pypi: analysis | Projects | Ecosyste.ms: Papers

10.7554/eLife.38986

Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma
Cited by: 34
Author(s): Jianing Xu, Ed Reznik, Ho‐Joon Lee, Gunes Gundem, Philip Jonsson, Judy Sarungbam, Anna Bialik, Francisco Sanchez‐Vega, Chad J. Creighton, Jake G. Hoekstra, Li Zhang, Peter Sajjakulnukit, Daniel M. Kremer, Zachary P. Tolstyka, Jozefina Casuscelli, Steve Stirdivant, Jie Tang, Nikolaus Schultz, Paul S Jeng, Yiyu Dong, Wenjing Su, Emily H. Cheng, Paul Russo, Jonathan Coleman, Elli Papaemmanuil, Ying-Bei Chen, Victor E. Reuter, Chris Sander, Scott R. Kennedy, James J. Hsieh, Costas A. Lyssiotis, Satish K. Tickoo, A. Ari Hakimi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0117029

Functional Network Overlap as Revealed by fMRI Using sICA and Its Potential Relationships with Functional Heterogeneity, Balanced Excitation and Inhibition, and Sparseness of Neuron Activity
Cited by: 17
Author(s): Jiansong Xu, Vince D. Calhoun, Patrick D. Worhunsky, Hui Xiang, Jian Li, John T. Wall, Godfrey D. Pearlson, Marc N. Potenza
Software Mentions: 2
Published: over 11 years ago

10.1155/2014/450621

RNA Sequencing Reveals Upregulation of RUNX1-RUNX1T1 Gene Signatures in Clear Cell Renal Cell Carcinoma
Cited by: 14
Author(s): Zhenggang Xiong, Hongjie Yu, Yan Ding, Chenchen Feng, Hanming Wei, Sha Tao, Dan Huang, S. Lilly Zheng, Jielin Sun, Jianfeng Xu, Zhaoxi Fang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0230392

High-mobility group box 1 fragment suppresses adverse post-infarction remodeling by recruiting PDGFRα-positive bone marrow cells
Cited by: 13
Author(s): Tetsushi Goto, Katsuto Tamai, Ryohei Matsuura, Takashi Kido, Toru Kuratani, Kazuo Shimamura, Ryoto Sakaniwa, Akira Harada, Yoshiki Sawa
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0130326

Bayesian Spatial NBDA for Diffusion Data with Home-Base Coordinates
Cited by: 3
Author(s): Glenna Nightingale, Kevin N. Laland, William Hoppitt, Peter Nightingale
Software Mentions: 2
Published: about 11 years ago

10.3390/ijms16036496

Favourable IFNL3 Genotypes Are Associated with Spontaneous Clearance and Are Differentially Distributed in Aboriginals in Canadian HIV-Hepatitis C Co-Infected Individuals
Cited by: 5
Author(s): Nasheed Moqueet, Claire Infante–Rivard, Robert W. Platt, Jim Young, Curtis Cooper, Mark Hull, Sharon Walmsley, Marina B. Klein
Software Mentions: 2
Published: over 11 years ago

10.1155/2020/4045204

Global Analysis of Alternative Splicing Difference in Peripheral Immune Organs between Tongcheng Pigs and Large White Pigs Artificially Infected with PRRSV In Vivo
Cited by: 5
Author(s): Yu Zhang, Liyao Xue, Xu Hang, Wan Liang, Qingqing Wu, Qingde Zhang, Xiang Zhou, Bang Liu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0124806

Net Clinical Benefit of Oral Anticoagulants: A Multiple Criteria Decision Analysis
Cited by: 20
Author(s): Jason C. Hsu, Cheng Yang Hsieh, Yea Huei Kao Yang, Christine Y. Lu
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0202751

Long length of stay at the emergency department is mostly caused by organisational factors outside the influence of the emergency department: A root cause analysis
Cited by: 42
Author(s): Babiche E. J. M. Driesen, Bauke H.G. Van Riet, Lisa Verkerk, H. Jaap Bonjer, Hanneke Merten, Prabath W.B. Nanayakkara
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms20030602

Human Brain Endothelial CXCR2 is Inflammation-Inducible and Mediates CXCL5- and CXCL8-Triggered Paraendothelial Barrier Breakdown
Cited by: 24
Author(s): Axel Haarmann, Michael K. Schuhmann, Christine Silwedel, Camelia‐Maria Monoranu, Guido Stoll, Mathias Buttmann
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0177513

