bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0244065

A strategic expression method of miR-29b and its anti-fibrotic effect based on RNA-sequencing analysis
Cited by: 7
Author(s): Xiaoming Fan, Yingnyu Gao, Xiaolu Zhang, Haroon Y. Lughmani, David J. Kennedy, Steven T. Haller, Sandrine V. Pierre, Joseph I. Shapiro, Jiang Tian
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0181084

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure
Cited by: 6
Author(s): Julia Morud, Arghavan Ashouri, Erik Larsson, Mia Ericson, Bo Söderpalm
Software Mentions: 1
Published: about 8 years ago

10.3390/biom10010150

Identification of miRNAs Enriched in Extracellular Vesicles Derived from Serum Samples of Breast Cancer Patients
Cited by: 33
Author(s): Patrícia Midori Murobushi Ozawa, Evelyn Vieira, Débora S. Lemos, Ingrid L.M. Souza, Sı́lvio M. Zanata, Vânia C. S. Pankievicz, Thalita Regina Tuleski, Emanuel Maltempi de Souza, Pryscilla Fanini Wowk, Cı́cero de Andrade Urban, Fusakuni Kuroda, Rubens Silveira de Lima, Rodrigo Coutinho de Almeida, Daniela Fiori Gradia, Iglenir João Cavalli, Luciane R. Cavalli, Danielle Malheiros, Enilze M.S.F. Ribeiro
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21249754

Identification and Analysis of MicroRNAs Associated with Wing Polyphenism in the Brown Planthopper, Nilaparvata lugens
Cited by: 6
Author(s): Xu Le, Jiao Zhang, An-ran Zhan, Yaqin Wang, Xingzhou Ma, Wencai Jie, Zhenghong Cao, Mohamed A.A. Omar, Kang He, Fei Li
Software Mentions: 1
Published: over 4 years ago

10.1038/s41396-018-0077-1

Peatland Acidobacteria with a dissimilatory sulfur metabolism
Cited by: 121
Author(s): Bela Hausmann, Claus Pelikan, Craig W. Herbold, Stephan Köstlbacher, Mads Albertsen, Stephanie A. Eichorst, Tijana Glavina del Rio, Martin Huemer, Per Halkjær Nielsen, Thomas Rattei, Ulrich Stingl, Susannah G. Tringe, Daniela Trojan, Cécilia Wentrup, Dagmar Woebken, Michael Pester, Alexander Loy
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21249561

Abscisic Acid Inhibits Asymbiotic Germination of Immature Seeds of Paphiopedilum armeniacum
Cited by: 3
Author(s): Xin Xu, Lin Fang, Lin Li, Guohua Ma, Kunlin Wu, Songjun Zeng
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0235183

ZBTB38 is dispensable for antibody responses
Cited by: 4
Author(s): Rachel Wong, Deepta Bhattacharya
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0170999

Identification of MiR-21-5p as a Functional Regulator of Mesothelin Expression Using MicroRNA Capture Affinity Coupled with Next Generation Sequencing
Cited by: 20
Author(s): Chiara De Santi, Sebastian Vencken, Jonathon Blake, Bettina Haase, Vladimı́r Beneš, Federica Gemignani, Stefano Landi, Catherine M. Greene
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0252597

Wound healing with topical BRAF inhibitor therapy in a diabetic model suggests tissue regenerative effects
Cited by: 4
Author(s): Helena Escuin-Ordinas, Yining Liu, Lingyun Sun, Willy Hugo, Robert Dimatteo, Rong Huang, Paige Krystofinski, Ariel M. Azhdam, Jordan Lee, Begoña Comı́n-Anduix, Alistair J. Cochran, Roger S. Lo, Tatiana Segura, Philip O. Scumpia, Antoni Ribas
Software Mentions: 1
Published: about 4 years ago

10.1038/s41396-020-0715-2

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation
Cited by: 28
Author(s): Carolina Reyes, Logan H. Hodgskiss, Melina Kerou, Thomas Pribasnig, Sophie S. Abby, Barbara Bayer, Stephan M. Kraemer, Christa Schleper
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22010087

Transient Receptor Potential Ankyrin 1 (TRPA1) Is Involved in Upregulating Interleukin-6 Expression in Osteoarthritic Chondrocyte Models
Cited by: 20
Author(s): Elina Nummenmaa, Mari Hämäläinen, Antti Pemmari, Lauri J. Moilanen, Lauri Tuure, Riina Nieminen, Teemu Moilanen, Katriina Vuolteenaho, Eeva Moilanen
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0218220

Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq
Cited by: 10
Author(s): Cameron V. Sayer, Bidisha Barat, David L. Popham
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-4084-9

Transcriptome analysis reveals differences in mechanisms regulating cessation of luteal function in pregnant and non-pregnant dogs
Cited by: 18
Author(s): Sophie Zatta, Hubert Rehrauer, Aykut Gram, Alois Boos, Mariusz P. Kowalewski
Software Mentions: 1
Published: almost 8 years ago

