cran: gplots | Projects | Ecosyste.ms: Papers

10.18632/aging.101871

Anesthesia and surgery induce cognitive dysfunction in elderly male mice: the role of gut microbiota
Cited by: 46
Author(s): Gaofeng Zhan, Hua Duan, Niannian Huang, Yue Wang, Shan Li, Zhiqiang Zhou, Ning Yang, Ruiwei Jiang, Bin Zhu, Ling Yang, Yu Fan, Hui Xu, Chun Yang, Ailin Luo
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2018.02512

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants
Cited by: 51
Author(s): Elena Biagi, Arianna Aceti, Sara Quercia, Isadora Beghetti, Simone Rampelli, Silvia Turroni, Matteo Soverini, Angelo Vittorio Zambrini, Giacomo Faldella, Marco Candela, Luigi Corvaglia, Patrizia Brigidi
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.68466

LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells
Cited by: 10
Author(s): Bo-Ruei Chen, Yinan Wang, Anthony Tubbs, Dali Zong, Faith C Fowler, Nicholas Zolnerowich, Wei Wu, Amelia Bennett, Chun-Chin Chen, Wendy Feng, André Nussenzweig, Jessica K. Tyler, Barry P. Sleckman
Software Mentions: 3
Published: about 5 years ago

10.1155/2015/878546

Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools
Cited by: 20
Author(s): Zhenzhen Huang, Huilong Duan, Haomin Li
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0110664

Soil Temperature Determines the Reaction of Olive Cultivars to Verticillium dahliae Pathotypes
Cited by: 29
Author(s): Rocío Calderón, Carlos Lucena, J. L. Trapero-Casas, Pablo J. Zarco‐Tejada, Juan A Navas‐Cortés
Software Mentions: 3
Published: about 12 years ago

10.1186/s12870-021-02919-5

Superoxide dismutase (SOD) as a selection criterion for triticale grain yield under drought stress: a comprehensive study on genomics and expression profiling, bioinformatics, heritability, and phenotypic variability
Cited by: 39
Author(s): Armin Saed-Moucheshi, Fatemeh Sohrabi, Elham Fasihfar, Fatemeh Baniasadi, Mehrnaz Riasat, Ali-Akbar Mozafari
Software Mentions: 3
Published: over 5 years ago

10.1038/srep24180

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years
Cited by: 21
Author(s): Xiaotao Jiang, Feng Guo, Tong Zhang
Software Mentions: 3
Published: over 10 years ago

10.3390/cancers11101410

An IKK/NF-κB Activation/p53 Deletion Sequence Drives Liver Carcinogenesis and Tumor Differentiation
Cited by: 3
Author(s): Michael Svinarenko, Sarah‐Fee Katz, Umesh Tharehalli, Medhanie Mulaw, Harald J. Maier, Yoshiaki Sunami, Sarah Fischer, Yuexin Chen, Sabine Heurich, Lena Erkert, Andrea Tannapfel, Thomas Wirth, Reinhold Schirmbeck, Thomas Seufferlein, André Lechel
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0119741

Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance
Cited by: 12
Author(s): Silvia Pajares, Valeria Souza, Luis E. Eguiarte
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1006405

Signaling through Lrg1, Rho1 and Pkc1 Governs Candida albicans Morphogenesis in Response to Diverse Cues
Cited by: 30
Author(s): Jinglin Lucy Xie, Nora Grahl, Trevor J.L. Sless, Michelle Leach, Sang Hu Kim, Deborah A. Hogan, Nicole Robbins, Leah E. Cowen
Software Mentions: 3
Published: about 10 years ago

10.1155/2020/3075729

Comprehensive Analysis of lncRNAs Related to the Prognosis of Esophageal Cancer Based on ceRNA Network and Cox Regression Model
Cited by: 4
Author(s): Chao Li, Wu Yao, Congcong Zhao, Yang Guo, Jingjing Wei, Yuanmeng Qi, Ruoxuan Huang, Qiuyan Zhao, Changfu Hao
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-021-07426-3

