pypi: Pathway | Projects | Ecosyste.ms: Papers

10.7717/peerj.6152

Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (<i>Amphiprion clarkii</i>)
Cited by: 17
Author(s): Robert J. Holmberg, Eric Wilcox-Freeburg, Andrew L. Rhyne, Michael F. Tlusty, Alan Stebbins, Steven W. Nye, Aaron Honig, Amy E. Johnston, Christine M San Antonio, Bradford Bourque, Robyn Hannigan
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11440

Identification of the biological function of miR-9 in spinal cord ischemia-reperfusion injury in rats
Cited by: 2
Author(s): Fengshou Chen, Jie Han, Xiaoqian Li, Zaili Zhang, Dan Wang
Software Mentions: 1
Published: over 3 years ago

10.3390/ph6111429

Hedgehog Pathway Blockade Inhibits Melanoma Cell Growth in Vitro and in Vivo
Cited by: 37
Author(s): Kathryn E. O'Reilly, Eleazar Vega Saenz de Miera, Miguel F. Segura, Erica B. Friedman, Laura Poliseno, Sung Won Han, Judy Zhong, Jiří Zavadil, Anna C. Pavlick, Eva Hernando, Iman Osman
Software Mentions: 1
Published: about 11 years ago

10.14814/phy2.14373

The acute effects of growth hormone in adipose tissue is associated with suppression of antilipolytic signals
Cited by: 10
Author(s): Katrine Lundby Høyer, Morten Lyng Høgild, Edward O. List, Kevin Y. Lee, Emily Kissinger, Rita Sharma, Nils E. Magnusson, Vishwajeet Puri, John J. Kopchick, Jens Otto Lunde Jørgensen, Niels Jessen
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pbio.3000508

Cisd2 is essential to delaying cardiac aging and to maintaining heart functions
Cited by: 34
Author(s): Chi-Hsiao Yeh, Zhao Qing Shen, Shao Yu Hsiung, Po‐Kuei Wu, Yuan Teng, Yi Ju Chou, Su Wen Fang, Chian Feng Chen, Yu Yan, Lung‐Sen Kao, Chiang Kao, Ting Fen Tsai
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pbio.2005707

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation
Cited by: 71
Author(s): Oswaldo A. Lozoya, Inmaculada Martínez‐Reyes, Tianyuan Wang, Dagoberto Grenet, Pierre R. Bushel, Jianying Li, Navdeep S. Chandel, Richard P. Woychik, Janine H. Santos
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1005432

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells
Cited by: 10
Author(s): Aurélien Naldi, Romain M. Larive, Urszula Czerwińska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1004176

Extensive Decoupling of Metabolic Genes in Cancer
Cited by: 27
Author(s): Ed Reznik, Chris Sander
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1004714

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
Cited by: 296
Author(s): David Lamparter, Daniel Marbach, Rico Rueedi, Zoltán Kutalik, Sven Bergmann
Software Mentions: 1
Published: almost 9 years ago

10.1371/currents.RRN1180

Genetic Testing for CYP450 Polymorphisms to Predict Response to Clopidogrel: current evidence and test availabilityApplication: Pharmacogenomics
Cited by: 13
Author(s): Renée M. Ned
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pgen.1004458

Age-Associated Sperm DNA Methylation Alterations: Possible Implications in Offspring Disease Susceptibility
Cited by: 224
Author(s): Timothy G. Jenkins, Kenneth I. Aston, Christian Pflueger, Bradley R. Cairns, Douglas T. Carrell
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003542

Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle
Cited by: 89
Author(s): Haiqing Fu, Alika K. Maunakea, Melvenia M. Martin, Liang Huang, Zhang Ya, Michaël Ryan, RyangGuk Kim, Chii Meil Lin, Keji Zhao, Mirit I. Aladjem
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000080

BRCA1 and BRCA2 Missense Variants of High and Low Clinical Significance Influence Lymphoblastoid Cell Line Post-Irradiation Gene Expression
Cited by: 13
Author(s): Nicola Waddell, Anette ten Haaf, Anna Marsh, Julie K. Johnson, Logan C. Walker, kConFab Investigators, Milena Gongora, Melissa A. Brown, Piyush Grover, Mark Girolami, Sean M. Grimmond, Georgia Chenevix-Trench, Amanda B. Spurdle
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1000367

Genetic Mechanisms in Apc-Mediated Mammary Tumorigenesis
Cited by: 46
Author(s): Mari Kuraguchi, Nana Ohene-Baah, Dmitriy Sonkin, Roderick T. Bronson, Raju Kucherlapati
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pntd.0004965

DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions
Cited by: 22
Author(s): Prashanthi Karyala, Rahul Metri, Christopher Bathula, Syam K. Yelamanchi, Lipika Sahoo, Selvam Arjunan, Narayan P. Sastri, Nagasuma Chandra
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0003878

Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery
Cited by: 70
Author(s): Sean Ekins, Jair L. Siqueira-Neto, Laura-Isobel McCall, Malabika Sarker, Maneesh K. Yadav, Elizabeth L. Ponder, E. Adam Kallel, Danielle Kellar, Steven Chen, Michelle R. Arkin, Barry A. Bunin, James H. McKerrow, Carolyn Talcott
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0135788

SILAC-Based Mass Spectrometry Analysis Reveals That Epibrassinolide Induces Apoptosis via Activating Endoplasmic Reticulum Stress in Prostate Cancer Cells
Cited by: 16
Author(s): Pınar Obakan, Carlos Barrero, Ajda Çoker Gürkan, Elif Damla Arısan, Salim Merali, Narçın Palavan-Ünsal
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0218523

Potential distribution of dominant malaria vector species in tropical region under climate change scenarios
Cited by: 22
Author(s): Godwin E. Akpan, Kayode A. Adepoju, Olakunle R. Oladosu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0016894

SOD2 Deficient Erythroid Cells Up-Regulate Transferrin Receptor and Down-Regulate Mitochondrial Biogenesis and Metabolism
Cited by: 18
Author(s): Florent Martin, Xiuling Xu, Katharina von Löhneysen, Timothy J. Gilmartin, Jeffrey S. Friedman
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0066318

Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and the Subsequent Germ Line
Cited by: 156
Author(s): Michael K. Skinner, Carlos Guerrero-Bosagna, Eric Nilsson, Ramji Kumar Bhandari, John R. McCarrey
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0010023

Retinoic Acid Mediates Regulation of Network Formation by COUP-TFII and VE-Cadherin Expression by TGFβ Receptor Kinase in Breast Cancer Cells
Cited by: 17
Author(s): Priya Prahalad, Sivanesan Dakshanamurthy, Habtom W. Ressom, Stephen W. Byers
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0037697

BRCA1 Regulates Follistatin Function in Ovarian Cancer and Human Ovarian Surface Epithelial Cells
Cited by: 11
Author(s): Tejaswita M. Karve, Anju Preet, Rosie A. Sneed, Clara Salamanca, Xin Li, Jingwen Xu, Deepak Kumar, Eliot M. Rosen, Tapas Kumar Saha
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0043394

A Multi-Omics Analysis of Recombinant Protein Production in Hek293 Cells
Cited by: 100
Author(s): Stefanie Dietmair, Mark P. Hodson, Lake‐Ee Quek, Nicholas Timmins, Peter P. Gray, Lars K. Nielsen
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0046249

Dioxin (TCDD) Induces Epigenetic Transgenerational Inheritance of Adult Onset Disease and Sperm Epimutations
Cited by: 216
Author(s): Mohan Manikkam, Rebecca Tracey, Carlos Guerrero-Bosagna, Michael K. Skinner
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0117739

Comparison of the Transcriptomes of Mouse Skin Derived Precursors (SKPs) and SKP-Derived Fibroblasts (SFBs) by RNA-Seq
Cited by: 10
Author(s): Yujie Mao, Li Xiong, Siyu Wang, Jianqiao Zhong, Runhua Zhou, Li Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0034707

Nuclear Factor Kappa B Activation Occurs in the Amnion Prior to Labour Onset and Modulates the Expression of Numerous Labour Associated Genes
Cited by: 55
Author(s): Sheri Lim, David A. MacIntyre, Yun Sok Lee, Shirin Khanjani, Vasso Terzidou, Tiong Ghee Teoh, Phillip R. Bennett
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0055439

Quantitative 1H-NMR-Metabolomics Reveals Extensive Metabolic Reprogramming and the Effect of the Aquaglyceroporin FPS1 in Ethanol-Stressed Yeast Cells
Cited by: 25
Author(s): Artur B. Lourenço, Filipa Roque, Miguel C. Teixeira, José R. Ascenso, Isabel Sá‐Correia
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0215389

Progesterone receptor membrane component 1 inhibits tumor necrosis factor alpha induction of gene expression in neural cells
Cited by: 9
Author(s): Karlie A. Intlekofer, Kelsey J. Clements, H. Cary Woods, Hillary L. Adams, Alexander Suvorov, Sandra L. Petersen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0147421

