bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0107608

Depletion of the RNA-Binding Protein RBP33 Results in Increased Expression of Silenced RNA Polymerase II Transcripts in Trypanosoma brucei
Cited by: 10
Author(s): Sandra M. Fernández‐Moya, Mark Carrington, Antonio M. Estévez
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0034150

Differential Expression of miRNAs in Colorectal Cancer: Comparison of Paired Tumor Tissue and Adjacent Normal Mucosa Using High-Throughput Sequencing
Cited by: 141
Author(s): Julian Hamfjord, Astrid M. Stangeland, Timothy R. Hughes, Martina L. Skrede, Kjell Magne Tveit, Tone Ikdahl, Elin H. Kure
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0094352

MicroRNA Buffering and Altered Variance of Gene Expression in Response to Salmonella Infection
Cited by: 13
Author(s): Hua Bao, Arun Kommadath, Graham Plastow, Christopher K. Tuggle, Le Luo Guan, Paul Stothard
Software Mentions: 1
Published: over 12 years ago

10.1186/s12935-020-01295-8

Construction of a metastasis-associated ceRNA network reveals a prognostic signature in lung cancer
Cited by: 22
Author(s): Qing Cao, Zewen Dong, Shuzhen Liu, Guoyan An, Bianbian Yan, Lei Lei
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-39852-5

Suppression of glioblastoma by a drug cocktail reprogramming tumor cells into neuronal like cells
Cited by: 19
Author(s): Lei Gao, Shichao Huang, Hong Zhang, Wei Hua, Shunmei Xin, Lin Cheng, Wuqiang Guan, Yongchun Yu, Ying Mao, Gang Pei
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-3596-7

Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress
Cited by: 88
Author(s): Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, R. S. Tomar, Ashish Chaturvedi, Kishor Gaikwad, Madan Pal
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0224765

Identifying resurrection genes through the differentially expressed genes between Selaginella tamariscina (Beauv.) spring and Selaginella moellendorffii Hieron under drought stress
Cited by: 12
Author(s): Wei Gu, Aqin Zhang, Hongmei Sun, Yuchen Gu, Chao Ji, Rong Tian, Jin‐Ao Duan
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-3585-x

RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development
Cited by: 70
Author(s): Audrey M. V. Ah‐Fong, Kyoung Su Kim, Howard S. Judelson
Software Mentions: 1
Published: over 9 years ago

10.1186/s13058-018-1059-y

Metastatic breast cancer cells overexpress and secrete miR-218 to regulate type I collagen deposition by osteoblasts
Cited by: 53
Author(s): Xuxiang Liu, Minghui Cao, Melanie R. Palomares, Xiwei Wu, Arthur Li, Yan Wei, Miranda Fong, Wing-Chung Chan, Shizhen Emily Wang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0111006

Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains
Cited by: 11
Author(s): Vikash Pandey, Marc Sultan, Karl Kashofer, Markus Ralser, Vyacheslav Amstislavskiy, Julia Starmann, Ingrid Osprian, Christina Grimm, Hendrik Hache, Marie–Laure Yaspo, Holger Sültmann, Michael Trauner, Helmut Denk, Kurt Zatloukal, Hans Lehrach, Christoph Wierling
Software Mentions: 1
Published: about 12 years ago

10.3390/ijms22083882

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus
Cited by: 2
Author(s): Roberto Martín‐Hernández, Rossanna Rodríguez-Canul, Nuvia Kantún-Moreno, Miguel A. Olvera‐Novoa, Óscar Medina-Contreras, Cristobal Garikoitz-Legarda, Juan Carlos Triviño, Jesús Alejandro Zamora‐Briseño, Víctor May-Solis, Alicia Poot-Salazar, Juan Antonio Pérez-Vega, Judit Gil-Zamorano, George Grant, Alberto Dávalos, Leticia Olivera‐Castillo
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-40227-z

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development
Cited by: 2
Author(s): Vikram S. Shivakumar, Gabriel Johnson, Elizabeth A. Zimmer
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0130328

Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity
Cited by: 75
Author(s): Meenal Vyas, Tonja W. Fisher, Rong He, William M. Nelson, Guohua Yin, Joseph M. Cicero, Mark R. Willer, Ryan Kim, Robin Kramer, Greg A. May, John A. Crow, Carol Soderlund, David R. Gang, Judith K. Brown
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0017820

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays
Cited by: 206
Author(s): Daniel Bottomly, Nicole A.R. Walter, Jessica Ezzell Hunter, Priscila Darakjian, Sunita Kawane, Kari J. Buck, Robert P. Searles, Michael A. Mooney, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0104541

De Novo Transcriptome Assembly and Comparative Analysis of Differentially Expressed Genes in Prunus dulcis Mill. in Response to Freezing Stress
Cited by: 54
Author(s): S. A. Mousavi, Arghavan Alisoltani, Behrouz Shiran, Hossein Fallahi, Esmaeil Ebrahimie, Ali Imani, S. Houshmand
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0034940

Transcriptome Responses of Insect Fat Body Cells to Tissue Culture Environment
Cited by: 16
Author(s): Naoya Ogata, Takeshi Yokoyama, Kikuo Iwabuchi
Software Mentions: 1
Published: over 14 years ago