Transcriptome analysis of the transdifferentiation of canine BMSCs into insulin producing cells
Cited by: 2
Author(s): Jinglu Wang, Pengxiu Dai, Tong Zou, Yangou Lv, Wen Zhao, Xinke Zhang, Yihua Zhang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0185216

Aging and death-associated changes in serum albumin variability over the course of chronic hemodialysis treatment
Cited by: 17
Author(s): Yuichi Nakazato, R Kurane, Satoru Hirose, Akira Watanabe, Hiromi Shimoyama
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0078613

Distinct Phyllosphere Bacterial Communities on Arabidopsis Wax Mutant Leaves
Cited by: 77
Author(s): Eva E. Reisberg, U. Hildebrandt, Markus Riederer, Ute Hentschel
Software Mentions: 3
Published: about 13 years ago

10.7150/ijms.63402

Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer
Cited by: 8
Author(s): Chang Liu, Yu Pan, Qinyu Li, Yifan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4510-7

Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster
Cited by: 30
Author(s): Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-014-0412-4

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Cited by: 55
Author(s): Rebecca Worsley Hunt, Wyeth W. Wasserman
Software Mentions: 3
Published: over 12 years ago

10.1093/jxb/eraa264

The chromatin-modifying protein HUB2 is involved in the regulation of lignin composition in xylem vessels
Cited by: 4
Author(s): Bo Zhang, Bernadette Sztojka, Carolin Seyfferth, Sacha Escamez, Pál Miskolczi, Maxime Chantreau, L. Bako, Nicolas Delhomme, András Gorzsás, Rishikesh P. Bhalerao, Hannele Tuominen
Software Mentions: 3
Published: over 6 years ago

10.1155/2018/2837328

Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt
Cited by: 15
Author(s): Sally Ali Tawfik, Marwa Azab, Ali Abdellah Abdelrahman Ahmed, Dalia Mukhtar Fayyad
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13287-019-1209-x

Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature
Cited by: 76
Author(s): Lucas‐Sebastian Spitzhorn, Matthias Megges, Wasco Wruck, Shaifur Rahman, Jörg Otte, Özer Degistirici, Roland Meisel, Rüdiger V. Sorg, Richard O.C. Oreffo, James Adjaye
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/8831331

Differential Expression and PAH Degradation: What <i>Burkholderia vietnamiensi</i>s G4 Can Tell Us?
Cited by: 7
Author(s): Guilherme Pinto Cauduro, Ana Lusia Leal, Tiago Falcón Lopes, Marcela Marmitt, Victor Hugo Valiati
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-017-1251-x

Dynamic DNA methylation reconfiguration during seed development and germination
Cited by: 187
Author(s): Taiji Kawakatsu, Joseph R. Nery, Rosa Castanon, Joseph R. Ecker
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0171078

Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia
Cited by: 16
Author(s): Hannu Hotti, Peddinti Gopalacharyulu, Tuulikki Seppänen‐Laakso, Heiko Rischer
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-017-3663-0

Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs
Cited by: 22
Author(s): Dominik Terfehr, Tim A. Dahlmann, Ulrich Kück
Software Mentions: 3
Published: over 9 years ago

10.3390/nu10101492

Digestive Responses to Fortified Cow or Goat Dairy Drinks: A Randomised Controlled Trial
Cited by: 12
Author(s): Amber M. Milan, Alison J. Hodgkinson, Sarah M. Mitchell, Utpal Kumar Prodhan, Colin G. Prosser, Elizabeth Carpenter, Karl Fraser, David Cameron‐Smith
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-96331-6

Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina
Cited by: 1
Author(s): Rocío Pérez‐Portela, Álex García-Cisneros, Marta Campos-Canet, Creu Palacín
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers11081157

A Novel Type of Blood Biomarker: Distinct Changes of Cytokine-Induced STAT Phosphorylation in Blood T Cells Between Colorectal Cancer Patients and Healthy Individuals
Cited by: 14
Author(s): Jae Won Yun, Sejoon Lee, Hye Mi Kim, Sejong Chun, Edgar G. Engleman, Hee Cheol Kim, Eun Suk Kang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-021-07683-2

