bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/s12885-020-07598-3

Identification and validation of a six-gene signature associated with glycolysis to predict the prognosis of patients with cervical cancer
Cited by: 14
Author(s): Luya Cai, Chuan Hu, Shanshan Yu, Lixiao Liu, Xiaobo Yu, Jiahua Chen, Xuan Li, Fan Lin, Cheng Zhang, Wenfeng Li, Xiaojian Yan
Software Mentions: 1
Published: about 4 years ago

10.1186/s12977-018-0409-2

A CRISPR screen for factors regulating SAMHD1 degradation identifies IFITMs as potent inhibitors of lentiviral particle delivery
Cited by: 20
Author(s): Ferdinand Roesch, Molly OhAinle, Michael Emerman
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-3878-0

Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth
Cited by: 46
Author(s): Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J. Marsit, Jia Chen
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-016-0740-5

Fusarium oxysporum f.sp. radicis-lycopersici induces distinct transcriptome reprogramming in resistant and susceptible isogenic tomato lines
Cited by: 40
Author(s): Daniele Manzo, Francesca Ferriello, Gerardo Puopolo, A. Zoina, Daniela D’Esposito, Luca Tardella, Alberto Ferrarini, Maria Raffaella Ercolano
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.10769

Mitochondrial DNA copy number variation across human cancers
Cited by: 363
Author(s): Ed Reznik, Martin L. Miller, Yasin Şenbabaoğlu, Nadeem Riaz, Judy Sarungbam, Satish K. Tickoo, Hikmat Al‐Ahmadie, William Lee, Venkatraman Seshan, A. Ari Hakimi, Chris Sander
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-6-124

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
Cited by: 77
Author(s): Willem Albert Rensink, Yuandan Lee, Jia Liu, Stacey Iobst, Shuai Ouyang, C. Robin Buell
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0125026

Circulating MicroRNAs as Non-Invasive Biomarkers for Early Detection of Non-Small-Cell Lung Cancer
Cited by: 115
Author(s): Magdalena B. Wozniak, Ghislaine Scélo, David C. Muller, Anush Mukeria, Давид Заридзе, Paul Brennan
Software Mentions: 1
Published: over 9 years ago

10.1177/2472555220973597

CETSA MS Profiling for a Comparative Assessment of FDA-Approved Antivirals Repurposed for COVID-19 Therapy Identifies TRIP13 as a Remdesivir Off-Target
Cited by: 11
Author(s): Tomas Friman, Alexey Chernobrovkin, Daniel Martinez Molina, Laurence H. Arnold
Software Mentions: 1
Published: over 3 years ago

10.1136/thoraxjnl-2015-207236

Latrophilin receptors: novel bronchodilator targets in asthma
Cited by: 12
Author(s): Alen Faiz, Chantal Donovan, Maartje A.E. Nieuwenhuis, Maarten van den Berge, Dirkje S. Postma, Sean Yao, C Y Park, Robert Hirsch, J. J. Fredberg, Gavin Tjin, Andrew J. Halayko, Karen Limbert Rempel, Jeremy P. T. Ward, Tak H. Lee, Yohan Bossé, David C. Nickle, Ma’en Obeidat, Judith M. Vonk, Judith L. Black, Brian G. Oliver, Ramaswamy Krishnan, Brian J. McParland, Jane E. Bourke, Janette K. Burgess
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0127498

Englerin A Agonizes the TRPC4/C5 Cation Channels to Inhibit Tumor Cell Line Proliferation
Cited by: 80
Author(s): Cheryl Carson, Pichai Raman, Jennifer Tullai, Lei Xu, Martin Hénault, Emily Thomas, Suresh Yeola, Jianmin Lao, Mark J. McPate, J. Martin Verkuyl, George Marsh, Jason Sarber, Adam Amaral, Scott Bailey, Danuta Lubicka, Helen Trinh Pham, Nicolette Miranda, Jian Ding, Hui Tang, Haisong Ju, Pamela Tranter, Nan Ji, Philipp Krastel, Rishi K. Jain, Andrew Schumacher, Joseph Loureiro, Elizabeth George, Giuliano Berellini, Nathan T. Ross, Simon M. Bushell, Gül Erdemli, Jonathan M. Solomon
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-2988-4

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems
Cited by: 21
Author(s): Anne Abot, Grégory Arnal, Lucas Auer, Adèle Lazuka, Delphine Labourdette, Sophie Lamarre, Lidwine Trouilh, Élisabeth Laville, Vincent Lombard, Gabrielle Potocki-Véronèse, Bernard Henrissat, Michael O’Donohue, Guillermina Hernandez-Raquet, Claire Dumon, Véronique Anton Leberre
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0135852

LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods
Cited by: 15
Author(s): Ronny Feuer, Sebastian Vlaic, Janine Arlt, Oliver Sawodny, Uta Dahmen, Ulrich M. Zanger, Maria Thomas
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0194844

Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers
Cited by: 23
Author(s): A. Irigoyen, Cristina Jiménez-Luna, Manuel Benavides, Octavio Caba, Javier Gállego, Francisco M. Ortuño Guzman, Carmen Guillén Ponce, Ignacio Rojas, Enrique Aranda, Carolina Torres, José Luis Paniza Prados
Software Mentions: 1
Published: over 6 years ago

10.1016/j.toxrep.2019.09.010

Cross-species comparison of CAR-mediated procarcinogenic key events in a 3D liver microtissue model
Cited by: 6
Author(s): Simon Plummer, Bobby Beaumont, Stephanie Jean Wallace, Graeme Ball, Jayne Wright, Elizabeth McInnes, Richard A. Currie, Rich Peffer, David E. Cowie
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2229-14-108

Day and night heat stress trigger different transcriptomic responses in green and ripening grapevine (vitis vinifera) fruit
Cited by: 134
Author(s): Markus Rienth, Laurent Torregrosa, Nathalie Luchaire, Ratthaphon Chatbanyong, David Lecourieux, Mary T. Kelly, Charles Romieu
Software Mentions: 1
Published: over 10 years ago

10.1038/s41422-019-0181-4

AIF-regulated oxidative phosphorylation supports lung cancer development
Cited by: 56
Author(s): Rao S, Laura Mondragón, Blanka Pranjic, Toshikatsu Hanada, Gautier Stoll, Thomas Köcher, Peng Zhang, Alexander Jais, Alexander Lercher, Andréas Bergthaler, Daniel Schramek, Katharina Haigh, Valentina Sica, Marion Leduc, Nazanine Modjtahedi, Tsung-Pin Pai, Masahiro Onji, Iris Uribesalgo, Reiko Hanada, I. Kozieradzki, Rubina Koglgruber, Shane J. F. Cronin, Zhi‐Gang She, Franz Quehenberger, Helmut Popper, Lukas Kenner, Jody J. Haigh, Oliver Kepp, Malgorzata Rak, Kaican Cai, Guido Kroemer, Josef Penninger
Software Mentions: 1
Published: over 5 years ago

10.1186/s13148-019-0736-8

Random forest-based modelling to detect biomarkers for prostate cancer progression
Cited by: 66
Author(s): Réka Tóth, Heiko Schiffmann, Claudia Hube‐Magg, Franziska Büscheck, Doris Höflmayer, Sören Weidemann, Patrick Lebok, Christoph Fraune, Sarah Minner, Thorsten Schlomm, Guido Sauter, Christoph Plass, Yassen Assenov, Ronald Simon, Jan Meiners, Clarissa Gerhäuser
Software Mentions: 1
Published: about 5 years ago

10.3390/toxics8010012

Potential of Inactivated Bifidobacterium Strain in Attenuating Benzo(A)Pyrene Exposure-Induced Damage in Colon Epithelial Cells In Vitro
Cited by: 7
Author(s): Mengfan Xu, Lili Fu, Junwen Zhang, Tao Wang, Junfeng Fan, Baoqing Zhu, Piotr Dziugan, Bolin Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0092498

Impact of Cigarette Smoke on the Human and Mouse Lungs: A Gene-Expression Comparison Study
Cited by: 38
Author(s): Mathieu C. Morissette, Maxime Lamontagne, Jean‐Christophe Bérubé, Gordon J. Gaschler, Andrew Williams, Carole L. Yauk, Christian Couture, Michel Laviolette, James C. Hogg, Wim Timens, Sabina Halappanavar, Martin R. Stämpfli, Yohan Bossé
Software Mentions: 1
Published: over 10 years ago

10.1186/s13148-020-00930-5

Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Cited by: 9
Author(s): Laura Moody, Sylvia L. Crowder, Andrew D. Frugé, Julie L. Locher, Wendy Demark‐Wahnefried, Laura Q. Rogers, Ashley Delk-Licata, William R. Carroll, Sharon A. Spencer, Michael Black, John W. Erdman, Hong Chen, Yuan Pan, Anna E. Arthur
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2229-11-120

Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I
Cited by: 28
Author(s): Guo-Ling Nan, Arnaud Ronceret, Rachel Wang, John Fernandes, W. Zacheus Cande, Virginia Walbot
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12872-020-01701-z

Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis
Cited by: 7
Author(s): Dinghui Wang, Bin Liu, Tianhua Xiong, Wenlong Yu, Sheng Qiang
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers13164225

Tobacco Smoke and Electronic Cigarette Vapor Alter Enhancer RNA Expression That Can Regulate the Pathogenesis of Lung Squamous Cell Carcinoma
Cited by: 2
Author(s): Joseph C. Tsai, Omar A. Saad, Shruti Magesh, Jingyue Xu, Abby C Lee, Wei Tse Li, Jaideep Chakladar, Mark M. Fuster, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 1
Published: over 3 years ago