Analysis of Host Gene Expression Profile in HIV-1 and HIV-2 Infected T-Cells
Cited by: 18
Author(s): Krishnakumar Devadas, Santanu Biswas, Mohan Haleyurgirisetty, Owen Wood, Viswanath Ragupathy, Sherwin Lee, Indira Hewlett
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0079233

The Human Placental Sexome Differs between Trophoblast Epithelium and Villous Vessel Endothelium
Cited by: 96
Author(s): Silvija Cvitic, Mark S. Longtine, Hubert Hackl, Karin Wagner, Michael D. Nelson, Gernot Desoyé, Ursula Hiden
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0114009

Identification of MicroRNAs Linked to Regulators of Muscle Protein Synthesis and Regeneration in Young and Old Skeletal Muscle
Cited by: 70
Author(s): Evelyn Zacharewicz, Paul A. Della Gatta, John Reynolds, Andrew Garnham, Tamsyn M. Crowley, Aaron P. Russell, Séverine Lamon
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0046153

Proteins with Altered Levels in Plasma from Glioblastoma Patients as Revealed by iTRAQ-Based Quantitative Proteomic Analysis
Cited by: 64
Author(s): Poonam Gautam, Sudha C. Nair, Manoj Kumar Gupta, Rakesh Sharma, Ravindra Varma Polisetty, Megha S Uppin, Sundaram Challa, Aneel Kumar Puligopu, Praveen Ankathi, A K Purohit, Giriraj Ratan Chandak, H. C. Harsha, Ravi Sirdeshmukh
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0146756

A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast U.S. Continental Shelf
Cited by: 348
Author(s): Jonathan A. Hare, Wendy Morrison, Mark W. Nelson, Megan M. Stachura, Eric J. Teeters, Roger B. Griffis, Michael A. Alexander, James D. Scott, Larry Alade, Richard J. Bell, Antonie S. Chute, Kiersten L. Curti, Tobey H. Curtis, Daniel Kircheis, John F. Kocik, Sean M. Lucey, Camilla T. McCandless, Lisa M. Milke, David E. Richardson, Eric Robillard, Harvey J. Walsh, M. Conor McManus, Katrin E. Marancik, Carolyn A. Griswold
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0178809

De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.)
Cited by: 31
Author(s): Hui Xue, Shangyin Cao, Haoxian Li, Jie Zhang, Juan Niu, Lina Chen, Fuhong Zhang, Dan Zhao
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0036129

Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease
Cited by: 202
Author(s): Eric Nilsson, Ginger Larsen, Mohan Manikkam, Carlos Guerrero-Bosagna, Marina I. Savenkova, Michael K. Skinner
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0018399

Global Gene Expression Profiling of Endothelium Exposed to Heme Reveals an Organ-Specific Induction of Cytoprotective Enzymes in Sickle Cell Disease
Cited by: 25
Author(s): Samit Ghosh, Fang Tan, Tianwei Yu, Yuhua Li, Olufolake Adisa, Mario Mosunjac, Solomon F. Ofori-Acquah
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0177888

Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes
Cited by: 56
Author(s): Jing Cheng, Jia Huang, Shengjie Yuan, Shanshan Zhou, Wei Yan, Wei Shen, Yun Chen, Xi Xia, Aiyue Luo, Da Zhu, Shixuan Wang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0034519

A Gestational High Protein Diet Affects the Abundance of Muscle Transcripts Related to Cell Cycle Regulation throughout Development in Porcine Progeny
Cited by: 11
Author(s): Michael Oster, Eduard Muráni, C. C. Metges, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0090804

Genome-Wide Screen of DNA Methylation Changes Induced by Low Dose X-Ray Radiation in Mice
Cited by: 32
Author(s): Jingzi Wang, Youwei Zhang, Kai Xu, Xiaobei Mao, Lijun Xue, Fei Liu, Hongjun Yu, Longbang Chen, Xiaoyuan Chen
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0064954

Sorafenib Inhibits Epithelial-Mesenchymal Transition through an Epigenetic-Based Mechanism in Human Lung Epithelial Cells
Cited by: 32
Author(s): Jie Zhang, Yue‐Lei Chen, Guanyu Ji, Weiying Fang, Zhaowei Gao, Yi Liu, Jun Wang, Xiaoyan Ding, Fei Gao
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0060397

Study of Global Transcriptional Changes of N-GlcNAc2 Proteins-Producing T24 Bladder Carcinoma Cells under Glucose Deprivation
Cited by: 11
Author(s): Takahiro Isono, Tokuhiro Chano, Hidetoshi Okabe, Masafumi Suzaki
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0063912