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
Cited by: 11
Author(s): Aliki Xanthopoulou, Javier Montero‐Pau, Belén Picó, Panagiotis Boumpas, Eleni Tsaliki, Harry S. Paris, Athanasios Tsaftaris, Apostolos Kalivas, Ιfigeneia Mellidou, Ioannis Ganopoulos
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00075-16

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization
Cited by: 27
Author(s): Mengxin Zhao, Bo Sun, Linwei Wu, Qun Gao, Wang Feng, Chongqing Wen, Mengmeng Wang, Yuting Liang, Lauren Hale, Jizhong Zhou, Yunfeng Yang
Software Mentions: 3
Published: about 10 years ago

10.1186/s40594-021-00306-y

Am I getting through? Surveying students on what messages they recall from the first day of STEM classes
Cited by: 6
Author(s): Clara L. Meaders, Lillian G. Senn, Brian A. Couch, A. Kelly Lane, Marilyne Stains, MacKenzie R. Stetzer, Erin Vinson, Michelle K. Smith
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-6570-8

MicroRNA expression profile analysis in sperm reveals hsa-mir-191 as an auspicious omen of in vitro fertilization
Cited by: 37
Author(s): Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiang-Dong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang, Xiaoxi Sun
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0032080

Knockdown of SF-1 and RNF31 Affects Components of Steroidogenesis, TGFβ, and Wnt/β-catenin Signaling in Adrenocortical Carcinoma Cells
Cited by: 20
Author(s): Anna Ehrlund, Philip Jonsson, Lise Lotte Vedin, Cecilia Williams, Jan Åke Gustafsson, Eckardt Treuter
Software Mentions: 3
Published: over 14 years ago

10.1093/gbe/evv144

Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition
Cited by: 27
Author(s): John A. Burns, Amber Paasch, Apurva Narechania, Eun-Soo Kim
Software Mentions: 3
Published: over 11 years ago

10.3390/cancers13102499

Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma
Cited by: 3
Author(s): Lisanne Noordam, Zhouhong Ge, Hadiye Özturk, Michail Doukas, Shanta Mancham, Patrick P.C. Boor, Lucia Campos Carrascosa, Guoying Zhou, Thierry van den Bosch, Qiuwei Pan, Jan N.M. IJzermans, Marco J. Bruno, Dave Sprengers, Jaap Kwekkeboom
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13030550

Extracellular miRNAs as Predictive Biomarkers for Glypican-3-Derived Peptide Vaccine Therapy Response in Ovarian Clear Cell Carcinoma
Cited by: 6
Author(s): Makoto Ukai, Akira Yokoi, Kosuke Yoshida, Shiro Suzuki, Kiyosumi Shibata, Fumitaka Kikkawa, Tetsuya Nakatsura, Hiroaki Kajiyama
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.203451

Intravascular emboli relates to immunosuppressive tumor microenvironment and predicts prognosis in stage III colorectal cancer
Cited by: 1
Author(s): Xiangping Song, Di Xie, Fengbo Tan, Yuan Zhou, Yuqiang Li, Zhongyi Zhou, Qian Pei, Haiping Pei
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0161967

CYR61 and TAZ Upregulation and Focal Epithelial to Mesenchymal Transition May Be Early Predictors of Barrett’s Esophagus Malignant Progression
Cited by: 6
Author(s): Joana Cardoso, Marta Mesquita, António Dias Pereira, Mónica Bettencourt-Dias, Paula Chaves, José B. Pereira-Leal
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2229-13-14

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem
Cited by: 34
Author(s): Hardy Hall, Brian E. Ellis
Software Mentions: 3
Published: almost 14 years ago