10.1186/s13148-021-01048-y

Differential methylation EPIC analysis discloses cisplatin-resistance related hypermethylation and tumor-specific heterogeneity within matched primary and metastatic testicular germ cell tumor patient tissue samples
Cited by: 12
Author(s): João Lobo, Vera Constâncio, Pedro Leite‐Silva, Rita Guimarães, Mariana Cantante, Isaac Braga, Joaquina Maurício, Leendert H. J. Looijenga, Rui Henrique, Carmen Jerónimo
Software Mentions: 1
Published: over 3 years ago

10.3390/toxins10050199

Saccharomyces cerevisiae Boulardii Reduces the Deoxynivalenol-Induced Alteration of the Intestinal Transcriptome
Cited by: 18
Author(s): Imourana Alassane-Kpémbi, Philippe Pinton, Jean-François Hupé, Manon Neves, Yannick Lippi, Sylvie Combes, Mathieu Castex, Isabelle P. Oswald
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0069808

Differentiated Neuroprogenitor Cells Incubated with Human or Canine Adenovirus, or Lentiviral Vectors Have Distinct Transcriptome Profiles
Cited by: 18
Author(s): Stefania Piersanti, Letizia Astrologo, Valerio Licursi, Rossella Costa, Enrica Roncaglia, Aurélie Gennetier, Sandy Ibanes, Miguel Chillón, Rodolfo Negri, Enrico Tagliafico, Eric J. Kremer, Isabella Saggio
Software Mentions: 1
Published: over 11 years ago

10.1523/ENEURO.0181-17.2017

TU-Tagging: A Method for Identifying Layer-Enriched Neuronal Genes in Developing Mouse Visual Cortex
Cited by: 14
Author(s): Johanna Tomorsky, Leah DeBlander, Clifford Kentros, Chris Q. Doe, Cristopher M. Niell
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-12-501

Temporal transcriptome changes induced by MDV in marek's disease-resistant and -susceptible inbred chickens
Cited by: 35
Author(s): Ying Yu, Juan Luo, Apratim Mitra, Shuang Chang, Fei Tian, Huanmin Zhang, Ping Yuan, Huaijun Zhou, Jiuzhou Song
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0039980

Sex-Related Differences in Gene Expression by Porcine Aortic Valvular Interstitial Cells
Cited by: 58
Author(s): Chloé M. McCoy, Dylan Q. Nicholas, Kristyn S. Masters
Software Mentions: 1
Published: over 12 years ago

10.3390/toxins12100645

Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature
Cited by: 6
Author(s): Catherine Duport, Ludivine Rousset, Béatrice Alpha-Bazin, Jean Armengaud
Software Mentions: 1
Published: about 4 years ago

10.1186/s12870-020-2317-6

Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns
Cited by: 18
Author(s): Mao-Song Pei, Suhao Cao, Lei Wu, Guo‐Ming Wang, Zhihua Xie, Chao Gu, Shaoling Zhang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0115865

No Specific Gene Expression Signature in Human Granulosa and Cumulus Cells for Prediction of Oocyte Fertilisation and Embryo Implantation
Cited by: 25
Author(s): Tanja Burnik Papler, Eda Vrtačnik Bokal, Luca Lovrečić, Andreja Nataša Kopitar, Aleš Maver
Software Mentions: 1
Published: over 9 years ago

10.1186/s13148-018-0499-7

Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice
Cited by: 12
Author(s): Joana Frobel, Susann Rahmig, Julia Franzen, Claudia Waskow, Wolfgang Wagner
Software Mentions: 1
Published: over 6 years ago

10.3390/toxins12100621

Indoxyl Sulfate-Mediated Metabolic Alteration of Transcriptome Signatures in Monocytes of Patients with End-Stage Renal Disease (ESRD)
Cited by: 2
Author(s): Hee Young Kim, Su Jeong Lee, Yuri Hwang, Ga Hye Lee, Chae Eun Yoon, Hyeon Chang Kim, Tae Hyun Yoo, Won Woo Lee
Software Mentions: 1
Published: about 4 years ago

10.1186/s13148-018-0579-8

Loss of DNA methylation is related to increased expression of miR-21 and miR-146b in papillary thyroid carcinoma
Cited by: 24
Author(s): Isabella Maria Dias Payão Ortiz, Mateus Camargo Barros-Filho, Mariana Bisarro dos Reis, Caroline Moraes Beltrami, Fábio Albuquerque Marchi, Hellen Kuasne, Luísa Matos do Canto, Julia Bette Homem de Mello, Cecilie Abildgaard, Clóvis Antônio Lopes Pinto, Luiz Paulo Kowalski, Sílvia Regina Rogatto
Software Mentions: 1
Published: about 6 years ago