Choice of Bacterial Growth Medium Alters the Transcriptome and Phenotype of Salmonella enterica Serovar Typhimurium
Cited by: 37
Author(s): Jessica M A Blair, Grace E. Richmond, Andrew M. Bailey, Alasdair Ivens, Laura J. V. Piddock
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0023111

Influence of Stochastic Gene Expression on the Cell Survival Rheostat after Traumatic Brain Injury
Cited by: 32
Author(s): Daniel Rojo, Donald S. Prough, Michael T. Falduto, Deborah R. Boone, Maria‐Adelaide Micci, Kristen M. Kahrig, Jeanna M. Crookshanks, Arnaldo Jimenez, Tatsuo Uchida, Jeremy Cowart, Bridget E. Hawkins, Marcela A. Avila, Douglas S. DeWitt, Helen L. Hellmich
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0231124

Onset hyperalgesia and offset analgesia: Transient increases or decreases of noxious thermal stimulus intensity robustly modulate subsequent perceived pain intensity
Cited by: 11
Author(s): Benedict J. Alter, Mya S. Aung, Irina A. Strigo, Howard L. Fields
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0018551

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains
Cited by: 73
Author(s): Jerônimo C. Ruiz, Vívian D’Afonseca, Artur M. S. Silva, Amjad Ali, Anne Cybelle Pinto, Anderson Santos, Aryanne A. M. C. Rocha, Débora de Oliveira Lopes, Fernanda Alves Dorella, Luis Gustavo Carvalho Pacheco, Marcília Pinheiro da Costa, Meritxell Zurita-Turk, Núbia Seyffert, Pablo M. R. O. Moraes, Siomar C. Soares, Síntia Almeida, Thiago Luiz de Paula Castro, Vinícius Augusto Carvalho de Abreu, Eva Trost, Jan Baumbach, Andreas Tauch, Maria Paula Cruz Schneider, John Anthony McCulloch, Louise Cerdeira, Rommel Thiago Jucá Ramos, Adhemar Zerlotini, Anderson J. Dominitini, Daniela de Melo Resende, Elisângela Monteiro Coser, Luana Muniz de Oliveira, André Luiz Pedrosa, Carlos Ueira Vieira, C. T. Guimarães, Daniela C. Bartholomeu, Diana Magalhães de Oliveira, Fabrício R. Santos, Élida Mara Leite Rabelo, Francisco Pereira Lobo, Glória Regina Franco, Ana Flávia Dias Vieira da Costa, Ieso de Miranda Castro, Sílvia Regina Costa Dias, Jesus Aparecido Ferro, José Miguel Ortega, Luciano V. Paiva, Luiz Ricardo Goulart, Juliana Franco Almeida, M. I. T. Ferro, N. P. Carneiro, Paula R. K. Falcão, Priscila Grynberg, Santuza Maria Ribeiro Teixeira, Sérgio Hermínio Brommonschenkel, Sérgio C. Oliveira, Roberto Meyer, Robert J. Moore, Anderson Miyoshi, Guilherme Oliveira, Vasco Azevedo
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0092540

Pressure Pain Thresholds Increase after Preconditioning 1 Hz Repetitive Transcranial Magnetic Stimulation with Transcranial Direct Current Stimulation
Cited by: 11
Author(s): Tonya M. Moloney, Alice G. Witney
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0242978

Umbilical cord blood metabolome differs in relation to delivery mode, birth order and sex, maternal diet and possibly future allergy development in rural children
Cited by: 10
Author(s): Alastair B. Ross, Malin Barman, Olle Hartvigsson, Anna‐Carin Lundell, Otto Savolainen, Bill Hesselmar, Agnes E. Wold, Ann‐Sofie Sandberg
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0206407

Conditional deletion of Ahr alters gene expression profiles in hematopoietic stem cells
Cited by: 17
Author(s): JA Bennett, Singh Kp, Welle Sl, Boule La, Lawrence Bp, Gasiewicz Ta
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0125838

Molecular Heterogeneity in a Patient-Derived Glioblastoma Xenoline Is Regulated by Different Cancer Stem Cell Populations
Cited by: 27
Author(s): Jo Meagan Garner, David W. Ellison, David Finkelstein, Debolina Ganguly, Ziyun Du, Michelle Sims, Chuan Yang, Rodrigo B. Interiano, Andrew M. Davidoff, Lawrence M. Pfeffer
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0193181

Assessing the capability to experience a 'good death': A qualitative study to directly elicit expert views on a new supportive care measure grounded in Sen's capability approach
Cited by: 8
Author(s): Philip Kinghorn, Joanna Coast
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0202449