10.1186/s13073-019-0694-y

A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation
Cited by: 41
Author(s): Hannah Demond, Zahra Anvar, Bahia Namavar Jahromi, Ángela Sparago, Ankit Verma, Maryam Davari, Luciano Calzari, Silvia Russo, Mojgan Akbarzadeh‐Jahromi, David Gabriel Monk, Simon Andrews, Andrea Riccio, Gavin Kelsey
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0131292

An Insight into the Sialome of the Lone Star Tick, Amblyomma americanum, with a Glimpse on Its Time Dependent Gene Expression
Cited by: 95
Author(s): Shahid Karim, José M. C. Ribeiro
Software Mentions: 3
Published: over 11 years ago

10.18632/aging.101102

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells
Cited by: 15
Author(s): Ivan Petrov, Maria Suntsova, Olga Mutorova, Maxim Sorokin, Andrew Garazha, Elena Tarasovna Ilnitskaya, Pavel Spirin, Sergey Larin, Olga Kovalchuk, Vladimir Prassolov, Alex Zhavoronkov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0254541

Transcriptome profiling in susceptible and tolerant rubber tree clones in response to cassiicolin Cas1, a necrotrophic effector from Corynespora cassiicola
Cited by: 5
Author(s): Sébastien Ribeiro, Philippe Label, Dominique García, Pascal Montoro, Valérie Pujade-Renaud
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0117439

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae)
Cited by: 65
Author(s): Matteo Montagna, Bessem Chouaia, Giuseppe Mazza, Erica M. Prosdocimi, Elena Crotti, Valeria Mereghetti, Violetta Vacchini, Annamaria Giorgi, Alessio De Biase, S. Longo, Rita Cervo, G.C. Lozzia, Alberto Alma, Claudio Bandi, Daniele Daffonchio
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0082319

Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations
Cited by: 21
Author(s): Kirsten Ellegaard, Lisa Klasson, Siv G. E. Andersson
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0172521

Chronically dysregulated NOTCH1 interactome in the dentate gyrus after traumatic brain injury
Cited by: 16
Author(s): Noora Puhakka, Anna Bot, Niina Vuokila, Konrad J. Dębski, Katarzyna Łukasiuk, Asla Pitkänen
Software Mentions: 3
Published: over 9 years ago

10.3390/cancers13020298

Soluble and Exosome-Bound α-Galactosylceramide Mediate Preferential Proliferation of Educated NK Cells with Increased Anti-Tumor Capacity
Cited by: 3
Author(s): Arnika K. Wagner, Ulf Gehrmann, Stefanie Hiltbrunner, Valentina Carannante, Thuy T. Luu, Tanja I. Näslund, Hanna Brauner, Nadir Kadri, Klas Kärre, Susanne Gabrielsson
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0173106

Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model
Cited by: 3
Author(s): Sergey Malchenko, Simone Treiger Sredni, Yingtao Bi, Naira V. Margaryan, Jerusha Boyineni, Indra Mohanam, Tadanori Tomita, Ramana V. Davuluri, Marcelo B. Soares
Software Mentions: 3
Published: over 9 years ago

10.3390/molecules23102622

Monitoring Protein Dynamics in Protein O-Mannosyltransferase Mutants In Vivo by Tandem Fluorescent Protein Timers
Cited by: 9
Author(s): Joan Castells-Ballester, Ewa Zatorska, Matthias Meurer, Patrick Neubert, Anke Metschies, Michael Knop, Sabine Strahl
Software Mentions: 3
Published: about 8 years ago

10.1186/s13099-020-00351-y

Gut microbiome of native Arab Kuwaitis
Cited by: 6
Author(s): Erica L Plummer, Dieter Bulach, Glen P. Carter, M. John Albert
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-017-1575-2

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface
Cited by: 16
Author(s): Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D. Lange, Kathrin Kalies, Steffen Möller
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1004740