10.3390/biom11091265

Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression
Cited by: 0
Author(s): Zihao Liu, Yu Shi, Qun Lin, Wenqian Yang, Qing Luo, Yinghuan Cen, Juanmei Li, Xiaolin Fang, Wen Guo Jiang, Chang Gong
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms22010393

OsPP2C09 Is a Bifunctional Regulator in Both ABA-Dependent and Independent Abiotic Stress Signaling Pathways
Cited by: 17
Author(s): Myung Ki Min, Rigyeong Kim, Woo‐Jong Hong, Ki‐Hong Jung, Jong-Yeol Lee, Beom-Gi Kim
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0216862

Inflammatory response of mesenchymal stromal cells after in vivo exposure with selected trauma-related factors and polytrauma serum
Cited by: 15
Author(s): Elisa Maria Amann, Alexander Groß, Markus Rojewski, Hans A. Kestler, Miriam Kalbitz, Rolf E. Brenner, Markus Huber‐Lang, Hubert Schrezenmeier
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0221288

Fanconi-BRCA pathway mutations in childhood T-cell acute lymphoblastic leukemia
Cited by: 14
Author(s): Gayle P. Pouliot, James Degar, Laura Hinze, Bose Kochupurakkal, Chau D. Vo, Melissa Burns, Lisa A. Moreau, Chirag Ganesa, Justine E. Roderick, Sofie Peirs, Björn Menten, Mignon L. Loh, Stephen P. Hunger, Lewis B. Silverman, Marian H. Harris, Kristen E. Stevenson, David M. Weinstock, Andrew P. Weng, Pieter Van Vlierberghe, Alan D. D’Andrea, Alejandro Gutiérrez
Software Mentions: 1
Published: over 5 years ago

10.3390/biom10040501

BET Inhibitors Synergize with Carfilzomib to Induce Cell Death in Cancer Cells via Impairing Nrf1 Transcriptional Activity and Exacerbating the Unfolded Protein Response
Cited by: 18
Author(s): Janakiram R. Vangala, Ajay Potluri, Senthil K. Radhakrishnan
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0189886

Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study
Cited by: 7
Author(s): Valborg Guðmundsdóttir, Helle Pedersen, Karla V. Allebrandt, Caroline Brorsson, Nienke van Leeuwen, Karina Banasik, Anubha Mahajan, Christopher J. Groves, Martijn van de Bunt, Adem Y. Dawed, Andreas Fritsche, Harald Staiger, Annemarie M. Simonis-Bik, Joris Deelen, Mark H. H. Kramer, A.J.J. Dietrich, Thomas Hübschle, Gonneke Willemsen, Hans‐Ulrich Häring, Eco J. C. de Geus, Dorret I. Boomsma, Elisabeth M. W. Eekhoff, Jorge Ferrer, Mark I. McCarthy, Ewan R. Pearson, Ramneek Gupta, Søren Brunak, Leen M ’t Hart
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22010079

Ordinary Gasoline Emissions Induce a Toxic Response in Bronchial Cells Grown at Air-Liquid Interface
Cited by: 7
Author(s): Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Michal Šíma, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka, Pavel Rőssner
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0214296

Limited differential expression of miRNAs and other small RNAs in LPS-stimulated human monocytes
Cited by: 9
Author(s): Daniel Lu, Tracy M. Yamawaki, Hong Zhou, Wen-Yu Chou, Mark Chhoa, Edwin Lamas, Sabine Escobar, Heather A. Arnett, Huanying Ge, Todd Juan, Songli Wang, Chi-Ming Li
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-020-0594-6

Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus
Cited by: 49
Author(s): Namil Lee, Woori Kim, Jinkyoo Chung, Yong Jae Lee, Suhyung Cho, Kyoung‐Soon Jang, Sun Chang Kim, Jaehyung Kim, Byung-Kwan Cho
Software Mentions: 1
Published: over 5 years ago

10.1038/s41396-020-00785-x

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease
Cited by: 164
Author(s): Sang Moo Lee, Hyun Gi Kong, Geun Cheol Song, Choong‐Min Ryu
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0143944

Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event
Cited by: 10
Author(s): Stephanie M. Rosales, Rebecca Vega Thurber
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0106795

The Expression Pattern of microRNAs in Granulosa Cells of Subordinate and Dominant Follicles during the Early Luteal Phase of the Bovine Estrous Cycle
Cited by: 73
Author(s): Dessie Salilew‐Wondim, Ijaz Ahmad, Samuel Gebremedhn, Sudeep Sahadevan, Munir Hossain, F. Rings, M. Hoelker, Ernst Tholen, Christiane Neuhoff, Christian Looft, K. Schellander, Dawit Tesfaye
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0212031

Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue
Cited by: 25
Author(s): Christy L. Trejo, Miloš Babić, Elliot Imler, Migdalia Gonzalez, Sergei I. Bibikov, Peter J. Shepard, Harper VanSteenhouse, Joanne M. Yeakley, Bruce Seligmann
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-020-00840-7

Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium
Cited by: 34
Author(s): Nunzia Picone, Arjan Pol, Rob Mesman, Maartje A. H. J. van Kessel, Geert Cremers, A.H. van Gelder, Theo A. van Alen, Mike S. M. Jetten, Sebastian Lücker, Huub J. M. Op den Camp
Software Mentions: 1
Published: over 4 years ago

10.1038/s41396-020-00811-y

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy
Cited by: 69
Author(s): Frank X. Ferrer‐González, Brittany Widner, Nicole R. Holderman, John Glushka, Arthur S. Edison, Elizabeth B. Kujawinski, Mary Ann Moran
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0146636

Genetic Signature of Resistance to White Band Disease in the Caribbean Staghorn Coral Acropora cervicornis
Cited by: 36
Author(s): Silvia Libro, Steven V. Vollmer
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5594-4

Differential expression profiling of ΔlitR and ΔrpoQ mutants reveals insight into QS regulation of motility, adhesion and biofilm formation in Aliivibrio salmonicida
Cited by: 12
Author(s): Miriam Khider, Erik Hjerde, Hilde Hansen, Nils Peder Willassen
Software Mentions: 1
Published: over 6 years ago

10.3390/biom9120823

Genome-Wide Analysis of Abscisic Acid Biosynthesis, Catabolism, and Signaling in Sorghum Bicolor under Saline-Alkali Stress
Cited by: 12
Author(s): Siqi Ma, Li-Yun Lin, Chen Meng, Chao Zhou, Jie Fu, Xiangling Shen, Chengsheng Zhang, Yiqiang Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41396-020-0707-2

Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails
Cited by: 16
Author(s): Corinna Breusing, Jessica Mitchell, Jennifer A. Delaney, Sean P. Sylva, Jeffrey S. Seewald, Peter R. Girguis, Roxanne A. Beinart
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0243178

Gene expression profiles of esophageal squamous cell cancers in Hodgkin lymphoma survivors versus sporadic cases
Cited by: 2
Author(s): Berbel L.M. Ykema, Sanne Hoefnagel, Lisanne S. Rigter, Liudmila L. Kodach, Gerrit A. Meijer, Flora E. van Leeuwen, Hina Khan, Pétur Snæbjörnsson, Berthe M.P. Aleman, Annegien Broeks, Sybren L. Meijer, Kenneth K. Wang, Beatriz Carvalho, Kausilia K. Krishnadath, Monique E. van Leerdam
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0094839

Profiles of Extracellular miRNA in Cerebrospinal Fluid and Serum from Patients with Alzheimer's and Parkinson's Diseases Correlate with Disease Status and Features of Pathology
Cited by: 300
Author(s): Kasandra Burgos, Ivana Malenica, Raghu Metpally, Amanda Courtright, Benjamin Rakela, Thomas G. Beach, Holly A. Shill, Charles H. Adler, Marwan N. Sabbagh, Stephen Villa, Waibhav Tembe, David W. Craig, Kendall Van Keuren‐Jensen
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0210064

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms
Cited by: 107
Author(s): Megan R. Sanctuary, Jennifer N. Kain, Shin-Yu Chen, Karen M. Kalanetra, Danielle G. Lemay, Destanie R. Rose, Houa Yang, Daniel J. Tancredi, J. Bruce German, Carolyn M. Slupsky, Paul Ashwood, David A. Mills, Jennifer T. Smilowitz, Kathleen Angkustsiri
Software Mentions: 1
Published: over 6 years ago

10.7150/ijbs.55873

The histone demethylase KDM2B regulates human primordial germ cell-like cells specification
Cited by: 4
Author(s): Weiyan Yuan, Zhaokai Yao, Veeramohan Veerapandian, Xinyan Yang, Xiaoman Wang, Dingyao Chen, Linzi Ma, Chaohui Li, Yi Zheng, Fang Luo, Xiaoyang Zhao
Software Mentions: 1
Published: over 4 years ago

10.7150/ijbs.58422

Long noncoding RNA SH3PXD2A-AS1 promotes colorectal cancer progression by regulating p53-mediated gene transcription
Cited by: 6
Author(s): Pingfu Hou, Tian Lin, Sen Meng, Meilin Shi, Fang Chen, Tao Jiang, Zhongwei Li, Minle Li, Sufang Chu, Junnian Zheng, Jing Bai
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0223274

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome
Cited by: 34
Author(s): Pablo Arroyo, Brian Ho, Lillian Sau, Scott T. Kelley, Varykina G. Thackray
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0256112

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms
Cited by: 8
Author(s): Anja Lührmann, Ksenia Ovadenko, Justinus Hellmich, Christoph Sudendey, Vitaly Belik, Jürgen Zentek, Wilfried Vahjen
Software Mentions: 1
Published: almost 4 years ago