An integrative analysis of tissue-specific transcriptomic and metabolomic responses to short-term dietary methionine restriction in mice
Cited by: 30
Author(s): Sujoy Ghosh, Laura A. Forney, Desiree Wanders, Kirsten P. Stone, Thomas W. Gettys
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms20174267

Ceritinib-Induced Regression of an Insulin-Like Growth Factor-Driven Neuroepithelial Brain Tumor
Cited by: 10
Author(s): Alexandra Russo, Claudia Paret, Francesca Alt, Jürgen Burhenne, Margaux Fresnais, Wolfgang Wagner, Martin Gläser, Hannah Bender, Sabrina Huprich, Patrick N. Harter, Katharina Filipski, Nadine Lehmann, Nora Backes, Lea Roth, Larissa Seidmann, Clemens Sommer, Marc A. Brockmann, Torsten Pietsch, Marie A. Neu, Arthur Wingerter, Jörg Faber
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms20246252

The Major Factors Causing the Microspore Abortion of Genic Male Sterile Mutant NWMS1 in Wheat (Triticum aestivum L.)
Cited by: 17
Author(s): Junchang Li, Jing Zhang, Huijuan Li, Hao Niu, Qiaoqiao Xu, Zhixin Jiao, Junhang An, Yumei Jiang, Qiaoyun Li, Jishan Niu
Software Mentions: 2
Published: over 6 years ago

10.1155/2021/5587441

Identification of Molecular Characteristics and New Prognostic Targets for Thymoma by Multiomics Analysis
Cited by: 4
Author(s): Dazhong Liu, Pengfei Zhang, Jichun Zhao, Lei Yang, Wei Wang
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms21113783

Genome-Wide Identification of Epigenetic Regulators in Quercus suber L.
Cited by: 6
Author(s): Helena G. Silva, Rómulo Sacramento Sobral, Alexandre Papadopoulos Magalhães, Leonor Morais-Cecílio, Maria Manuela Ribeiro Costa
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms21228730

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer
Cited by: 60
Author(s): Pamela Vernocchi, Tommaso Gili, Federica Conte, Federica Del Chierico, Giorgia Conta, Alfredo Miccheli, Andrea Botticelli, Paola Paci, Guido Caldarelli, Marianna Nuti, Paolo Marchetti, Lorenza Putignani
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0055137

Construction and Analysis of the Model of Energy Metabolism in E. coli
Cited by: 4
Author(s): Zixiang Xu, Xiao Sun, Jibin Sun
Software Mentions: 2
Published: over 13 years ago

10.3390/ijms22020712

An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates
Cited by: 3
Author(s): Daeun Kim, Jaeseung Song, Sora Lee, Junghyun Jung, Wonhee Jang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0088896

Long-Term Effects of Gestational Nicotine Exposure and Food-Restriction on Gene Expression in the Striatum of Adolescent Rats
Cited by: 5
Author(s): Nicholas E. Ilott, Tomasz Schneider, Jonathan Mill, Leonard C. Schalkwyk, Giovana Brolese, Lisiane Bizarro, I. P. Stolerman, Emma Dempster, Philip Asherson
Software Mentions: 2
Published: over 12 years ago

10.3390/ijms22052452

A Systems Biology Approach to Investigating the Interaction between Serotonin Synthesis by Tryptophan Hydroxylase and the Metabolic Homeostasis
Cited by: 11
Author(s): Suhyeon Park, Yumin Kim, Jibeom Lee, Jeong Yun Lee, Hail Kim, Sunjae Lee, Chang‐Myung Oh
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22073489

CRISPR-Cas9–Mediated TIM3 Knockout in Human Natural Killer Cells Enhances Growth Inhibitory Effects on Human Glioma Cells
Cited by: 30
Author(s): Takayuki Morimoto, Tsutomu Nakazawa, Ryosuke Matsuda, Fusanori Nishimura, Mitsutoshi Nakamura, Shuichi Yamada, Ichiro Nakagawa, Young-Soo Park, Takahiro Tsujimura, Hiroyuki Nakase
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0063644

Identification of Altered Metabolic Pathways in Plasma and CSF in Mild Cognitive Impairment and Alzheimer’s Disease Using Metabolomics
Cited by: 338
Author(s): Eugenia Trushina, Tumpa Dutta, Xuan Mai T. Persson, Michelle M. Mielke, Ronald C. Petersen
Software Mentions: 2
Published: about 13 years ago