10.3390/cells8121601

Rewiring of Lipid Metabolism and Storage in Ovarian Cancer Cells after Anti-VEGF Therapy
Cited by: 22
Author(s): Matteo Curtarello, Martina Tognon, Carolina Venturoli, Micol Silic-Benussi, Angela Grassi, Martina Verza, Sonia Minuzzo, Marica Pinazza, Valentina Brillo, Giovanni Tosi, Ruggero Ferrazza, Graziano Guella, Egidio Iorio, Adrien Godfroid, Nor Eddine Sounni, Alberto Amadori, Stefano Indraccolo
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0162750

Transcriptomic Analysis of Persistent Infection with Foot-and-Mouth Disease Virus in Cattle Suggests Impairment of Apoptosis and Cell-Mediated Immunity in the Nasopharynx
Cited by: 22
Author(s): Michael Eschbaumer, Carolina Stenfeldt, George R. Smoliga, Juan M. Pacheco, Luis L. Rodrı́guez, Robert W. Li, James Zhu, Jonathan Arzt
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0084033

Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome
Cited by: 34
Author(s): Abdessamad El Kaoutari, Fabrice Armougom, Quentin Leroy, B. Vialettes, Matthieu Million, Didier Raoult, Bernard Henrissat
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0058199

An Antibody-Based Leukocyte-Capture Microarray for the Diagnosis of Systemic Lupus Erythematosus
Cited by: 9
Author(s): Ming‐Wei Lin, Joshua W. K. Ho, Leonard C. Harrison, Cristobal G. dos Remedios, Stephen Adelstein
Software Mentions: 1
Published: over 11 years ago

10.1186/s40035-020-00194-2

Paroxetine ameliorates prodromal emotional dysfunction and late-onset memory deficit in Alzheimer’s disease mice
Cited by: 11
Author(s): Penghui Ai, Si Chen, Xiandong Liu, Xiaona Zhu, Yuan‐Bo Pan, Donghan Feng, Shengdi Chen, Nan‐Jie Xu, Suya Sun
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0029457

Convergent Differential Regulation of Parvalbumin in the Brains of Vocal Learners
Cited by: 42
Author(s): Erina Hara, Miriam V. Rivas, James M. Ward, Kazuo Okanoya, Erich D. Jarvis
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12967-015-0506-0

DNA methylation analysis of phenotype specific stratified Indian population
Cited by: 43
Author(s): Harish Rotti, Sandeep Mallya, Shama Prasada Kabekkodu, Sanjiban Chakrabarty, Sameer Bhale, Ramachandra Bharadwaj, Balakrishna K Bhat, Amrish P Dedge, Vikram Ram Dhumal, G G Gangadharan, P. M. Gopinath, Periyasamy Govindaraj, Kalpana Joshi, Paturu Kondaiah, Sreekumaran Nair, SN Venugopalan Nair, Jayakrishna Nayak, B V Prasanna, Pooja Shintre, Mayura Sule, Kumarasamy Thangaraj, Bhushan Patwardhan, Marthanda Varma Sankaran Valiathan, Kapaettu Satyamoorthy
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2229-13-27

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
Cited by: 48
Author(s): Hyun Jo Koo, Eric T. McDowell, Xiaoqiang Ma, Kevin Greer, Jeremy Kapteyn, Zhengzhi Xie, Anne Descour, Hye Ran Kim, Yeisoo Yu, David Kudrna, Rod A. Wing, Carol Soderlund, David R. Gang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0212662

Synovial fluid proteome changes in ACL injury-induced posttraumatic osteoarthritis: Proteomics analysis of porcine knee synovial fluid
Cited by: 18
Author(s): A. M. Kiapour, Jakob T. Sieker, Benedikt L. Proffen, TuKiet T. Lam, Braden C. Fleming, Martha M. Murray
Software Mentions: 1
Published: over 5 years ago

10.1186/s13148-018-0490-3

Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study
Cited by: 19
Author(s): Yan Cheng, Cátia Monteiro, Andreia Matos, Jiaying You, Avelino Fraga, Carina Pereira, Victoria Catalán, Amaia Rodrı́guez, Javier Gómez-Ambrosi, Gema Frühbeck, Ricardo Ribeiro, Pingzhao Hu
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2229-11-173

SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus
Cited by: 135
Author(s): Steven G. Hussey, Eshchar Mizrachi, Antanas Spokevicius, Gerd Bossinger, David Kenneth Berger, Alexander Andrew Myburg
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13148-018-0591-z

Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality
Cited by: 33
Author(s): Xinyu Zhang, Ying Hu, Bradley E. Aouizerat, Gang Peng, Vincent C. Marconi, Michael J. Corley, Todd Hulgan, Kendall Bryant, Hongyu Zhao, John H. Krystal, Amy C. Justice, Ke Xu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-016-2623-4

Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes
Cited by: 37
Author(s): Sonia Paco, Manuela Hummel, Virginia Plá, Lauro Sumoy, Fernando Aguado
Software Mentions: 1
Published: over 8 years ago

