Park, Sandeep Tripathi, Carrie Freeman, Yunjia Zhang, Rebecca Sowers, Jeremy Rosenblum, David S. Geller, Bang H. Hoang, Jonathan Gill, Richard Görlick
Software Mentions: 4
Published: about 7 years ago

10.1161/CIRCULATIONAHA.120.046672

Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis
Cited by: 192
Author(s): Gabriel F. Alencar, Katherine Owsiany, Santosh Karnewar, Katyayani Sukhavasi, Giuseppe Mocci, Anh Nguyen, Corey Williams, Sohel Shamsuzzaman, Michal Mokrý, Christopher A. Henderson, Ryan M. Haskins, Richard A. Baylis, Aloke V. Finn, Coleen A. McNamara, Eli R. Zunder, Vamsidhar R M Venkata, Gérard Pasterkamp, Johan Björkegren, Stefan Bekiranov, Gary K. Owens
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.01063

α7 Nicotinic Acetylcholine Receptor Signaling Modulates Ovine Fetal Brain Astrocytes Transcriptome in Response to Endotoxin
Cited by: 16
Author(s): Mingju Cao, James W. MacDonald, Hai L. Liu, Molly Weaver, Marina Farrel Cortês, Lucien Daniel Durosier, Patrick Burns, Gilles Fecteau, André Desrochers, Jay Schulkin, Marta C. Antonelli, Raphael Bernier, Michael O. Dorschner, Theo K. Bammler, Martin G. Frasch
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1004790

Pathway-Based Genomics Prediction using Generalized Elastic Net
Cited by: 82
Author(s): Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart
Software Mentions: 4
Published: about 8 years ago

10.1038/srep15782

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Cited by: 213
Author(s): Christian Milani, Gabriele Andrea Lugli, Sabrina Duranti, Francesca Turroni, Leonardo Mancabelli, Chiara Ferrario, Marta Mangifesta, Arancha Hevia, Alice Viappiani, Matthias Scholz, Stefania Arioli, Borja Sánchez, Jonathan A. Lane, Doyle V. Ward, Rita M. Hickey, Diego Mora, Nicola Segata, Abelardo Margollés, Douwe van Sinderen, Marco Ventura
Software Mentions: 4
Published: over 8 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-899

Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: over 9 years ago

10.3389/fneur.2020.00590

Preeclampsia Drives Molecular Networks to Shift Toward Greater Vulnerability to the Development of Autism Spectrum Disorder
Cited by: 4
Author(s): Qinglian Xie, Zhe Li, Yan Wang, Shan Zaidi, Ancha Baranova, Fuquan Zhang, Hongbao Cao
Software Mentions: 4
Published: almost 4 years ago

10.1084/jem.20190730

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid
Cited by: 47
Author(s): Guillermo L. Lehmann, Christin Hanke-Gogokhia, Yang Hu, Rohan Bareja, Zelda Salfati, Michael Ginsberg, Daniel J. Nolan, Santiago P. Méndez-Huergo, Tomás Dalotto-Moreno, Alexandre Wojcinski, Francisca Ochoa, Siyuan Zeng, Juan P. Cerliani, Lampros Panagis, Patrick J. Zager, Robert F. Mullins, Shuntaro Ogura, Gerard A. Lutty, Jakyung Bang, Jonathan H. Zippin, Carmelo Romano, Gabriel A. Rabinovich, Olivier Elemento, Alexandra L. Joyner, Shahin Rafii, Enrique Rodríguez-Boulan, Ignacio Benedicto
Software Mentions: 4
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

10.1186/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

10.1186/1471-2164-16-S11-S4

A method for developing regulatory gene set networks to characterize complex biological systems
Cited by: 1
Author(s): Chayaporn Suphavilai, Zhu Li, Jake Y. Chen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-018-2183-5

INBIA: a boosting methodology for proteomic network inference
Cited by: 2
Author(s): Davide Stefano Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.2834

Transcriptome analysis of the oriental melon (Cucumis meloL. var.makuwa) 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.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: almost 3 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/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

10.3389/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

Projects: pypi: Pathway

Papers Mentioning Pathway 827