10.1111/acel.13229

Underlying features of epigenetic aging clocks in vivo and in vitro
Cited by: 84
Author(s): Zuyun Liu, Diana Leung, Kyra Thrush, Wei Zhao, Scott Ratliff, Toshiko Tanaka, Lauren Schmitz, Jennifer A. Smith, Luigi Ferrucci, Morgan E. Levine
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22189957

Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula
Cited by: 8
Author(s): Xia Yin, Yang Jiao, Lin Ma, Yan Su, Yongzhen Pang
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0231021

Exploitation of local and global information in predictive processing
Cited by: 1
Author(s): Daniel S. Kluger, Nico Broers, Marlen A. Roehe, Moritz F. Wurm, Niko A. Busch, Ricarda Ines Schubotz
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/3962146

TPPP3 Associated with Prognosis and Immune Infiltrates in Head and Neck Squamous Carcinoma
Cited by: 9
Author(s): Zheng Yang, Xiaohong Li, Jingyu Li, Qingde Su, Yuling Qiu, Zunni Zhang, Liqian Zhang, Wuning Mo
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0106050

Tau Overexpression Impacts a Neuroinflammation Gene Expression Network Perturbed in Alzheimer’s Disease
Cited by: 87
Author(s): Paul D. Wes, Amy Easton, John P. Corradi, Donna M. Barten, Nino Devidze, Lynn B. DeCarr, Amy Truong, Aiqing He, Nestor X. Barrezueta, Craig Polson, Clotilde Bourin, Marianne E. Flynn, Stefanie Keenan, Regina Lidge, Jere E. Meredith, JoAnne E. Natale, Sethu Sankaranarayanan, Gregory Cadelina, Charlie Albright, Angela Cacace
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12862-016-0733-x

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Cited by: 61
Author(s): Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C. Willison, Richard E. Lenski, Orkun S. Soyer, Dominique Schneider
Software Mentions: 2
Published: almost 10 years ago

10.1155/2020/1392674

Increased Expression of LYNX1 in Ovarian Serous Cystadenocarcinoma Predicts Poor Prognosis
Cited by: 3
Author(s): Hui Liu, Ao Wang, Yu Ma
Software Mentions: 2
Published: over 5 years ago

10.1016/j.isci.2020.101497

Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation
Cited by: 23
Author(s): Shijun Xiao, Zhenbo Mou, Dingding Fan, Zhou He, Ming Zou, Yu Zeng, Chaowei Zhou, Ruibin Yang, Jiaqi Liu, Shilin Zhu, Yajuan Li, Yanchao Liu, Fei Liu, Wanliang Wang, Benhe Zeng, Hong Li, Di Wang, Haiping Li
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12876-018-0927-3

Helicobacter pylori infections in Ethiopia; prevalence and associated factors: a systematic review and meta-analysis
Cited by: 30
Author(s): Addisu Melese, Chalachew Genet, Balew Zeleke, Tesfaye Andualem
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.9626

Transcriptomic and proteomic analysis of mouse radiation-induced acute myeloid leukaemia (AML)
Cited by: 6
Author(s): Christophe Badie, Agnieszka Blachowicz, Žarko Barjaktarović, Rosemary Finnon, Arlette Michaux, Hakan Sarioglu, Natalie Brown, Grainne Manning, Mohammed Abderrafi Benotmane, Soile Tapio, Joanna Polańska, Simon Bouffler
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0211095

Mapping and quantification of ferruginous outcrop savannas in the Brazilian Amazon: A challenge for biodiversity conservation
Cited by: 34
Author(s): Pedro Walfir M. Souza-Filho, Tereza Cristina Giannini, Rodolfo Jaffé, Ana María Giulietti, Diogo C. Santos, Wilson R. Nascimento, José Tasso Felix Guimarães, Marlene Furtado da Costa, Vera Lúcia Imperatriz-Fonseca, José Oswaldo Siqueira
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0087225

Nanoscale Effects of Ethanol and Naltrexone on Protein Organization in the Plasma Membrane Studied by Photoactivated Localization Microscopy (PALM)
Cited by: 24
Author(s): Steven J. Tobin, Eliedonna E. Cacao, Daniel Wing Wo Hong, Lars Terenius, Vladana Vukojević, Tijana Jovanovic-Talisman
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0023525

OASIS: Online Application for the Survival Analysis of Lifespan Assays Performed in Aging Research
Cited by: 256
Author(s): Jae-Seong Yang, Hyun Jun Nam, Mihwa Seo, Seong Kyu Han, Y. S. Choi, Hong Gil Nam, Seung-Jae Lee, Sanguk Kim
Software Mentions: 2
Published: about 15 years ago