GATA4 inhibits cell differentiation and proliferation in pancreatic cancer
Cited by: 18
Author(s): Yan Gong, Liang Zhang, Aiqun Zhang, Xin Chen, Peng Gao, Qiang Zeng
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0087602

Direct and Indirect Targets of the E2A-PBX1 Leukemia-Specific Fusion Protein
Cited by: 32
Author(s): Christofer Diakos, Yuanyuan Xiao, Shichun Zheng, Leo Kager, Michael Dworzak, Joseph L. Wiemels
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0135720

Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq
Cited by: 41
Author(s): Fangyan Chen, Changjian Zhang, Xiaodong Jia, Shuo Wang, Jing Wang, Yong Chen, Jingya Zhao, Shen Tian, Xiaonan Han, Li Han
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0188997

Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle
Cited by: 43
Author(s): M. Neupane, T. W. Geary, J. N. Kiser, Gregory W. Burns, P. J. Hansen, Thomas E. Spencer, Holly L. Neibergs
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0112189

Expression Profiling of Rectal Tumors Defines Response to Neoadjuvant Treatment Related Genes
Cited by: 33
Author(s): Pablo Palma, Carlos Cano, Raquel Conde-Muíño, A. Comino, Pablo Bueno, José Antonio Ferrón, Marta Cuadros
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0156469

Correction: Correlative Gene Expression to Protective Seroconversion In Rift Valley Vaccinates
Cited by: 0
Author(s): Richard C. Laughin, Kenneth L. Drake, John C. Morrill, L. Garry Adams
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0067472

Predicting and Analyzing Interactions between Mycobacterium tuberculosis and Its Human Host
Cited by: 36
Author(s): Holifidy Rapanoel, Gaston K. Mazandu, Nicola Mulder
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0050054

Altered Gene Expression Pattern in Peripheral Blood Mononuclear Cells in Patients with Acute Myocardial Infarction
Cited by: 69
Author(s): Marek Kiliszek, Beata Burzyńska, Marcin Michalak, Monika Góra, Aleksandra Winkler, Agata Maciejak, Agata Leszczynska, Ewa Gajda, Janusz Kochanowski, Grzegorz Opolski
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0078489

Differential Stress Transcriptome Landscape of Historic and Recently Emerged Hypervirulent Strains of Clostridium difficile Strains Determined Using RNA-seq
Cited by: 23
Author(s): Joy Scaria, Chunhong Mao, Jenn Wei Chen, Sean P. McDonough, Bruno W. S. Sobral, Yung Fu Chang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0124899

Increased MicroRNA-34b and -34c Predominantly Expressed in Stromal Tissues Is Associated with Poor Prognosis in Human Colon Cancer
Cited by: 47
Author(s): Yukiharu Hiyoshi, Aaron J. Schetter, Hirokazu Okayama, Kentaro Inamura, Katsuhiro Anami, Giang Huong Nguyen, Izumi Horikawa, Jason E. Hawkes, Elise D. Bowman, Suet Yi Leung, Curtis C. Harris
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0064544

Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation
Cited by: 28
Author(s): Irina Bonzheim, Martin Irmler, Margit Klier-Richter, Julia Steinhilber, Nataša Anastasov, Sabine Schäfer, Patrick Adam, Johannes Beckers, Mark Raffeld, Falko Fend, Leticia Quintanilla-Martı́nez
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0158101

Meta-Analysis of Genome-Wide Association Studies and Network Analysis-Based Integration with Gene Expression Data Identify New Suggestive Loci and Unravel a Wnt-Centric Network Associated with Dupuytren’s Disease
Cited by: 25
Author(s): Kerstin Becker, Sabine Siegert, Mohammad Reza Toliat, Juanjiangmeng Du, Ramona Casper, Guido H. Dolmans, Paul M. N. Werker, Sigrid Tinschert, André Franke, Christian Gieger, Konstantin Strauch, Michael Nothnagel, Peter Nürnberg, Hans Christian Hennies
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0099757

Integrative Analyses of Hepatic Differentially Expressed Genes and Blood Biomarkers during the Peripartal Period between Dairy Cows Overfed or Restricted-Fed Energy Prepartum
Cited by: 35
Author(s): Khuram Shahzad, Massimo Bionaz, Erminio Trevisi, Giuseppe Bertoni, Sandra L. Rodriguez-Zas, Juan J. Loor
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0162566

Phenotypic and Molecular Alterations in the Mammary Tissue of R-Spondin1 Knock-Out Mice during Pregnancy
Cited by: 3
Author(s): Sead Chadi, Jacqueline Polyte, Lucas Lefèvre, Johan Castille, Aude Ehanno, Johann Laubier, Florence Jaffrézic, Fabienne Le Provost
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0016913