10.1186/s13148-020-0820-0

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci
Cited by: 52
Author(s): Mark W. Logue, Mark W. Miller, Erika J. Wolf, Bertrand R. Huber, Filomene G. Morrison, Zhenwei Zhou, Yuanchao Zheng, Alicia K. Smith, Nikolaos P. Daskalakis, Andrew Ratanatharathorn, Monica Uddin, Caroline M. Nievergelt, Allison Ashley‐Koch, Dewleen G. Baker, Jean C. Beckham, Melanie E. Garrett, Marco P. Boks, Elbert Geuze, Gerald A. Grant, Michael A. Hauser, Ronald C. Kessler, Nathan A. Kimbrel, Adam X. Maihofer, Christine E. Marx, Xuejun Qin, Victoria B. Risbrough, Bart P. F. Rutten, Murray B. Stein, Robert J. Ursano, Eric Vermetten, Christiaan H. Vinkers, Erin B. Ware, Annjanette Stone, Steven A. Schichman, Regina E. McGlinchey, William Milberg, Jasmeet P. Hayes, Mieke Verfaellie
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0231108

Probing lasting cryoinjuries to oocyte-embryo transcriptome
Cited by: 9
Author(s): Binnur Eroglu, Edyta Szurek, Peter Z. Schall, Keith E. Latham, Ali Eroğlu
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.58396

A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress
Cited by: 116
Author(s): Madlen Stephani, Lorenzo Picchianti, Alexander Gajic, Rebecca Beveridge, Emilio Skarwan, Víctor Sánchez de Medina Hernández, Azadeh Mohseni, Marion Clavel, Yonglung Zeng, Christin Naumann, Mateusz Matuszkiewicz, Eleonora Turco, Christian Loefke, Baiying Li, Gerhard Dürnberger, Michael Schutzbier, Hsiao Tieh Chen, Alibek Abdrakhmanov, Adriana Savova, Khong Sam Chia, Armin Djamei, Irene Schaffner, Steffen Abel, Liwen Jiang, Karl Mechtler, Fumiyo Ikeda, Sascha Martens, Tim Clausen, Yasin Dagdas
Software Mentions: 1
Published: over 4 years ago

10.1186/s12885-021-08293-7

A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma
Cited by: 5
Author(s): Zhiying Chen, Jiahui Wei, Min Li, Yufei Zhao
Software Mentions: 1
Published: over 3 years ago

10.1038/tp.2016.131

MicroRNAs as biomarkers for major depression: a role for let-7b and let-7c
Cited by: 94
Author(s): Anand Gururajan, Marie Naughton, Karen A. Scott, Richard M. O’Connor, Gerard M. Moloney, Gerard Clarke, Joshua L. Dowling, Annabel Walsh, Muhammad Ismail, George Shorten, Lucinda V. Scott, Declan M. McLoughlin, John F. Cryan, Timothy G. Dinan
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0114481

Immediate and Persistent Transcriptional Correlates of Long-Term Sensitization Training at Different CNS Loci in Aplysia californica
Cited by: 10
Author(s): Samantha Herdegen, Catherine Conte, Saman Kamal, Robert Calin-Jageman, Irina Calin‐Jageman
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-12-490

Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
Cited by: 59
Author(s): Florbela A. Vieira, Sílvia F. Gregório, Serena Ferraresso, Michael A. S. Thorne, Rita A. Costa, Massimo Milan, Luca Bargelloni, Melody S. Clark, Adelino V.M. Canário, Deborah M. Power
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0053467

Fine Mapping Links the FTa1 Flowering Time Regulator to the Dominant Spring1 Locus in Medicago
Cited by: 28
Author(s): Chin Chin Yeoh, Martin Balcerowicz, Lulu Zhang, Mauren Jaudal, Lysiane Brocard, Pascal Ratet, Joanna Putterill
Software Mentions: 1
Published: almost 12 years ago

10.1038/tp.2016.78

Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3
Cited by: 27
Author(s): Bianca Pfaffenseller, Pedro Vieira da Silva Magalhães, Marco Antônio De Bastiani, Mauro A. A. Castro, Amelia L. Gallitano, Flávio Kapczinski, Fábio Klamt
Software Mentions: 1
Published: over 8 years ago

10.1111/eva.12394

Adaptation to climate change: trade‐offs among responses to multiple stressors in an intertidal crustacean
Cited by: 52
Author(s): Morgan W. Kelly, Melissa B. DeBiasse, Vidal A. Villela, Hope L. Roberts, Colleen F. Cecola
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0057458

Estrogen Signalling and the Metabolic Syndrome: Targeting the Hepatic Estrogen Receptor Alpha Action
Cited by: 49
Author(s): Marko Matic, Galyna Bryzgalova, Hui Gao, Per Antonson, Patricia Humire, Yoko Omoto, Neil Portwood, Camilla Pramfalk, Suad Efendić, Per Olof Berggren, Jan Åke Gustafsson, Karin Dahlman-Wright
Software Mentions: 1
Published: almost 12 years ago