10.18632/oncotarget.18978

EB1 protein alteration characterizes sporadic but not ulcerative colitis associated colorectal cancer
Cited by: 6
Author(s): Timo Gemoll, Sophie L. Kollbeck, Karl Karstens, Gia G. Hò, Sonja Hartwig, Sarah Strohkamp, Katharina Schillo, Christoph Thorns, Martina Oberländer, Kathrin Kalies, Stefan Lehr, Jens K. Habermann
Software Mentions: 2
Published: about 9 years ago

10.1186/s12863-020-00853-3

Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23
Cited by: 25
Author(s): Khanam Taslima, Stefanie Wehner, John B. Taggart, Hugues de Verdal, John A. H. Benzie, Michaël Bekaert, Brendan McAndrew, David J. Penman
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.20537

Identification of candidate genes related to pancreatic cancer based on analysis of gene co-expression and protein-protein interaction network
Cited by: 10
Author(s): Tiejun Zhang, Xiaojuan Wang, Z.Q. Yue
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.21546

Identification of hub genes related to silicone-induced immune response in rats
Cited by: 5
Author(s): Xiaolu Huang, Yiwen Zhou, Wenhui Liu, Haizhou Li, Xiao Liang, Rui Jin, Hengyu Du, Jianjun He, Bangda Chai, Ran Duan, Qingfeng Li
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.22009

The WAVE3-YB1 interaction regulates cancer stem cells activity in breast cancer
Cited by: 21
Author(s): Kamila Błędzka, Barbara J. Schiemann, William P. Schiemann, Paul L. Fox, Edward F. Plow, Khalid Sossey‐Alaoui
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.22402

NMR-based metabolomic techniques identify potential urinary biomarkers for early colorectal cancer detection
Cited by: 41
Author(s): Zhening Wang, Yan Lin, Jiahao Liang, Yao Huang, Changchun Ma, Xingmu Liu, Ju-Rong Yang
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.23254

Long non-coding RNA GAS5 and ZFAS1 are prognostic markers involved in translation targeted by miR-940 in prostate cancer
Cited by: 30
Author(s): Xin Chen, Chao Yang, Shengli Xie, Edwin Cheung
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0065324

To Clone or Not to Clone? Induced Pluripotent Stem Cells Can Be Generated in Bulk Culture
Cited by: 34
Author(s): Charlotte A. Willmann, Hatim Hemeda, Lisa A. Pieper, Michael Lenz, Jie Qin, Sylvia Joussen, Stephanie Sontag, Paul Wanek, Bernd Denecke, H Schüler, Martin Zenke, Wolfgang Wagner
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0157893

Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia
Cited by: 7
Author(s): Yee Ling Lau, Wenn-Chyau Lee, Junhui Chen, Zhisheng Zhong, Jianbo Jian, Amirah Amir, Fei Wen Cheong, Jia-Siang Sum, Mun-Yik Fong
Software Mentions: 2
Published: about 10 years ago

10.18632/oncotarget.24047

Molecular characterization of breast cancer cell response to metabolic drugs
Cited by: 22
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Jorge M. Arevalillo, Mariana Díaz-Almirón, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Hilario Navarro, Rosa Aras-López, Irene Dapía, Rocío López-Vacas, Paolo Nanni, Sara Llorente-Armijo, Pedro Arias, Alberto M. Borobia, Paloma Maı́n, Jaime Feliú, Enrique Espinosa, Juan Ángel Fresno Vara
Software Mentions: 2
Published: over 8 years ago

10.1002/cjp2.191

Overactivation of the <scp>IGF</scp> signalling pathway in osteosarcoma: a potential therapeutic target?
Cited by: 5
Author(s): Baptiste Ameline, Michal Kováč, Michaela Nathrath, Maxim Barenboim, Olaf Witt, Andreas H. Krieg, Daniel Baumhoer
Software Mentions: 2
Published: over 5 years ago

10.3390/jpm10040282

Digital Phenotyping and Patient-Generated Health Data for Outcome Measurement in Surgical Care: A Scoping Review
Cited by: 16
Author(s): Prakash Jayakumar, Eugenia Lin, Vincent P Galea, Abraham J Mathew, Nikhil Panda, Imelda Vetter, Alex B. Haynes
Software Mentions: 2
Published: over 5 years ago