10.7150/ijbs.58026

Deciphering the effects of PYCR1 on cell function and its associated mechanism in hepatocellular carcinoma
Cited by: 6
Author(s): Yijuan Xu, Wenpu Zuo, Xiao Wang, Qinle Zhang, Xiang Gan, Nguan Soon Tan, Wenxian Jia, Jiayi Liu, Zhouquan Li, Bo Zhou, Dong Zhao, Zhibin Xie, Yanjun Tan, Shu Zheng, Chengwu Liu, Hongtao Li, Zhijian Chen, Xiaoli Yang, Zhichuan Huang
Software Mentions: 1
Published: over 4 years ago

10.7150/ijbs.58657

Protopanaxadiol improves endometriosis associated infertility and miscarriage in sex hormones receptors-dependent and independent manners
Cited by: 11
Author(s): Zhen‐Zhen Lai, Hui‐Li Yang, Jing Shi, Hui‐Hui Shen, Yan Wang, Kai‐Kai Chang, Tao Zhang, Jiang‐Feng Ye, Jiansong Sun, Xue Qiu, Ming‐Qing Li
Software Mentions: 1
Published: over 4 years ago

10.1186/s13046-018-0897-x

Vitexin compound 1, a novel extraction from a Chinese herb, suppresses melanoma cell growth through DNA damage by increasing ROS levels
Cited by: 48
Author(s): Nian Liu, Kuan Song Wang, Min Qi, Ying Zhou, Guang Zeng, Juan Tao, Jiayi Zhou, Jiang Lin Zhang, Xiang Chen, Cong Peng
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0224429

Transcriptional foliar profile of the C3-CAM bromeliad Guzmania monostachia
Cited by: 7
Author(s): Helenice Mercier, Maria Aurineide Rodrigues, Sónia Cristina da Silva Andrade, Luiz Lehmann Coutinho, Bruno Nobuya Katayama Gobara, Alejandra Matiz, Paulo Tamaso Mioto, Ana Zangirólame Gonçalves
Software Mentions: 1
Published: over 5 years ago

10.1186/s13046-019-1032-3

PAGE4 promotes prostate cancer cells survive under oxidative stress through modulating MAPK/JNK/ERK pathway
Cited by: 18
Author(s): Chengcheng Lv, Shui Fu, Qingzhuo Dong, Zi Yu, Gejun Zhang, Chuize Kong, Cheng Fu, Yu Zeng
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0257417

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium
Cited by: 3
Author(s): Ningning Zhang, Zhanwei Teng, Pengtao Li, Tong Fu, Hongxia Lian, Linfeng Wang, Gao Teng-yun
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-015-1436-1

Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae
Cited by: 32
Author(s): Inna Biryukova, Tao Ye
Software Mentions: 1
Published: over 10 years ago

10.1186/s13046-019-1241-9

Minichromosome maintenance 3 promotes hepatocellular carcinoma radioresistance by activating the NF-κB pathway
Cited by: 29
Author(s): Qing Yang, Binhui Xie, Hui Tang, Meng Wang, Changchang Jia, Xiaomei Zhang, Yi Zhang, Jianwen Zhang, Heping Li, Binsheng Fu
Software Mentions: 1
Published: about 6 years ago

10.1186/s13046-019-1427-1

Impact of Docetaxel on blood-brain barrier function and formation of breast cancer brain metastases
Cited by: 9
Author(s): Simon Bernatz, Elena I. Ilina, Kavi Devraj, Patrick N. Harter, Klaus Mueller, Sascha Kleber, Yannick Braun, Cornelia Penski, Christoph Renner, Rashi Halder, Lukas Jennewein, Christine Solbach, Frits Thorsen, Bernhard Paulweber, Axel Mischo, Michel Mittelbronn
Software Mentions: 1
Published: over 5 years ago

10.3390/biom11010041

isomiRs–Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?
Cited by: 10
Author(s): Ilias Glogovitis, Galina Yahubyan, Thomas Würdinger, Danijela Koppers-Lalić, Vesselin Baev
Software Mentions: 1
Published: over 4 years ago

10.1186/s13046-020-01815-4

Impact of the acidic environment on gene expression and functional parameters of tumors in vitro and in vivo
Cited by: 13
Author(s): Mandy Rauschner, Luisa Lange, Thea Hüsing, Sarah Reime, Alexander Nolze, Marcel Maschek, Oliver Thews, Anne Riemann
Software Mentions: 1
Published: over 4 years ago

10.1186/s13046-021-01875-0

A preliminary study of micro-RNAs as minimally invasive biomarkers for the diagnosis of prostate cancer patients
Cited by: 16
Author(s): Simona Giglio, Cosimo De Nunzio, Roberto Cirombella, Antonella Stoppacciaro, Omar Faruq, Stefano Volinia, Gustavo Baldassarre, Andrea Tubaro, Hideshi Ishii, Carlo M. Croce, Andrea Vecchione
Software Mentions: 1
Published: over 4 years ago