Characterization of CD8+ T Cell Differentiation following SIVΔnef Vaccination by Transcription Factor Expression Profiling
Cited by: 14
Author(s): James M. Billingsley, Premeela A. Rajakumar, Michelle Connole, Nadine C. Salisch, Sama Adnan, Yury V. Kuzmichev, Henoch S. Hong, R. Keith Reeves, Hyung-Joo Kang, Wenjun Li, Qingsheng Li, Ashley T. Haase, R. Paul Johnson
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0169805

Novel Analysis of Immune Cells from Nasal Microbiopsy Demonstrates Reliable, Reproducible Data for Immune Populations, and Superior Cytokine Detection Compared to Nasal Wash
Cited by: 47
Author(s): Simon P. Jochems, Katherine Piddock, Jamie Rylance, Hugh Adler, Beatriz F. Carniel, Andrea Collins, Jenna F. Gritzfeld, Carole A. Hancock, Helen Hill, Jesús Reiné, Alexandra L. Seddon, Carla Solórzano, Syba Sunny, A Zachary Trimble, A. Wright, Seher Zaidi, Stephen B. Gordon, Daniela M. Ferreira
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12870-020-02384-6

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Cited by: 13
Author(s): Beáta Strejčková, Radim Čegan, Aleš Pečinka, Zbyněk Milec, Jan Šafář
Software Mentions: 3
Published: about 6 years ago

10.1186/s12870-018-1373-7

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance
Cited by: 24
Author(s): Ana Paula Zotta Mota, Bruna Vidigal, Étienne Danchin, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, David J. Bertioli, Ana Cláudia Guerra Araújo, Ana Cristina Miranda Brasileiro, P. M. Guimarães
Software Mentions: 3
Published: over 8 years ago

10.1186/s12964-019-0332-8

Low levels of pyruvate induced by a positive feedback loop protects cholangiocarcinoma cells from apoptosis
Cited by: 12
Author(s): Mingming Zhang, Yida Pan, Dehua Tang, Robert Dorfman, Lei Xu, Qian Zhou, Lixing Zhou, Yuming Wang, Li Yang, Yuyao Yin, Bo Kong, Helmut Frieß, Shimin Zhao, Jian‐Lin Wu, Lei Wang, Xiaoping Zou
Software Mentions: 3
Published: over 7 years ago

10.1002/iid3.246

Flow Plex —A tool for unbiased comprehensive flow cytometry data analysis
Cited by: 0
Author(s): Johannes Nowatzky, Ezra Resnick, Julia Manasson, Cristy Stagnar, Arshed Al-Obeidi, Olivier Manches
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-020-01677-0

Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus
Cited by: 25
Author(s): Hans Kristian Mattila, Mari Mäkinen, Taina Lundell
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008212

Longevity is determined by ETS transcription factors in multiple tissues and diverse species
Cited by: 21
Author(s): A. Dobson, Richard Boulton-McDonald, Lara Houchou, Tatiana Svermova, Zhijian Ren, Jeremie Subrini, Mireya Vazquez-Prada, Mimoza Hoti, María Rodríguez López, Rita Ibrahim, Afroditi Gregoriou, Alexis Gkantiragas, Jürg Bähler, Marina Ezcurra, Nazif Alic
Software Mentions: 3
Published: over 7 years ago

10.1016/j.molcel.2017.01.030

Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways
Cited by: 33
Author(s): Jérôme Jullien, Munender Vodnala, Vincent Pasque, Mami Oikawa, Kazuaki Miyamoto, George E. Allen, Sarah-Anne David, Vincent Brochard, Stan Wang, Charles R. Bradshaw, Haruhiko Koseki, Vittorio Sartorelli, Nathalie Beaujean, J. B. Gurdon
Software Mentions: 3
Published: over 9 years ago

10.1186/s13024-021-00482-z

The TGFβ/Notch axis facilitates Müller cell-to-epithelial transition to ultimately form a chronic glial scar
Cited by: 15
Author(s): Federica Maria Conedera, Ana Maria Quintela Pousa, Nadia Mercader, Markus Tschopp, Volker Enzmann
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-06778-6

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen
Cited by: 18
Author(s): Andreína I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvécio Della Coletta-Filho, Rodrigo P. P. Almeida
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0148771