10.3390/cells9030617

BMP-9 Modulates the Hepatic Responses to LPS
Cited by: 13
Author(s): H Gaitantzi, J Karch, Lena Germann, Chen Cai, Vanessa Rausch, Emrullah Birgin, Nuh N. Rahbari, Tatjana Seitz, Claus Hellerbrand, Courtney König, Hellmut G. Augustin, Carolin Mogler, Carolina De La Torre, Norbert Gretz, Timo Itzel, Andreas Teufel, Matthias P. Ebert, Katja Breitkopf‐Heinlein
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-14-121

Comparative transcriptomics reveals different strategies of Trichodermamycoparasitism
Cited by: 222
Author(s): Lea Atanasova, Stéphane Le Crom, Sabine Gruber, Fanny Coulpier, Verena Seidl‐Seiboth, Christian P. Kubicek, Irina S. Druzhinina
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.stem.2012.02.023

The Germ Cell Determinant Blimp1 Is Not Required for Derivation of Pluripotent Stem Cells
Cited by: 22
Author(s): Siqin Bao, Harry G. Leitch, Astrid Gillich, Jennifer Nichols, Fuchou Tang, Shinseog Kim, Caroline Lee, Thomas P. Zwaka, Xihe Li, M. Azim Surani
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-016-2424-9

Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice
Cited by: 7
Author(s): Tenzin Nyima, Michael Müller, Guido Hooiveld, Melissa J. Morine, Marco Scotti
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2229-10-134

Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses
Cited by: 13
Author(s): Shailendra Sharma, Nese Sreenivasulu, Vokkaliga T. Harshavardhan, Christiane Seiler, Shiveta Sharma, Zaynali Nezhad Khalil, Eduard Akhunov, Sunish K. Sehgal, Marion S. Röder
Software Mentions: 1
Published: almost 15 years ago

10.1038/srep03372

Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture
Cited by: 29
Author(s): Carola I. Weidner, Thomas Walenda, Qiong Lin, M Wölfler, Bernd Denecke, Ivan G. Costa, Martin Zenke, Wolfgang Wagner
Software Mentions: 1
Published: about 11 years ago

10.1186/s40164-018-0105-x

Understanding metabolic changes in aging bone marrow
Cited by: 12
Author(s): Kwasi M. Connor, Young Hsu, Pardeep K. Aggarwal, Stephen Capone, Anthony Colombo, Giridharan Ramsingh
Software Mentions: 1
Published: over 6 years ago

10.1038/s12276-019-0255-x

microRNA-328 in exosomes derived from M2 macrophages exerts a promotive effect on the progression of pulmonary fibrosis via FAM13A in a rat model
Cited by: 57
Author(s): Meng Yao, Weihong Zhang, Wentao Ma, Qiuhong Liu, Xing Liu, Guiqiu Zhao
Software Mentions: 1
Published: over 5 years ago

10.1038/s12276-021-00651-6

Plasma extracellular vesicle delivery of miR-210-3p by targeting ATG7 to promote sepsis-induced acute lung injury by regulating autophagy and activating inflammation
Cited by: 16
Author(s): Guang Li, Bo Wang, Xiangchao Ding, Xinghua Zhang, Jian Tang, Hongyuan Lin
Software Mentions: 1
Published: over 3 years ago

10.1038/srep05008

PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression
Cited by: 13
Author(s): Juan Wang, Xueqiu Lin, Su Wang, Chenfei Wang, Qixuan Wang, Xikun Duan, Peng Lü, Qian Wang, Chengyang Wang, X. Shirley Liu, Jinyan Huang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0080171

Links between the Oncoprotein YB-1 and Small Non-Coding RNAs in Breast Cancer
Cited by: 38
Author(s): Cherie Blenkiron, Daniel Hurley, Sandra Fitzgerald, Cristin G. Print, Annette Lasham
Software Mentions: 1
Published: about 11 years ago

10.3892/etm.2014.2041

Identification of dysregulated miRNAs and their regulatory signature in glioma patients using the partial least squares method
Cited by: 11
Author(s): Jiajun Shou, Shaohua Gu, Wentao Gu
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0164985

MicroRNA-941 Expression in Polymorphonuclear Granulocytes Is Not Related to Granulomatosis with Polyangiitis
Cited by: 7
Author(s): Jesper Brink Svendsen, Bo Baslund, Elisabeth Præstekjær Cramer, Nicolas Rapin, Niels Borregaard, Jack B. Cowland
Software Mentions: 1
Published: about 8 years ago

10.1186/s12967-019-2042-9

Metabolic profiling reveals distinct metabolic alterations in different subtypes of pituitary adenomas and confers therapeutic targets
Cited by: 8
Author(s): Jiaxuan Feng, Hua Gao, Qi Zhang, Yang Zhou, Chuzhong Li, Sida Zhao, Liu Hong, Jinjin Yang, Shuyu Hao, Hong Wan, Zhengping Zhuang, Guowang Xu, Yazhou Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0054248