10.1038/s41388-020-01495-6

SUV39H1 regulates the progression of MLL-AF9-induced acute myeloid leukemia
Cited by: 12
Author(s): Yajing Chu, Yangpeng Chen, Huibin Guo, Mengke Li, Bichen Wang, Deyang Shi, Xuelian Cheng, Jian Guan, Xiaomin Wang, Chenghai Xue, Tao Cheng, Jun Shi, Weiping Yuan
Software Mentions: 1
Published: almost 5 years ago

10.1523/ENEURO.0232-21.2021

Heterogeneous Expression of Nuclear Encoded Mitochondrial Genes Distinguishes Inhibitory and Excitatory Neurons
Cited by: 10
Author(s): Meghan E. Wynne, Alicia R. Lane, Kaela S. Singleton, Stephanie A. Zlatic, Avanti Gokhale, Erica Werner, Duc M. Duong, Jennifer Q. Kwong, Amanda Crocker, Víctor Faúndez
Software Mentions: 1
Published: about 4 years ago

10.1038/s41388-021-01685-w

Cancer-associated fibroblast secretion of PDGFC promotes gastrointestinal stromal tumor growth and metastasis
Cited by: 21
Author(s): Hyunho Yoon, Chih Min Tang, Sudeep Banerjee, Mayra Yebra, Sangkyu Noh, Adam M. Burgoyne, Jorge de la Torre, Martina De Siena, Mengyuan Liu, Lillian R. Klug, Yoon Young Choi, Mojgan Hosseini, Antonio L. Delgado, Zhiyong Wang, Randall French, Andrew M. Lowy, Ronald P. DeMatteo, Michael C. Heinrich, Alfredo A. Molinolo, J. Silvio Gutkind, Olivier Harismendy, Jason K. Sicklick
Software Mentions: 1
Published: over 4 years ago

10.3390/biomedicines8040088

A Non-Coding RNA Landscape of Bronchial Epitheliums of Lung Cancer Patients
Cited by: 12
Author(s): Yanli Luo, V.K. Holden, Pushpawallie Dhilipkannah, Janaki Deepak, Nevins W. Todd, Feng Jiang
Software Mentions: 1
Published: over 5 years ago

10.1523/ENEURO.0208-17.2017

Genetic Pathways of Neuroregeneration in a Novel Mild Traumatic Brain Injury Model in Adult Zebrafish
Cited by: 25
Author(s): Amanda L. Maheras, Brian Dix, Olivia M. S. Carmo, Aleena Young, Vanessa N. Gill, Julia Sun, Aleah R. Booker, Helen A. Thomason, Anastasia E. Ibrahim, Lauren Stanislaw, Jennifer C. Dallego, Cat N. Ngo, Audrey Chen, Barbara K. Fortini, Rory Spence
Software Mentions: 1
Published: over 7 years ago

10.3390/biomedicines8060147

Transcriptome-Wide Analysis of CXCR5 Deficient Retinal Pigment Epithelial (RPE) Cells Reveals Molecular Signatures of RPE Homeostasis
Cited by: 11
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Anthony Mukwaya, Huang Hu
Software Mentions: 1
Published: about 5 years ago

10.1038/s41388-021-01814-5

USP22 promotes HER2-driven mammary carcinoma aggressiveness by suppressing the unfolded protein response
Cited by: 20
Author(s): Evangelos Prokakis, Anna Dyas, Regina Grün, Sonja Fritzsche, Upasana Bedi, Zahra Basir Kazerouni, Robyn Laura Kosinsky, Steven A. Johnsen, Florian Wegwitz
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0234837

A tale of two fish: Comparative transcriptomics of resistant and susceptible steelhead following exposure to Ceratonova shasta highlights differences in parasite recognition
Cited by: 15
Author(s): Damien Barrett, Jerri L. Bartholomew
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0223177

Transcriptome analysis of PK-15 cells in innate immune response to porcine deltacoronavirus infection
Cited by: 18
Author(s): Shan Jiang, Fuqiang Li, Xiuli Li, Lili Wang, Li Zhang, Chao Lu, Zheng Li, Yan Mi
Software Mentions: 1
Published: almost 6 years ago

10.3390/nu11102310

Loss of Diurnal Oscillatory Rhythms in Gut Microbiota Correlates with Changes in Circulating Metabolites in Type 2 Diabetic db/db Mice
Cited by: 35
Author(s): Eleni Beli, Samantha Prabakaran, Preethi Krishnan, Carmella Evans‐Molina, Maria B. Grant
Software Mentions: 1
Published: almost 6 years ago