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis
Cited by: 41
Author(s): Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean May, Festo Massawe, Sean Mayes, Jamie Twycross
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12943-020-01301-7

Targeting CDK7 suppresses super enhancer-linked inflammatory genes and alleviates CAR T cell-induced cytokine release syndrome
Cited by: 12
Author(s): Wei Ye, Chong Li, Huifang Bian, Wei Qian, Kaizhou Jin, Tianmin Xu, Xiaomao Guo, Lu Xia, Fengtao Su
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-3203-3

Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology
Cited by: 33
Author(s): Robert Jackson, Bruce A. Rosa, Sonia Lameiras, Sean Cuninghame, Josee Bernard, Wely B. Floriano, Paul F. Lambert, Alain Nicolas, Ingeborg Zehbe
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3237-6

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe
Cited by: 64
Author(s): Yuriko Harigaya, Roy Parker
Software Mentions: 3
Published: about 10 years ago

10.1093/infdis/jiu615

Gene Expression and Cytokine Profile Correlate With Mycobacterial Growth in a Human BCG Challenge Model
Cited by: 29
Author(s): Magali Matsumiya, Iman Satti, Agnieszka Chomka, Stephanie A. Harris, Lisa Stockdale, Joel N. Meyer, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: about 12 years ago

10.1172/jci.insight.97018

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site
Cited by: 16
Author(s): Hao Cheng, Sebastian K. Grimm, M.S.A. Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, G. Donofrio, Gunilla B. Karlsson Hedestam, Mattia Bonsignori, Barton F. Haynes, Timothy Lahey, Isaac Maro, C. Fordham von Reyn, Miroslaw K. Gorny, Susan Zolla‐Pazner, Bruce D. Walker, Galit Alter, Dennis R. Burton, Merlin L. Robb, Shelly J. Krebs, Michael S. Seaman, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 3
Published: over 8 years ago

10.3390/nu9030233

Integration of Traditional and Metabolomics Biomarkers Identifies Prognostic Metabolites for Predicting Responsiveness to Nutritional Intervention against Oxidative Stress and Inflammation
Cited by: 15
Author(s): You Jin Kim, Iksoo Huh, Ji Yeon Kim, Saejong Park, Sung Ha Ryu, Kyu Bong Kim, Suhkmann Kim, Taesung Park, Oran Kwon
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0054379

Characterization of the Vaginal Micro- and Mycobiome in Asymptomatic Reproductive-Age Estonian Women
Cited by: 199
Author(s): Tiina Drell, Triin Lillsaar, Lea Tummeleht, Jaak Simm, Anu Aaspõllu, Edda Väin, Ivo Saarma, Andres Salumets, Gilbert Donders, Madis Metsis
Software Mentions: 3
Published: almost 14 years ago

10.1186/s13024-018-0280-6

The Trem2 R47H Alzheimer’s risk variant impairs splicing and reduces Trem2 mRNA and protein in mice but not in humans
Cited by: 83
Author(s): Xianyuan Xiang, Thomas M. Piers, Benedikt Wefers, Kaichuan Zhu, Anna Mallach, Bettina Brunner, Gernot Kleinberger, Wilbur M. Song, Marco Colonna, Jochen Herms, Wolfgang Wurst, Jennifer M. Pocock, Christian Haass
Software Mentions: 3
Published: about 8 years ago

10.26508/lsa.201800205

Innate extracellular vesicles from melanoma patients suppress β-catenin in tumor cells by miRNA-34a
Cited by: 22
Author(s): Jung-Hyun Lee, Jochen Dindorf, Martin Eberhardt, Xin Lai, Christian Ostalecki, Nina Koliha, Stefani Gross, Katja Blume, Heiko Bruns, Stefan Wild, Gerold Schuler, Julio Vera, Andreas S. Baur
Software Mentions: 3
Published: over 7 years ago