10.4103/0975-7406.76463

Differential scanning calorimetry: An invaluable tool for a detailed thermodynamic characterization of macromolecules and their interactions
Cited by: 278
Author(s): Michael Chiu, Elmar J. Prenner
Software Mentions: 2
Published: over 15 years ago

10.3390/biom11040579

Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors
Cited by: 5
Author(s): Alex R. Medeiros, Leonardo L. G. Ferreira, Márcia Regina de Souza, Celso de Oliveira Rezende, Rocio Marisol Espinoza Chávez, Luiz C. Dias, Adriano D. Andricopulo
Software Mentions: 2
Published: over 5 years ago

10.1262/jrd.2018-136

Glycerol kinase 2 is essential for proper arrangement of crescent-like mitochondria to form the mitochondrial sheath during mouse spermatogenesis
Cited by: 27
Author(s): Keisuke Shimada, Hirotaka Kato, Haruhiko Miyata, Masahito Ikawa
Software Mentions: 2
Published: over 7 years ago

10.1186/s12967-020-02630-3

A machine learning-based clinical tool for diagnosing myopathy using multi-cohort microarray expression profiles
Cited by: 6
Author(s): Andrew Tran, Chris J. Walsh, Jane Batt, Claudia C. dos Santos, Pingzhao Hu
Software Mentions: 2
Published: over 5 years ago

10.1186/1479-5876-4-29

Gene expression in acute Stanford type A dissection: a comparative microarray study
Cited by: 44
Author(s): Barbara Theresia Weis-Müller, Olga Modlich, Irina Drobinskaya, Derya Unay, Rita Huber, Hans Bojar, Jochen D. Schipke, P. Feindt, E. Gams, Wolfram Müller, Timm O. Goecke, W. Sandmann
Software Mentions: 2
Published: about 20 years ago

10.1186/s12864-019-5722-1

Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio)
Cited by: 14
Author(s): Shahrbanou Hosseini, Ngoc-Thuy Ha, Henner Simianer, Clemens Falker‐Gieske, Bertram Brenig, André Franke, Gabriele Hörstgen‐Schwark, Jens Tetens, Sebastian Herzog, Ahmad Sharifi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0020763

A Systems Level, Functional Genomics Analysis of Chronic Epilepsy
Cited by: 63
Author(s): Kellen D. Winden, Stanislav L. Karsten, Anatol Bragin, Lili C. Kudo, Lauren Gehman, Josephine Ruidera, Daniel H. Geschwind, Jerome Engel
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0107559

Gene Expression and Pathway Analysis of Effects of the CMAH Deactivation on Mouse Lung, Kidney and Heart
Cited by: 15
Author(s): Deug-Nam Kwon, Byungsoo Chang, Jin‐Hoi Kim
Software Mentions: 2
Published: almost 12 years ago

10.3390/nu10091255

Lactobacillus acidophilus DDS-1 Modulates the Gut Microbiota and Improves Metabolic Profiles in Aging Mice
Cited by: 57
Author(s): Ravichandra Vemuri, Rajaraman Eri, Rohit Gundamaraju, Shakuntla Gondalia, Avinash V. Karpe, David J. Beale, Christopher Martoni, Rajaraman Eri
Software Mentions: 2
Published: almost 8 years ago

10.3390/nu12103140

Statistical and Machine-Learning Analyses in Nutritional Genomics Studies
Cited by: 14
Author(s): Leila Khorraminezhad, Mickaël Leclercq, Arnaud Droit, Jean‐François Bilodeau, Iwona Rudkowska
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-14-436

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules
Cited by: 15
Author(s): Katrina Williams, William A Bryant, Victoria A Jenkins, Geraint Barton, Adam A. Witney, John W. Pinney, Brian D. Robertson
Software Mentions: 2
Published: about 13 years ago

10.3390/nu13061788

Hepatic Nfe2l2 Is Not an Essential Mediator of the Metabolic Phenotype Produced by Dietary Methionine Restriction
Cited by: 4
Author(s): Fei Han, Kirsten P. Stone, Sujoy Ghosh, Laura A. Forney, Landon C. Sims, Leighann Y Vincik, Thomas W. Gettys
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0210008

Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum
Cited by: 10
Author(s): Deepanwita Banerjee, Anu Raghunathan
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0193271

Placental CpG methylation of infants born extremely preterm predicts cognitive impairment later in life
Cited by: 26
Author(s): Sloane K. Tilley, Elizabeth M. Martin, Lisa Smeester, Robert M. Joseph, Karl Kuban, Timothy Heeren, Olaf Dammann, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0211502