10.3390/biomedicines9080949

Evaluation of β-Catenin Inhibition of Axitinib and Nitazoxanide in Human Monocyte-Derived Dendritic Cells
Cited by: 1
Author(s): Waqas Azeem, Ragnhild Maukon Bakke, Benjamin Gabriel, Silke Appel, Anne Margrete Øyan, Karl‐Henning Kalland
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms22031390

Novel Identified Circular Transcript of RCAN2, circ-RCAN2, Shows Deviated Expression Pattern in Pig Reperfused Infarcted Myocardium and Hypoxic Porcine Cardiac Progenitor Cells In Vitro
Cited by: 4
Author(s): Julia Mester-Tonczar, Patrick Einzinger, Johannes Winkler, Nina Kastner, Andreas Spannbauer, Katrin Zlabinger, Denise Traxler, Dominika Lukovic, Ena Hašimbegović, Georg Goliasch, Noémi Pávó, Mariann Gyöngyösi
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0137548

Neurotranscriptomics: The Effects of Neonatal Stimulus Deprivation on the Rat Pineal Transcriptome
Cited by: 28
Author(s): Stephen W. Hartley, Steven L. Coon, Luis Savastano, James C. Mullikin, Nisc Comparative Sequencing Program, Cong Fu, David C. Klein
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0205055

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density
Cited by: 10
Author(s): Wei Zheng, Kairui Wang, Yijun Sun, Shiu‐Ming Kuo
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0203160

Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug
Cited by: 24
Author(s): Courtney Davis-Vogel, Brandon Van Allen, John L. Van Hemert, Amit Sethi, Mark E. Nelson, Dipali G. Sashital
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0175041

Inositol 1, 4, 5-trisphosphate-dependent nuclear calcium signals regulate angiogenesis and cell motility in triple negative breast cancer
Cited by: 15
Author(s): Erika S. Guimarães, Rosângela Pinheiro Gonçalves Machado, Matheus de Castro Fonseca, Andressa França, Luciana Estefani Drumond de Carvalho, Ana Cândida Araújo e Silva, Brígida Gomes Almeida, Puebla Cassini, Bárbara Hissa, Luciana E. Drumond, Carlos Alberto Gonçalves, Gabriel R. Fernandes, Marina De Brot, Márcio Flávio Dutra Moraes, Lucíola da Silva Barcelos, José Miguel Ortega, André G. Oliveira, M. Fátima Leite
Software Mentions: 1
Published: over 8 years ago

10.3390/biomedicines9070719

miR-208b Reduces the Expression of Kcnj5 in a Cardiomyocyte Cell Line
Cited by: 4
Author(s): Julia Hupfeld, Maximilian Ernst, Maria Knyrim, Stephanie Binas, Udo Kloeckner, Sindy Rabe, Katja Quarch, Danny Misiak, Matthew Fuszard, Claudia Großmann, Michael Gekle, Barbara Schreier
Software Mentions: 1
Published: about 4 years ago

10.3390/biomedicines8110450

Modulation of Small RNA Signatures in Schwann-Cell-Derived Extracellular Vesicles by the p75 Neurotrophin Receptor and Sortilin
Cited by: 12
Author(s): Nádia Pereira Gonçalves, Yan Yan, Maj Ulrichsen, Morten T. Venø, Ebbe Toftgaard Poulsen, Jan J. Enghild, Jørgen Kjems, Christian Bjerggaard Vægter
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0202351

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus)
Cited by: 18
Author(s): Eyal Hallali, Fotini Kokou, T.K. Chourasia, Tali Nitzan, Pazit Con, Sheenan Harpaz, Itzhak Mizrahi, Avner Cnaani
Software Mentions: 1
Published: almost 7 years ago

10.1002/JLB.5HI0119-018R

Frontline Science: Endotoxin-induced immunotolerance is associated with loss of monocyte metabolic plasticity and reduction of oxidative burst
Cited by: 35
Author(s): Inge Grondman, Rob J. W. Arts, Rebecca M. Koch, Guus P Leijte, Jelle Gerretsen, Niklas Bruse, Rosalie W.M. Kempkes, Rob ter Horst, Matthijs Kox, Peter Pickkers, Mihai G. Netea, Mark S. Gresnigt
Software Mentions: 1
Published: about 6 years ago

10.1194/jlr.RA120000888

Angiopoietin-like protein 3 governs LDL-cholesterol levels through endothelial lipase-dependent VLDL clearance
Cited by: 104
Author(s): René Adam, Ivory J. Mintah, Corey A. Alexa-Braun, Lisa M. Shihanian, Joseph S. Lee, Poulabi Banerjee, Sara Hamon, Hye In Kim, Jonathan C. Cohen, Helen H. Hobbs, Cristopher V. Van Hout, Jesper Gromada, Andrew Murphy, George D. Yancopouloš, Mark W. Sleeman, Viktoria Gusarova
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0208344

De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing
Cited by: 9
Author(s): Sang-Ho Kang, Jong-Yeol Lee, Tae‐Ho Lee, Soo-Yun Park, Chang-Kug Kim
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-021-00957-4