Lack of RsmA-Mediated Control Results in Constant Hypervirulence, Cell Elongation, and Hyperflagellation in Pectobacterium wasabiae
Cited by: 25
Author(s): Viia Kõiv, Liis Andresen, Martin Broberg, Jekaterina Frolova, Panu Somervuo, Petri Auvinen, Minna Pirhonen, Tanel Tenson, Andres Mäe
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0140467

Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro
Cited by: 67
Author(s): Dessie Salilew‐Wondim, Éric Fournier, M. Hoelker, Mohammed Saeed‐Zidane, Ernst Tholen, Christian Looft, Christiane Neuhoff, U. Besenfelder, V. Havlíček, F. Rings, Dominic Gagné, Marc‐André Sirard, Claude Robert, Habib A. Shojaei Saadi, Ahmed Gad, K. Schellander, Dawit Tesfaye
Software Mentions: 1
Published: about 9 years ago

10.1038/srep09088

Blood cell transcriptomic-based early biomarkers of adverse programming effects of gestational calorie restriction and their reversibility by leptin supplementation
Cited by: 19
Author(s): Jadwiga Konieczna, Juana Sánchez, Mariona Palou, Catalina Picó, Andreu Taberner Palou
Software Mentions: 1
Published: over 9 years ago

10.1186/s12967-021-03006-x

Identification of proteins associated with development of psoriatic arthritis in peripheral blood mononuclear cells: a quantitative iTRAQ-based proteomics study
Cited by: 7
Author(s): Jie Zhu, Ling Han, Ruilai Liu, Zhenghua Zhang, Qiong Huang, Xu Fang, Yang Ke, Guangjian Huang, Zheng Zhang, Nikhil Yawalkar, Hui Deng, Kexiang Yan
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0063825

Global Gene Expression Profiling in PAI-1 Knockout Murine Heart and Kidney: Molecular Basis of Cardiac-Selective Fibrosis
Cited by: 33
Author(s): Asish K. Ghosh, Sheila B. Murphy, Raj Kishore, Douglas E. Vaughan
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0082473

Molecular Strategies of the Caenorhabditis elegans Dauer Larva to Survive Extreme Desiccation
Cited by: 97
Author(s): Cihan Erkut, Andrej Vasilj, Sebastian Boland, Bianca Habermann, Andrej Shevchenko, Teymuras V. Kurzchalia
Software Mentions: 1
Published: almost 11 years ago

10.3390/cancers11101536

Understanding the Interplay between COX-2 and hTERT in Colorectal Cancer Using a Multi-Omics Analysis
Cited by: 24
Author(s): Georgios D. Ayiomamitis, George Notas, Thivi Vasilakaki, Aikaterini Tsavari, Styliani Vederaki, T. Theodosopoulos, Elias Kouroumalis, Apostolos Zaravinos
Software Mentions: 1
Published: about 5 years ago

10.1523/ENEURO.0310-19.2019

TrkB Signaling Influences Gene Expression in Cortistatin-Expressing Interneurons
Cited by: 8
Author(s): Kristen R. Maynard, Alisha Kardian, Joanne M. Hill, Yishan Mai, Brianna K. Barry, Henry L. Hallock, Andrew E. Jaffe
Software Mentions: 1
Published: almost 5 years ago

10.1038/srep12393

Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer’s disease
Cited by: 102
Author(s): Xinzhong Li, Jintao Long, Taigang He, Robert Belshaw, James A. Scott
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0044609

In Vivo Functional Requirement of the Mouse Ifitm1 Gene for Germ Cell Development, Interferon Mediated Immune Response and Somitogenesis
Cited by: 10
Author(s): Ingeborg Klymiuk, Lukas Kenner, Thure Adler, Dirk H. Busch, Auke Boersma, Martin Irmler, Valérie Gailus‐Durner, Helmut Fuchs, Nicole R. Leitner, Mathias Müller, Ralf Kühn, Michaela Schlederer, Irina Treise, Martin Hrabé de Angelis, Johannes Beckers
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0020043

Differential Proteomics in Dequeened Honeybee Colonies Reveals Lower Viral Load in Hemolymph of Fertile Worker Bees
Cited by: 21
Author(s): Dries Cardoen, Ulrich Ernst, Matthias Van Vaerenbergh, Bart Boerjan, Dirk C. de Graaf, Tom Wenseleers, Liliane Schoofs, Peter Verleyen
Software Mentions: 1
Published: over 13 years ago

10.1038/srep13895

Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays
Cited by: 40
Author(s): Parvez Syed, S. Gupta, Saket Choudhary, Narendra Goud Pandala, Apurva Atak, Annie Richharia, Manubhai Kp, Heng Zhu, Sridhar Epari, Santosh Noronha, Aliasgar Moiyadi, Sanjeeva Srivastava
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0086490