Switching between reading tasks leads to phase-transitions in reading times in L1 and L2 readers
Cited by: 3
Author(s): Sebastian Wallot, Jun Taek Lee, Damian G. Kelty-Stephen
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0064181

Suppression and Activation of the Malignant Phenotype by Extracellular Matrix in Xenograft Models of Bladder Cancer: A Model for Tumor Cell “Dormancy”
Cited by: 15
Author(s): Robert E. Hurst, Paul Hauser, Kimberly D. Kyker, Jonathan E. Heinlen, Jason P. Hodde, Michael C. Hiles, Stanley D. Kosanke, Mikhail G. Dozmorov, Michael A. Ihnat
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0159790

Phylogeography of Libanotis buchtormensis (Umbelliferae) in Disjunct Populations along the Deserts in Northwest China
Cited by: 7
Author(s): Ping Wang, Xianzhi Zhang, Nan Tang, Jianjun Liu, Liang Xu, Kai Wang
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0160574

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers
Cited by: 15
Author(s): Michelle Davison, Todd J. Treangen, Sergey Koren, Mihai Pop, Devaki Bhaya
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0164627

Comparing Eye Tracking with Electrooculography for Measuring Individual Sentence Comprehension Duration
Cited by: 13
Author(s): Jana Müller, Dorothea Wendt, Birger Kollmeier, Thomas Brand
Software Mentions: 2
Published: almost 10 years ago

10.1042/BSR20204359

Identified a disintegrin and metalloproteinase with thrombospondin motifs 6 serve as a novel gastric cancer prognostic biomarker by bioinformatics analysis
Cited by: 4
Author(s): Yazhen Zhu, Yi Liu, Xiwen Liao, Shuang Luo
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0096841

HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering
Cited by: 3
Author(s): Yen-Jen Lin, Yu-Tin Chen, Shu-Ni Hsu, Chieh Yu Peng, Chuan‐Yi Tang, Tzu‐Chen Yen, Wu‐Chiao Hsieh
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0134014

Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine
Cited by: 21
Author(s): Daniel Montezano, Laura Meek, Rashmi Gupta, Luiz E. Bermudez, J.C.M. Bermudez
Software Mentions: 2
Published: about 11 years ago

10.1186/s12864-019-5495-6

A unique insight into the MiRNA profile during genital chlamydial infection
Cited by: 13
Author(s): Ifeyinwa Benyeogor, Tankya Simoneaux, Yuehao Wu, Stephanie Lundy, Zenas George, Khamia Ryans, Danielle McKeithen, Roshan Pais, Debra Ellerson, W. Walter Lorenz, Tolulope Omosun, Winston E. Thompson, Francis O. Eko, Carolyn M. Black, Uriel Blás-Machado, Joseph U. Igietseme, Qing He, Yusuf Omosun
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-10-130

Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae
Cited by: 33
Author(s): William J. Jo, Jeung Hyoun Kim, Eric Oh, Daniel Jaramillo, Patricia S. Holman, Alex Loguinov, Adam P. Arkin, Corey Nislow, Guri Giaever, Chris D. Vulpe
Software Mentions: 2
Published: over 17 years ago

10.1186/s12864-021-07510-8

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization
Cited by: 18
Author(s): Yun Dai, Xiao Sun, Chenggang Wang, Fĕi Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun, Shujiang Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0011031

Acetaminophen Modulates the Transcriptional Response to Recombinant Interferon-β
Cited by: 16
Author(s): Aaron Farnsworth, Anathea S. Flaman, Shiv S. Prasad, Caroline Gravel, Andrew Williams, Carole L. Yauk, Xuguang Li
Software Mentions: 2
Published: about 16 years ago

10.1038/s41408-020-00344-9

In vitro and ex vivo gene expression profiling reveals differential kinetic response of HSPs and UPR genes is associated with PI resistance in multiple myeloma
Cited by: 9
Author(s): Amit Mitra, Harish Kumar, Vijay Ramakrishnan, Li Chen, Linda B. Baughn, Santosh Kumar, S. Vincent Rajkumar, Brian G. Van Ness
Software Mentions: 2
Published: about 6 years ago

10.1038/s41413-019-0055-x

Extra-skeletal manifestations in mice affected by Clcn7-dependent autosomal dominant osteopetrosis type 2 clinical and therapeutic implications
Cited by: 12
Author(s): Antonio Maurizi, Mattia Capulli, A Curle, Rajvi Patel, Argia Ucci, JA Cortes, H Oxford, Shireen R. Lamandé, J Bateman, Nadia Rucci, Anna Teti
Software Mentions: 2
Published: about 7 years ago