Robust biomarker discovery for hepatocellular carcinoma from high-throughput data by multiple feature selection methods
Cited by: 13
Author(s): Zishuang Zhang, Zhi-Ping Liu
Software Mentions: 1
Published: almost 4 years ago

10.1194/jlr.RA119000446

Liver-specific ceramide reduction alleviates steatosis and insulin resistance in alcohol-fed mice
Cited by: 18
Author(s): Jason Correnti, Chun-Yao Lin, Jascha Brettschneider, Amy Kuriakose, Sookyoung Jeon, Eleonora Scorletti, Amanke Oranu, Dru McIver-Jenkins, Isabelle Kaneza, Delfin Buyco, Yedidya Saiman, Emma E. Furth, Josepmaría Argemi, Ramón Bataller, William L. Holland, Rotonya M. Carr
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-018-5125-8

Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors
Cited by: 13
Author(s): Ajay Kumar Mishra, G Duraisamy, Manish Khare, Tomáš Kocábek, Jernej Jakše, J. Břı́za, Josef Patzak, Teruo Shimmen, J. Matoušek
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0157828

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data
Cited by: 8
Author(s): Gregory R. Smith, Marc R. Birtwistle
Software Mentions: 1
Published: about 9 years ago

10.1021/acs.jmedchem.1c00644

Structural Fine-Tuning of Desmuramylpeptide NOD2 Agonists Defines Their <i>In Vivo</i> Adjuvant Activity
Cited by: 11
Author(s): Samo Guzelj, Sanja Nabergoj, Martina Gobec, Stane Pajk, Veronika Klančič, Bram Slütter, Ruža Frkanec, Adela Štimac, Primož Šket, Janez Plavec, Irena Mlinarič-Raščan, Žiga Jakopin
Software Mentions: 1
Published: about 4 years ago

10.1186/s12920-018-0469-0

Regulatory network analysis reveals the oncogenesis roles of feed-forward loops and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 6
Author(s): Mengxuan Xia, Qiong Zhang, Mei Luo, Pan Li, Yingxue Wang, Qian Lei, An‐Yuan Guo
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0181101

The nature of the GRE influences the screening for GR-activity enhancing modulators
Cited by: 8
Author(s): Karen Dendoncker, Steven Timmermans, Kelly Van Looveren, Lode De Cauwer, Karolien De Bosscher, Claude Libert
Software Mentions: 1
Published: about 8 years ago

10.1093/jmcb/mjy066

The HDAC3 enzymatic activity regulates skeletal muscle fuel metabolism
Cited by: 31
Author(s): Shuangxi Song, Yu Wen, Hui Tong, Emanuele Loro, Yingyun Gong, Jidong Liu, Sungguan Hong, Lei Li, Tejvir S. Khurana, Maoping Chu, Zheng Sun
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0240939

Transcriptomic analysis of seed germination improvement of Andrographis paniculata responding to air plasma treatment
Cited by: 4
Author(s): Jiayun Tong, Rui He, Xiaoting Tang, Mingzhi Li, Jie Wan
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0213872

Alterations of the MEK/ERK, BMP, and Wnt/β-catenin pathways detected in the blood of individuals with lymphatic malformations
Cited by: 8
Author(s): Tae-Han Kim, E. Tafoya, Malcolm P. Chelliah, Ramrada Lekwuttikarn, Li Jiang, Kavita Y. Sarin, Joyce Teng
Software Mentions: 1
Published: over 6 years ago

10.1093/jmcb/mjy065

Metabolic regulation of T cell development by Sin1–mTORC2 is mediated by pyruvate kinase M2
Cited by: 22
Author(s): Xue Ouyang, Yijie Han, Guojun Qu, Man Li, Ningbo Wu, Hongzhi Liu, Omotooke Arojo, Haixiang Sun, Xiaobo Liu, Dou Liu, Lei Chen, Qiang Zou, Bing Su
Software Mentions: 1
Published: over 6 years ago

10.1016/j.yjmcc.2019.11.157

Angiotensin peptide synthesis and cyclic nucleotide modulation in sympathetic stellate ganglia
Cited by: 6
Author(s): Emma N. Bardsley, Oliver C. Neely, David J. Paterson
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0244364

Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective
Cited by: 2
Author(s): Nourolah Soltani, Margaret Staton, Kimberly D. Gwinn
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms22041670

C1q/TNF-Related Protein 3 (CTRP-3) Deficiency of Adipocytes Affects White Adipose Tissue Mass but Not Systemic CTRP-3 Concentrations
Cited by: 5
Author(s): Andreas Schmid, M Roderfeld, Jonas Gehl, Elke Roeb, Andrea Nist, Ho‐Ryun Chung, Thorsten Stiewe, Thomas Karrasch, Andréas Schäffler
Software Mentions: 1
Published: over 4 years ago