Analysis of the Transcriptional Program of Developing Induced Regulatory T Cells
Cited by: 16
Author(s): Iryna Prots, Alla Skapenko, Peter E. Lipsky, Hendrik Schulze‐Koops
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0034833

Phase I Clinical Trial of Systemically Administered TUSC2(FUS1)-Nanoparticles Mediating Functional Gene Transfer in Humans
Cited by: 139
Author(s): Charles Lu, David J. Stewart, John Lee, Lin Ji, Rajagopal Ramesh, Gitanjali Jayachandran, Maria I. Nuñez, Ignacio I. Wistuba, Jeremy J. Erasmus, Marshall E. Hicks, Elizabeth A. Grimm, James M. Reuben, Veerabhadran Baladandayuthapani, Nancy Smyth Templeton, John D. McMannis, Jack A. Roth
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0071958

A Genome-Wide Association Study of Total Serum and Mite-Specific IgEs in Asthma Patients
Cited by: 25
Author(s): Jeong Hyun Kim, Hyun Sub Cheong, Jong Suk Park, An Soo Jang, Soo Taek Uh, Yong Hoon Kim, Mi Kyeong Kim, Inseon S. Choi, Sang Heon Cho, Byoung Whui Choi, Joon Seol Bae, Choon-Sik Park, Hyoung Doo Shin
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0126599

Resveratrol Ameliorates Imiquimod-Induced Psoriasis-Like Skin Inflammation in Mice
Cited by: 75
Author(s): Thomas Kjær, Kasper Thorsen, Niels Jessen, Karin Stenderup, Steen B. Pedersen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0181201

Biological control of Heterodera glycines by spore-forming plant growth-promoting rhizobacteria (PGPR) on soybean
Cited by: 56
Author(s): Ni Xiang, Kathy Lawrence, Joseph W. Kloepper, P. A. Donald, John A. McInroy
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0008918

Automated Network Analysis Identifies Core Pathways in Glioblastoma
Cited by: 317
Author(s): Ethan Cerami, Emek Demir, Nikolaus Schultz, Barry S. Taylor, Chris Sander
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0059908

Few Single Nucleotide Variations in Exomes of Human Cord Blood Induced Pluripotent Stem Cells
Cited by: 29
Author(s): Rui Su, Yadong Yang, Amanda Neises, Kimberly J. Payne, Jasmin Wang, Kasthuribai Viswanathan, Edward K. Wakeland, Xiangdong Fang, Xiao Bing Zhang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0037884

Phenotypic and Transcriptomic Response of Auxotrophic Mycobacterium avium Subsp. paratuberculosis leuD Mutant under Environmental Stress
Cited by: 14
Author(s): Jenn Wei Chen, Joy Scaria, Yung Fu Chang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0006958

Intestinal Microbiota Regulate Xenobiotic Metabolism in the Liver
Cited by: 199
Author(s): Britta Björkholm, Chek Mei Bok, Annelie Lundin, Joseph Rafter, Martin L. Hibberd, Sven Pettersson
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pone.0053310

Exome Capture Sequencing of Adenoma Reveals Genetic Alterations in Multiple Cellular Pathways at the Early Stage of Colorectal Tumorigenesis
Cited by: 38
Author(s): Dongkai Zhou, Yang Liu, Liangtao Zheng, Weiting Ge, Dan Li, Yong Zhang, Xueda Hu, Zhibo Gao, Jinghong Xu, Yanqin Huang, Hanguang Hu, Hang Zhang, Hao Zhang, Mingming Liu, Huanming Yang, Lei Zheng, Shu Zheng
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0036324

Transcriptome Sequencing of and Microarray Development for a Helicoverpa zea Cell Line to Investigate In Vitro Insect Cell-Baculovirus Interactions
Cited by: 28
Author(s): Quan Nguyen, Robin W. Palfreyman, Leslie C. L. Chan, Steven Reid, Lars K. Nielsen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0147837

Role of Periostin in Adhesion and Migration of Bone Remodeling Cells
Cited by: 35
Author(s): Teresa Cobo, Cristina G. Viloria, Laura Solares, Tania Fontanil, Elena González-Chamorro, Félix de Carlos, Juan Cobo, Santiago Cal, Álvaro J. Obaya
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0178391

Comparison of the adolescent and adult mouse prefrontal cortex proteome
Cited by: 15
Author(s): Abigail E. Agoglia, Sarah E. Holstein, Amanda Small, Marina Spanos, Brainard Burrus
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0126928