10.1038/s41413-020-00120-2

MEF2C regulates osteoclastogenesis and pathologic bone resorption via c-FOS
Cited by: 25
Author(s): Takayuki Fujii, Koichi Murata, Se-Hwan Mun, Seyeon Bae, Ye Ji Lee, Tannia Pannellini, Ki‐Woon Kang, David J. Oliver, Kyung‐Hyun Park‐Min, Lionel B. Ivashkiv
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0151436

Understory Plant Community Composition Is Associated with Fine-Scale Above- and Below-Ground Resource Heterogeneity in Mature Lodgepole Pine (Pinus contorta) Forests
Cited by: 16
Author(s): Anne C.S. McIntosh, S. Ellen Macdonald, Sylvie A. Quideau
Software Mentions: 2
Published: over 10 years ago

10.1038/s41416-018-0196-5

MiR-532-5p suppresses renal cancer cell proliferation by disrupting the ETS1-mediated positive feedback loop with the KRAS-NAP1L1/P-ERK axis
Cited by: 58
Author(s): Wei Zhai, Junjie Ma, Ronggang Zhu, Chun‐Fang Xu, Jin Zhang, Yonghui Chen, Zhiguo Chen, Dongkui Gong, Jiayi Zheng, Chen Chen, Saiyang Li, Butang Li, Yiran Huang, Wei Xue, Junhua Zheng
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0019328

Identification of Hyaloperonospora arabidopsidis Transcript Sequences Expressed during Infection Reveals Isolate-Specific Effectors
Cited by: 57
Author(s): Adriana Cabral, Joost H. M. Stassen, Michael Seidl, Jaqueline Bautor, Jane E. Parker, Guido Van den Ackerveken
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0256710

Inter-metropolitan land price characteristics and pattern in the Beijing-Tianjin-Hebei urban agglomeration, China
Cited by: 4
Author(s): Pengfei An, Can Li, Yajing Duan, Jun Ge, Xiangbo Feng
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0232160

The hepatic transcriptome of the turkey poult (Meleagris gallopavo) is minimally altered by high inorganic dietary selenium
Cited by: 4
Author(s): Rachel M Taylor, Kristelle M. Mendoza, Juan E. Abrahante, Kent M. Reed, Roger A. Sunde
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-5195-7

Genetic ancestry, admixture and health determinants in Latin America
Cited by: 68
Author(s): Emily T. Norris, Lu Wang, Andrew B. Conley, Lavanya Rishishwar, Leonardo Mariño-Ramírez, Augusto Valderrama-Aguirre, I. King Jordan
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-11-194

Evidence of perturbations of cell cycle and DNA repair pathways as a consequence of human and murine NF1-haploinsufficiency
Cited by: 17
Author(s): Alexander Pemov, Caroline Park, Karlyne M. Reilly, Douglas R. Stewart
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0211291

Aberrant FAM64A mRNA expression is an independent predictor of poor survival in pancreatic cancer
Cited by: 50
Author(s): Yan Jiao, Zhuo Fu, Yanqing Li, Wei Zhang, Yahui Liu
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-5880-1

Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs
Cited by: 23
Author(s): Siriluck Ponsuksili, Nares Trakooljul, Basavaraj Sajjanar, Frieder Hadlich, Eduard Muráni, Klaus Wimmers
Software Mentions: 2
Published: about 7 years ago

10.1186/bcr3567

An optimized five-gene multi-platform predictor of hormone receptor negative and triple negative breast cancer metastatic risk
Cited by: 28
Author(s): Christina Yau, John J. Sninsky, Shirley Kwok, Alice Wang, Amy C. Degnim, James N. Ingle, Cheryl Gillett, Andrew Tutt, Fred Waldman, Dan H. Moore, Laura J. Esserman, Christopher C. Benz
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0102498

Sediment and Turbidity Associated with Offshore Dredging Increase Coral Disease Prevalence on Nearby Reefs
Cited by: 166
Author(s): F. Joseph Pollock, Joleah B. Lamb, Stuart N. Field, Scott F. Heron, Britta Schaffelke, George Shedrawi, David G. Bourne, Bette L. Willis
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0065571