10.1007/s00109-021-02089-9

LMO3 reprograms visceral adipocyte metabolism during obesity
Cited by: 3
Author(s): Gabriel Wagner, Anna Fenzl, Josefine Lindroos-Christensen, Elisa Einwallner, Julia Husa, Nadine Witzeneder, Sabine Rauscher, Marion Gröger, Sophia Derdak, Thomas Mohr, Hedwig Sutterlüty, Florian Klinglmüller, Silviya Wolkerstorfer, Martina Fondi, Gregor Hoermann, Lei Cao, Oswald Wagner, Florian W. Kiefer, Harald Esterbauer, Martin Bilban
Software Mentions: 1
Published: about 4 years ago

10.1186/s12920-021-00875-5

Coding and non-coding RNA interactions reveal immune-related pathways in peripheral blood mononuclear cells derived from patients with proliferative vitreoretinopathy
Cited by: 5
Author(s): Yicheng Ni, Fangyuan Liu, Xiao Hu, Yingyan Qin, Zhaotian Zhang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0217276

Inhibition of immune checkpoints PD-1, CTLA-4, and IDO1 coordinately induces immune-mediated liver injury in mice
Cited by: 29
Author(s): Timothy Affolter, Heather P. Llewellyn, Derek W. Bartlett, Qing Zong, Shuhua Xia, Vince R. Torti, Changhua Ji
Software Mentions: 1
Published: about 6 years ago

10.1186/s12920-018-0389-z

Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer
Cited by: 18
Author(s): So Yeon Kim, Tae Rim Kim, Hyun-Hwan Jeong, Kyung-Ah Sohn
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0177928

Serum microRNA signatures as "liquid biopsies" for interrogating hepatotoxic mechanisms and liver pathogenesis in human
Cited by: 38
Author(s): Julian Krauskopf, Theo M. de Kok, Shelli Schomaker, Mark Gosink, Deborah A. Burt, Patricia Chandler, Roscoe L. Warner, Kent J. Johnson, Florian Caiment, Jos Kleinjans, Jiri Aubrecht
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0233646

Gut microbial diversity, inflammation, and oxidative stress are associated with tacrolimus dosing requirements early after heart transplantation
Cited by: 13
Author(s): Douglas L. Jennings, Bruno Bohn, A.M. Zuver, Duygu Onat, M. Gaine, E.A. Royzman, Jonathan Hupf, Danielle L. Brunjes, F. Latif, Susan Restaino, A.R. Garan, V.K. Topkara, Hiroo Takayama, Koji Takeda, Yoshifumi Naka, Maryjane Farr, Renu Nandakumar, Anne Catrin Uhlemann, P.C. Colombo, Ryan T. Demmer, M. Yuzefpolskaya
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22042181

Altered Expression of OsAAP3 Influences Rice Lesion Mimic and Leaf Senescence by Regulating Arginine Transport and Nitric Oxide Pathway
Cited by: 12
Author(s): Qilang Wei, Zhenwei Yan, Yifan Xiong, Zhongming Fang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0250649

Novel dopamine receptor 3 antagonists inhibit the growth of primary and temozolomide resistant glioblastoma cells
Cited by: 3
Author(s): Sarah Williford, Catherine Libby, Adetokunbo Ayokanmbi, Arphaxad Otamias, Juan Gordillo, Emily R. Gordon, Sara J. Cooper, Matthew Redmann, Yanjie Li, Corinne E. Griguer, Jianhua Zhang, Марек Напиерала, Subramaniam Ananthan, Anita B. Hjelmeland
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0194522

A bi-stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer
Cited by: 4
Author(s): Sachi Horibata, Edward J. Rice, Hui Zheng, Chinatsu Mukai, Tinyi Chu, Brooke A. Marks, Scott A. Coonrod, Charles G. Danko
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0177901

The role of the zinc finger protein ZC3H32 in bloodstream-form Trypanosoma brucei
Cited by: 18
Author(s): Claudius Klein, Monica Terrao, Christine Clayton
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1005691

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression
Cited by: 24
Author(s): David B. West, Eric K. Engelhard, Michael Adkisson, Alessia Nava, Julia V. Kirov, Andreanna Cipollone, Brandon Willis, Jared Rapp, Pieter J. de Jong, Kevin C K Lloyd
Software Mentions: 1
Published: over 9 years ago

10.1186/s12916-020-01899-x

EPHA7 mutation as a predictive biomarker for immune checkpoint inhibitors in multiple cancers
Cited by: 25
Author(s): Zhen Zhang, Haoxiang Wu, Wu-Hao Lin, Zi‐Xian Wang, Lu-Ping Yang, Zhao-Lei Zeng, Hongyu Luo
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-15-557

Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae
Cited by: 49
Author(s): Inna Biryukova, Tao Ye, Elena A. Levashina
Software Mentions: 1
Published: over 11 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583