Zebrafish Bone and General Physiology Are Differently Affected by Hormones or Changes in Gravity
Cited by: 68
Author(s): Jessica Aceto, Rasoul Nourizadeh-Lillabadi, Raphaël Marée, Nadia Dardenne, Nathalie Jeanray, Louis Wehenkel, Peter Aleström, Jack J. W. A. van Loon, Marc Müller
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0129762

Plasma Proteomic Profiling in Hereditary Breast Cancer Reveals a BRCA1-Specific Signature: Diagnostic and Functional Implications
Cited by: 19
Author(s): Domenica Scumaci, Laura Tammè, Claudia Vincenza Fiumara, Giusi Pappaianni, Antonio Concolino, Emanuela Leone, Maria Concetta Faniello, Barbara Quaresima, Enrico Ricevuto, Francesco Costanzo, Giovanni Cuda
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0183650

Effects of explicit cueing and ambiguity on the anticipation and experience of a painful thermal stimulus
Cited by: 6
Author(s): Lincoln M. Tracy, Stephen Gibson, Nellie Georgiou‐Karistianis, Melita J. Giummarra
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0239460

Prehospital use of a modified HEART Pathway and point-of-care troponin to predict cardiovascular events
Cited by: 10
Author(s): Jason P. Stopyra, Anna C. Snavely, Lane M. Smith, Roger Harris, R. Darrell Nelson, James E. Winslow, Roy L. Alson, Gregory J. Pomper, Robert F. Riley, Nicklaus P. Ashburn, Nella Hendley, Jeremiah Gaddy, Tyler Woodrum, Louis Fornage, David A. Conner, Manrique Alvarez, Adam Pflum, Lauren E. Koehler, Chadwick D. Miller, Simon A. Mahler
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0127332

Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis)
Cited by: 73
Author(s): Huamei Yue, Chuangju Li, Hao Du, Shuhuan Zhang, Qiwei Wei
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0170855

Transcriptome Sequencing of Gracilariopsis lemaneiformis to Analyze the Genes Related to Optically Active Phycoerythrin Synthesis
Cited by: 19
Author(s): Xiaoyun Huang, Xiaonan Zang, Fei Wu, Yuming Jin, Haitao Wang, Chang Liu, Yating Ding, Bian He, Dongfang Xiao, Xinwei Song, Li Zhu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0054524

Human Embryonic Stem Cell Derived Mesenchymal Progenitors Express Cardiac Markers but Do Not Form Contractile Cardiomyocytes
Cited by: 27
Author(s): Christophe Michel Raynaud, Najeeb Halabi, David A. Elliott, Jennifer Pasquier, Andrew G. Elefanty, Arash Rafii
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0018540

Evaluation of 309 Environmental Chemicals Using a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity Assay
Cited by: 62
Author(s): Kelly J. Chandler, Marianne Barrier, Susan Jeffay, Harriette P. Nichols, Nicole Kleinstreuer, Amar V. Singh, David M. Reif, Nisha S. Sipes, Richard S. Judson, David J. Dix, Robert J. Kavlock, E. Sidney Hunter, Thomas B. Knudsen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0104127

Profiling of Luteal Transcriptome during Prostaglandin F2-Alpha Treatment in Buffalo Cows: Analysis of Signaling Pathways Associated with Luteolysis
Cited by: 17
Author(s): Kunal B. Shah, Sudeshna Tripathy, Hepziba Suganthi, R. Medhamurthy
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0115383

Mutation Profiling in Cholangiocarcinoma: Prognostic and Therapeutic Implications
Cited by: 347
Author(s): Chaitanya Churi, Rachna T. Shroff, Ying Wáng, Asif Rashid, Hyunseon C. Kang, J. Weatherly, Mingxin Zuo, Ralph Zinner, David S. Hong, Funda Meric‐Bernstam, Filip Jankú, Christopher H. Crane, Lopa Mishra, J.N. Vauthey, Robert A. Wolff, Gordon B. Mills, Milind Javle
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0103794

Interleukin-1/Toll-Like Receptor-Induced Nuclear Factor Kappa B Signaling Participates in Intima Hyperplasia after Carotid Artery Balloon Injury in Goto-Kakizaki Rats: A Potential Target Therapy Pathway
Cited by: 4
Author(s): Xiaotian Zhang, Yi Wang, Wenjing Hu, Dongye Li, Zhongmin Zhou, Defeng Pan, Wanling Wu, Tongda Xu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0091397