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia
Cited by: 36
Author(s): Qiaojun Wen, Linda Y. Liu, Ting Yang, Cantas Alev, Shao-Yi Wu, David K. Stevenson, Guojun Sheng, Atul J. Butte, Xuefeng B. Ling
Software Mentions: 2
Published: about 13 years ago

10.1186/s13058-019-1142-z

Parity predisposes breasts to the oncogenic action of PAPP-A and activation of the collagen receptor DDR2
Cited by: 18
Author(s): Elizabeth Slocum, Amanda Craig, Augusto Villanueva, Doris Germain
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-9-105

MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters
Cited by: 25
Author(s): Philip Law, Clotilde Claudel‐Renard, Fourie Joubert, Abraham I. Louw, David Kenneth Berger
Software Mentions: 2
Published: over 18 years ago

10.1186/bcr3689

Parity-related molecular signatures and breast cancer subtypes by estrogen receptor status
Cited by: 35
Author(s): Melissa Rotunno, Xuezheng Sun, Jonine D. Figueroa, Mark E. Sherman, Montserrat García-Closas, Paul S. Meltzer, Tyisha Williams, Sallie S. Schneider, D. Joseph Jerry, Xiaohong R. Yang, Melissa A. Troester
Software Mentions: 2
Published: over 12 years ago

10.1186/s40478-019-0705-7

Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis
Cited by: 14
Author(s): Jeroen Melief, Marie Orre, Koen Bossers, C.G. van Eden, Karianne Schuurman, Matthew R. J. Mason, Joost Verhaagen, Jörg Hamann, Inge Huitinga
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0246259

Prediction of 72-hour mortality in patients with extremely high serum C-reactive protein levels using a novel weighted average of risk scores
Cited by: 5
Author(s): Kai Saito, Hitoshi Sugawara, Kiyoshi Ichihara, Takushi X. Watanabe, Akira Ishii, Takeo Fukuchi
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0170458

Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function
Cited by: 10
Author(s): Chris McDermott-Roe, Marion Leleu, Glenn C. Rowe, Oleg Palygin, John D. Bukowy, Judy Kuo, Monika Rech, Steffie Hermans-Beijnsberger, S. Schaefer, Eleonora Adami, Esther E. Creemers, Matthias Heinig, Blanche Schroen, Zoltàn Arany, Enrico Petretto, Aron M. Geurts
Software Mentions: 2
Published: over 9 years ago

10.1186/s12935-021-01938-4

NEIL3 may act as a potential prognostic biomarker for lung adenocarcinoma
Cited by: 14
Author(s): Chun‐Mei Zhao, Jian Liu, Haomiao Zhou, Qian Xin, Hui Sun, Xuewen Chen, Miaosen Zheng, Tingting Bian, Lei Liu, Yifei Liu, Jianguo Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-14-102

Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence
Cited by: 26
Author(s): Yi Kan Wang, Cristin G. Print, Edmund J. Crampin
Software Mentions: 2
Published: over 13 years ago

10.1186/s40478-017-0424-x

A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis
Cited by: 54
Author(s): Johnathan Cooper‐Knock, Claire Green, Gabriel Altschuler, Wenbin Wei, Joanna J. Bury, Paul R. Heath, Matthew Wyles, Catherine Gelsthorpe, J. Robin Highley, Alejandro Lorente-Pons, Tim Beck, Kathryn Doyle, Karel Otero, Bryan J. Traynor, Janine Kirby, Pamela J. Shaw, Winston Hide
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0158767

Assessing Progress, Impact, and Next Steps in Rolling Out Voluntary Medical Male Circumcision for HIV Prevention in 14 Priority Countries in Eastern and Southern Africa through 2014
Cited by: 44
Author(s): Katharine Kripke, Emmanuel Njeuhmeli, Julia Samuelson, Melissa Schnure, Shona Dalal, Timothy M.M. Farley, Catherine Hankins, Anne Thomas, Jason Reed, Peter Stegman, Naomi Bock
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0067489

Fetal DNA Methylation Associates with Early Spontaneous Preterm Birth and Gestational Age
Cited by: 84
Author(s): Sasha Parets, Karen N. Conneely, Varun Kilaru, Stephen J. Fortunato, Tariq Ali Syed, George R. Saade, Alicia K. Smith, Ramkumar Menon
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0118466

Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition
Cited by: 40
Author(s): Khyobeni Mozhui, Alicia K. Smith, Frances A. Tylavsky
Software Mentions: 2
Published: over 11 years ago

Projects: pypi: analysis

Science Score: 90/100

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Papers Mentioning analysis 2,036