10.1186/s13048-021-00814-z

Plasma-derived exosomal miR-4732-5p is a promising noninvasive diagnostic biomarker for epithelial ovarian cancer
Cited by: 28
Author(s): Jingjing Liu, Ji Geun Yoo, Jung Ho, Yoon Young Jung, Sanha Lee, Soo Young Hur, Youn Jin Choi
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0186173

The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts
Cited by: 24
Author(s): David B. Carlini, Daniel W. Fong
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-019-42010-6

A Network-guided Association Mapping Approach from DNA Methylation to Disease
Cited by: 16
Author(s): Yandan Lin, De-Shuang Huang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-6370-1

Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes
Cited by: 14
Author(s): Ruihong Wang, Pengda Ma, Chen Li, Lingang Xiao, Zongsuo Liang, Juane Dong
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0256875

Transcriptome characterization and expression profile of Coix lacryma-jobi L. in response to drought
Cited by: 9
Author(s): Guidong Miao, Yan Qin, Jihua Guo, Qingxia Zhang, Yingying Bao
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-015-2082-3

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer
Cited by: 51
Author(s): Manuel Saiselet, David Gacquer, Alex Spinette, Ligia Craciun, Myriam Decaussin‐Petrucci, Guy Andry, Vincent Detours, Carine Maenhaut
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-018-5128-5

Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-κB pathway in porcine intestinal epithelial cell line
Cited by: 37
Author(s): Xuelian Ma, Xiaomin Zhao, Zhichao Zhang, Jianxiong Guo, Lijuan Guan, Juejun Li, Mi Mi, Yong Huang, Dewen Tong
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-42025-z

Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians
Cited by: 11
Author(s): Kiyono Sekii, Shunta Yorimoto, Hikaru Okamoto, Nanna Nagao, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryo Furukawa, Shuji Shigenobu, Kazuya Kobayashi
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0206159

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs
Cited by: 45
Author(s): Mathilde Le Sciellour, Étienne Labussière, Olivier Zemb, David Renaudeau
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0084386

Genetic Analysis of Benzothiophene Biodesulfurization Pathway of Gordonia terrae Strain C-6
Cited by: 31
Author(s): Wei Wang, Ting Ma, Kehui Lian, Yue Zhang, Huimei Tian, Kaihua Ji, Guoqiang Li
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0103567

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy
Cited by: 44
Author(s): Jacqueline D. Farrell, Stephen Byrne, Cristiana Paina, Torben Asp
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0242179

MiR-424-5p regulates cell cycle and inhibits proliferation of hepatocellular carcinoma cells by targeting E2F7
Cited by: 24
Author(s): Yichao Zhao, Chaoqian Zhu, Qing Chang, Peng Peng, Jie Yang, Chunmei Liu, Yang Liu, Xiaonan Chen, Yuanguang Liu, Ran Cheng, Yijie Wu, Xiaotang Wu, Liang Hu, Jun Yin
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0135670

Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, George E. Liu, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0169177

Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss
Cited by: 27
Author(s): Shugen Wei, Xiaojun Ma, Limei Pan, Miao Jin, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanjun Guan, Changming Mo, Hao Huang, Maoshan Chen
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13058-018-0963-5

Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis
Cited by: 14
Author(s): Maria B. Padua, Poornima Bhat‐Nakshatri, Manjushree Anjanappa, Mayuri Prasad, Yangyang Hao, Xi Rao, Sheng Liu, Jun Wan, Yunlong Liu, Kyle McElyea, Max Jacobsen, George E. Sandusky, Sandra K. Althouse, Susan M. Perkins, Harikrishna Nakshatri
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0245613

A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection
Cited by: 7
Author(s): Kai Zhu, Li‐Tao Yang, Chengxi Li, Prakash Lakshmanan, Yong‐Xiu Xing, Yang–Rui Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0156780

Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy
Cited by: 11
Author(s): Xihui Sheng, Ligang Wang, Hemin Ni, Lixian Wang, Xiaolong Qi, Shuhan Xing, Yong Guo
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22094910

Extracellular Vesicles in Synovial Fluid from Rheumatoid Arthritis Patients Contain miRNAs with Capacity to Modulate Inflammation
Cited by: 15
Author(s): Andrew D Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C Pang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 5 years ago

10.1186/s12995-021-00332-0

Genome-wide mRNA profiling identifies the NRF2-regulated lymphocyte oxidative stress status in patients with silicosis
Cited by: 1
Author(s): Zhao Yi, Guangcui Xu, Haibin Li, Meiyu Chang, Chuan Xiong, Yingjun Tao, Yi Guan, Yuchun Li, Sanqiao Yao
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0199264

A CRISPR screen identifies MAPK7 as a target for combination with MEK inhibition in KRAS mutant NSCLC
Cited by: 15
Author(s): Nicholas Dompe, Christiaan Klijn, Sara A. Watson, Katherine R. Welker Leng, Jenna Port, Trinna Cuellar, Colin Watanabe, Benjamin Haley, Richard M. Neve, Marie Evangelista, David Stokoe
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0196681