Genome and Transcriptome Analysis of the Basidiomycetous Yeast Pseudozyma antarctica Producing Extracellular Glycolipids, Mannosylerythritol Lipids
Cited by: 34
Author(s): Tomotake Morita, Hideaki Koike, Hiroko Hagiwara, Emi Ito, Masayuki Machida, Shun Sato, Hiroshi Habe, Daï Kitamoto
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-9-78

Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)
Cited by: 47
Author(s): Robert B. Page, S. Randal Voss, Amy Samuels, Jeramiah J. Smith, Srikrishna Putta, Christopher K. Beachy
Software Mentions: 1
Published: almost 17 years ago

10.1038/srep15007

Junb controls lymphatic vascular development in zebrafish via miR-182
Cited by: 22
Author(s): Kristin Kiesow, Katrin Bennewitz, Laura Gutierrez-Miranda, Sandra J. Stoll, Bettina Hartenstein, Peter Angel, Jens Krøll, Marina Schorpp-Kistner
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0003279

Single-Species Microarrays and Comparative Transcriptomics
Cited by: 17
Author(s): Frédéric J. J. Chain, Dora Ilieva, Ben Evans
Software Mentions: 1
Published: about 16 years ago

10.12688/f1000research.8210.2

A curated transcriptome dataset collection to investigate the development and differentiation of the human placenta and its associated pathologies
Cited by: 10
Author(s): Alexandra K. Marr, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Damien Chaussabel, Tomoshige Kino
Software Mentions: 1
Published: over 8 years ago

10.12688/f1000research.16172.2

Strigolactone GR24 upregulates target genes of the cytoprotective transcription factor Nrf2 in skeletal muscle
Cited by: 1
Author(s): Shalem Modi, Tarja Kokkola
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0068415

Gene Expression Profiling of Immune-Competent Human Cells Exposed to Engineered Zinc Oxide or Titanium Dioxide Nanoparticles
Cited by: 87
Author(s): Soile Tuomela, Reija Autio, Tina Buerki-Thurnherr, Osman Arslan, Andrea Kunzmann, Britta Andersson-Willman, Peter Wick, Sanjay Mathur, Annika Scheynius, Harald F. Krug, Bengt Fadeel, Riitta Lahesmaa
Software Mentions: 1
Published: over 11 years ago

10.1038/srep15214

Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection
Cited by: 39
Author(s): Abhijit Maji, Richa Misra, Anupam Mondal, Dhirendra Kumar, Divya Bajaj, Abhinav Singhal, Gunjan Arora, Amit Bhaduri, Andaleeb Sajid, Sugandha Bhatia, Sompal Singh, Harshvardhan Singh, V. Pandu Ranga Rao, Debasis Dash, E. Shalini, Joy Sarojini Michael, Anil Chaudhary, Rajesh S. Gokhale, Yogendra Singh
Software Mentions: 1
Published: about 9 years ago

10.1186/s12885-019-5927-3

Estimation of immune cell content in tumor using single-cell RNA-seq reference data
Cited by: 28
Author(s): Xiaoqing Yu, Yian Ann Chen, José R. Conejo-Garcia, Christine H. Chung, Xuefeng Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0070320

Partial Restoration of Macrophage Alteration from Diet-Induced Obesity in Response to Porphyromonas gingivalis Infection
Cited by: 6
Author(s): Guilhem Richard, Niraj Trivedi, Călin Belta, Salomon Amar
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0041041

Role of Heat-Stable Enterotoxins in the Induction of Early Immune Responses in Piglets after Infection with Enterotoxigenic Escherichia coli
Cited by: 59
Author(s): Michaela Loos, Marisa Geens, Stijn Schauvliege, Frank Gasthuys, Jan van der Meulen, J. Daniel Dubreuil, Bruno Goddeeris, Theodoor Niewold, Eric Cox
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0159010

Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment – A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine
Cited by: 11
Author(s): Katri Koli, Eva Sutinen, Mikko Rönty, Pia Rantakari, Vittorio Fortino, Ville Pulkkinen, Dario Greco, Petra Sipilä, Marjukka Myllärniemi
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0194229

Pure flavonoid epicatechin and whole genome gene expression profiles in circulating immune cells in adults with elevated blood pressure: A randomised double-blind, placebo-controlled, crossover trial
Cited by: 25
Author(s): Diederik Esser, Johanna M. Geleijnse, Juri C. Matualatupauw, James I Dower, Daan Kromhout, P.C.H. Hollman, Lydia A. Afman
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0207470

CRB3 and the FERM protein EPB41L4B regulate proliferation of mammary epithelial cells through the release of amphiregulin
Cited by: 2
Author(s): Stephanie Walker, Laura M. Selfors, Ben Margolis, Joan S. Brugge
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0058104

Identification and Characterization of MicroRNAs Controlled by the Osteoblast-Specific Transcription Factor Osterix
Cited by: 46
Author(s): Chen Qin, Wenbin Liu, Krishna M. Sinha, Hideyo Yasuda, Benoít de Crombrugghe
Software Mentions: 1
Published: over 11 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776