Kinetic Analysis of Mouse Brain Proteome Alterations Following Chikungunya Virus Infection before and after Appearance of Clinical Symptoms
Cited by: 34
Author(s): Christophe Fraisier, Penelope Koraka, Maya Belghazi, Mahfoud Bakli, Samuel Granjeaud, Matthieu Pophillat, Stephanie M. Lim, Albert D. M. E. Osterhaus, Benedict Martina, Luc Camoin, Lionel Almeras
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0078171

Transcriptional Profiling of MEq-Dependent Genes in Marek’s Disease Resistant and Susceptible Inbred Chicken Lines
Cited by: 16
Author(s): Sugalesini Subramaniam, Likit Preeyanon, Hans H. Cheng
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0211614

Is there an association between consent rates in Swiss hospitals and critical care staffs' attitudes towards organ donation, their knowledge and confidence in the donation process?
Cited by: 6
Author(s): Isabelle Keel, Roger Schürch, Julius Weiss, Marcel Zwahlen, Franz F. Immer
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0111515

Discoidin Domain Receptor 1 Contributes to Tumorigenesis through Modulation of TGFBI Expression
Cited by: 23
Author(s): Nandini Rudra-Ganguly, Christine Lowe, Michael D. Mattie, Mi-Sook Chang, Daulet Satpayev, Alla Verlinsky, Zili An, Liping Hu, Peng Yang, Pia M. Challita-Eid, David R. Stover, Daniel S. Pereira
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0144158

Photoperiodic Modulation of Circadian Clock and Reproductive Axis Gene Expression in the Pre-Pubertal European Sea Bass Brain
Cited by: 18
Author(s): Rute Martins, Ana Gómez, Silvia Zanuy, Manuel Carrillo, Adelino V. M. Canário
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0126566

Molecular Mechanism of the Cell Death Induced by the Histone Deacetylase Pan Inhibitor LBH589 (Panobinostat) in Wilms Tumor Cells
Cited by: 19
Author(s): Yan-Fang Tao, Zhiheng Li, Liang‐Guo Xu, Fang Fang, Jun Lu, Gang Li, Liu Cao, Nana Wang, Xiaohong Du, Lichao Sun, Wei Zhao, Pei-Fang Xiao, He Zhao, Su Guang-Hao, Yanhong Li, Yiping Li, Yiming Xu, Huiting Zhou, Yi Wu, Meifang Jin, Lin Liu, Jian Ni, Shaoyan Hu, Xiaoyan Zhu, Xing Feng, Jian Wang, Jian Pan
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0065128

Transcriptome Analysis Reveals Novel Entry Mechanisms and a Central Role of SRC in Host Defense during High Multiplicity Mycobacterial Infection
Cited by: 9
Author(s): Jay Zhang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0080480

Comparative N-Glycoproteomic and Phosphoproteomic Profiling of Human Placental Plasma Membrane between Normal and Preeclampsia Pregnancies with High-Resolution Mass Spectrometry
Cited by: 19
Author(s): Fuqiang Wang, Ling Wang, Zhonghua Shi, Gaolin Liang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0078847

Continuous Hypoxic Culturing of Human Embryonic Stem Cells Enhances SSEA-3 and MYC Levels
Cited by: 35
Author(s): Elisa Närvä, Juha-Pekka Pursiheimo, Asta Laiho, Nelly Rahkonen, Maheswarareddy Emani, Miro Viitala, Kirsti Laurila, Roosa Sahla, Riikka Lund, Harri Lähdesmäki, Panu Jaakkola, Riitta Lahesmaa
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0067237

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy
Cited by: 9
Author(s): Tejaswini Narayanan, Shankar Subramaniam
Software Mentions: 1
Published: over 11 years ago

10.3390/cancers11121832

Targeting STAT3 and STAT5 in Tumor-Associated Immune Cells to Improve Immunotherapy
Cited by: 32
Author(s): Grégory Verdeil, Toby Lawrence, A.M. Schmitt-Verhulst, Nathalie Auphan-Anezin
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers12010241

1H-NMR Based Serum Metabolomics Highlights Different Specific Biomarkers between Early and Advanced Hepatocellular Carcinoma Stages
Cited by: 36
Author(s): Andrea Casadei‐Gardini, Laura Del Coco, Giorgia Marisi, Fabio Conti, Giulia Rovesti, Paola Ulivi, Matteo Canale, Giovanni Luca Frassineti, Francesco Giuseppe Foschi, Serena Longo, Francesco Paolo Fanizzi, Anna Maria Giudetti
Software Mentions: 1
Published: almost 5 years ago

Projects: pypi: Pathway

Papers Mentioning Pathway 827