10.1038/s41419-018-0671-1

Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells
Cited by: 30
Author(s): Sofia B. Winge, Marlene Danner Dalgaard, Kirstine Belling, James C. Jensen, John Nielsen, Lise Aksglæde, Mikkel Heide Schierup, Søren Brunak, Niels E. Skakkebæk, Anders Juul, Ewa Rajpert‐De Meyts, Kristian Almstrup
Software Mentions: 3
Published: over 8 years ago

10.1038/cddis.2017.426

Common microRNA–mRNA interactions exist among distinct porcine iPSC lines independent of their metastable pluripotent states
Cited by: 8
Author(s): Shiqiang Zhang, Youlong Xie, Hongxia Cao, Huayan Wang
Software Mentions: 3
Published: about 9 years ago

10.1155/2019/7376034

Identification of Potential Biomarkers and Survival Analysis for Head and Neck Squamous Cell Carcinoma Using Bioinformatics Strategy: A Study Based on TCGA and GEO Datasets
Cited by: 37
Author(s): Yujie Shen, Jinhui Liu, Liqing Zhang, Shikun Dong, Jiacheng Zhang, Yaqin Liu, Han Zhou, Wei Dong
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: over 11 years ago

10.1186/s13068-014-0171-1

System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation
Cited by: 83
Author(s): Luís Valledor, Takeshi Furuhashi, Luis Recuenco-Muñoz, Stefanie Wienkoop, Wolfram Weckwerth
Software Mentions: 3
Published: almost 12 years ago

10.1016/j.jbc.2021.100285

Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice
Cited by: 4
Author(s): Katarína Lopušná, Paweł Nowialis, Jana Opavska, Ajay Abraham, Alberto Riva, Staci L. Haney, René Opavský
Software Mentions: 3
Published: almost 6 years ago

10.1002/jcsm.12099

Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness
Cited by: 48
Author(s): Roland W. J. Hangelbroek, Parastoo Fazelzadeh, Michael Tieland, Mark V. Boekschoten, Guido Hooiveld, John van Duynhoven, James A. Timmons, Lex B. Verdijk, Lisette C. P. G. M. de Groot, Luc J. C. van Loon, Michael Müller
Software Mentions: 3
Published: almost 11 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: about 9 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: about 7 years ago

10.7150/jca.30336

Prognostic Value of Survival of MicroRNAs Signatures in Non-small Cell Lung Cancer
Cited by: 20
Author(s): Bin Chen, Tianshun Gao, Weiwei Yuan, Weihong Zhao, Tza‐Huei Wang, Jianqing Wu
Software Mentions: 3
Published: almost 8 years ago

10.7150/jca.31287

Comprehensive investigation of key biomarkers and pathways in hepatitis B virus-related hepatocellular carcinoma
Cited by: 9
Author(s): Xiwen Liao, Tingdong Yu, Chengkun Yang, Ketuan Huang, Xiangkun Wang, Chuangye Han, Rui Huang, Xiaoguang Liu, Yu Liu, Guangzhi Zhu, Hao Su, Wei Qin, Deng Jun, Xianmin Zeng, Bowen Han, Quanfa Han, Zheng-Qian Liu, Xin Zhou, Junqi Liu, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Lei Lü, Xinping Ye, Tao Peng
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41419-019-1570-9

BRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition
Cited by: 30
Author(s): Nunzio Del Gaudio, Antonella Di Costanzo, Ning Qing Liu, Lidio Conte, Antimo Migliaccio, Michiel Vermeulen, Joost H.A. Martens, Hendrik G. Stunnenberg, Angela Nebbioso, Lucia Altucci
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0118201

A Combined Gene Signature of Hypoxia and Notch Pathway in Human Glioblastoma and Its Prognostic Relevance
Cited by: 45
Author(s): Khushboo Irshad, Saroj Kant Mohapatra, Chitrangda Srivastava, Harshit Garg, Seema Mishra, Bhawana Dikshit, Chitra Sarkar, Deepak Gupta, P. Sarat Chandra, Parthaprasad Chattopadhyay, Subrata Sinha, Kunzang Chosdol
Software Mentions: 3
Published: over 11 years ago

10.1111/jcmm.14664

The non‐coding RNome after splenectomy
Cited by: 12
Author(s): Mihnea P. Dragomir, Ștefan Tudor, Kan Okubo, Masayoshi Shimizu, Meng Chen, Dana Elena Giza, Weixiang He, Cristina Ivan, C Vasilescu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0217431

Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary
Cited by: 27
Author(s): Dongmei Wu, Qiu-Ping Dai, Xuezhu Liu, Yingping Fan, Jianxin Wang
Software Mentions: 3
Published: over 7 years ago

10.1242/bio.014308

Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
Cited by: 40
Author(s): Catriona Manville, Kayleigh A. Smith, Zbysław Sońdka, Holly Ashlene Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham Jackson, Caroline A. Austin
Software Mentions: 3
Published: about 11 years ago

10.1186/s13321-018-0257-z

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking
Cited by: 5
Author(s): George Van Den Driessche, Denis Fourches
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1005748

Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
Cited by: 91
Author(s): Jesse R. Raab, Samuel Resnick, Terry Magnuson
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0233380

Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing
Cited by: 11
Author(s): Akihiro Sakai, Mizuo Ando, Takahito Fukusumi, Shuling Ren, Chao Liu, Jesse R. Qualliotine, Sunny Haft, Sayed Sadat, Yuki Saito, Theresa Guo, Guiyin Xu, Roman Šášik, Kathleen M. Fisch, J. Silvio Gutkind, Elana J. Fertig, Alfredo A. Molinolo, Joseph A. Califano
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0109710

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease
Cited by: 74
Author(s): HeeKuk Park, Jong Wook Shin, Sang-Gue Park, Wonyong Kim
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0118424

Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach
Cited by: 38
Author(s): Katharina Debowski, Rita Warthemann, Jana Lentes, Gabriela Salinas-Riester, Ralf Dressel, Daniel Langenstroth, Jörg Gromoll, Erika Sasaki, Rüdiger Behr
Software Mentions: 3
Published: over 11 years ago

10.1007/s00359-018-1252-6

Candidate genes for cooperation and aggression in the social wasp Polistes dominula
Cited by: 17
Author(s): Fabio Manfredini, Mark J. F. Brown, Amy L. Toth
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-9-37

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
Cited by: 38
Author(s): Rekin’s Janky, Jacques van Helden
Software Mentions: 3
Published: almost 19 years ago

10.1093/jxb/ert234

Nitrogen metabolism of two contrasting poplar species during acclimation to limiting nitrogen availability
Cited by: 172
Author(s): Jie Luo, Hong Li, Tong‐Xian Liu, Andrea Polle, Changhui Peng, Zhibin Luo
Software Mentions: 3
Published: about 13 years ago

10.1093/jxb/erv532

Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins
Cited by: 27
Author(s): Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding
Software Mentions: 3
Published: almost 11 years ago

10.1186/s11658-018-0090-4

Essential genes of the macrophage response to Staphylococcus aureus exposure
Cited by: 6
Author(s): Aixia Sun, Hongwei Zhang, Feng Pang, Guifen Niu, Jianzhong Chen, Fei Chen, Jian Zhang
Software Mentions: 3
Published: over 8 years ago

10.1093/jxb/erx391

Sugar metabolism reprogramming in a non-climacteric bud mutant of a climacteric plum fruit during development on the tree
Cited by: 36
Author(s): Macarena Farcuh, Bosheng Li, Rosa M. Rivero, Lyudmila Shlizerman, Avi Sadka, Eduardo Blumwald
Software Mentions: 3
Published: almost 9 years ago

10.1093/jxb/eraa123

Pre-akinete formation in Zygnema sp. from polar habitats is associated with metabolite re-arrangement
Cited by: 18
Author(s): Erwann Arc, Martina Pichrtová, Ilse Kranner, Andreas Holzinger
Software Mentions: 3
Published: over 6 years ago

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