Identification of cancer-related miRNA-lncRNA biomarkers using a basic miRNA-lncRNA network
Cited by: 51
Author(s): Guangle Zhang, Cong Pian, Zhi Chen, Jin Zhang, Mei‐Ling Xu, Liangyun Zhang, Yuanyuan Chen
Software Mentions: 1
Published: over 8 years ago

10.3390/brainsci11070913

Characterization of Early Life Stress-Affected Gut Microbiota
Cited by: 12
Author(s): Noriyoshi Usui, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0193009

Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories
Cited by: 12
Author(s): Matthew C. Hale, Garrett J. McKinney, Frank P. Thrower, Krista M. Nichols
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms22105088

Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination
Cited by: 5
Author(s): Yu Wu, Lamei Zheng, Bing Jie, Huimin Liu, Genfa Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0210414

The transcriptome sequencing and functional analysis of eyestalk ganglions in Chinese mitten crab (Eriocheir sinensis) treated with different photoperiods
Cited by: 4
Author(s): Yangyang Pang, Cong Zhang, Minjie Xu, Genyong Huang, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 1
Published: almost 8 years ago

10.3390/brainsci9070155

Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption
Cited by: 16
Author(s): Robert Hitzemann, Ovidiu D. Iancu, Cheryl Reed, Harue Baba, Denesa R. Lockwood, Tamara J. Phillips
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0149067

Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton
Cited by: 27
Author(s): Hisao Koga, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko Shibata, Masahiro Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, Hiroshi Wada
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0039914

A Retinoblastoma Orthologue Is a Major Regulator of S-Phase, Mitotic, and Developmental Gene Expression in Dictyostelium
Cited by: 11
Author(s): Kimchi Strasser, Gareth Bloomfield, Asa MacWilliams, Adriano Ceccarelli, Harry K. MacWilliams, Adrian Tsang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0118002

LSD1 Overexpression Is Associated with Poor Prognosis in Basal-Like Breast Cancer, and Sensitivity to PARP Inhibition
Cited by: 61
Author(s): Satoi Nagasawa, Anna S. Sedukhina, Yuko Nakagawa, Ichiro Maeda, Manabu Kubota, Shigeko Ohnuma, Koichiro Tsugawa, Tomohiko Ohta, Marta Roche-Molina, Juan A. Bernal, A.J. Narvaez, Anand D. Jeyasekharan, Ko Sato
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0110548

In-Depth Transcriptome Analysis of the Red Swamp Crayfish Procambarus clarkii
Cited by: 61
Author(s): Huangxuan Shen, Yacheng Hu, Yuanchao Ma, Xin Zhou, Zenghong Xu, Shui Yu, Chunyan Li, Peng Xu, Xin Sun
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0239617

Comparative transcriptome analysis reveals candidate genes related to cadmium accumulation and tolerance in two almond mushroom (Agaricus brasiliensis) strains with contrasting cadmium tolerance
Cited by: 3
Author(s): Penghu Liu, Zaixing Huang, Xuhui Luo, Hua Cai, Weng Bo-qi, Yixiang Wang, Li‐Song Chen
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-87991-5

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea
Cited by: 9
Author(s): Debasish B. Krishnatreya, Pooja Moni Baruah, Bhaskar Dowarah, Soni Chowrasia, Tapan Kumar Mondal, Niraj Agarwala
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0137726

Social Regulation of Gene Expression in Threespine Sticklebacks
Cited by: 23
Author(s): Anna K. Greenwood, Catherine L. Peichel
Software Mentions: 1
Published: about 11 years ago

10.1093/brain/awab123

Aromatic <scp>l</scp>-amino acid decarboxylase deficiency: a patient-derived neuronal model for precision therapies
Cited by: 14
Author(s): Giada Rossignoli, Karolin Krämer, Eleonora Lugarà, Haya Alrashidi, Simon Pope, Carmen De La Fuente Barrigon, Katy Barwick, Giovanni Bisello, Joanne Ng, John R. Counsell, Gabriele Lignani, Simon Heales, Mariarita Bertoldi, Serena Barral, Manju A. Kurian
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0130885

Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis
Cited by: 65
Author(s): Jie Ye, Tixu Hu, Congmei Yang, Hanxia Li, Mingze Yang, Raina Ijaz, Zhibiao Ye, Yuyang Zhang
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-021-88874-5

ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds
Cited by: 3
Author(s): Rocío Soledad Tognacca, Monica Carabelli, Giorgio Morelli, Ida Ruberti, Javier Francisco Botto
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0198221

AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection
Cited by: 34
Author(s): Audrey C. Papp, Abul K. Azad, Maciej Pietrzak, Amanda Williams, Samuel K. Handelman, Robert P. Igo, Catherine M. Stein, Katherine E. Hartmann, Larry S. Schlesinger, Wolfgang Sadée
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms22115877

The miR-106b/NR2F2-AS1/PLEKHO2 Axis Regulates Migration and Invasion of Colorectal Cancer through the MAPK Pathway
Cited by: 4
Author(s): Shuzhen Liu, Guoyan An, Qing Cao, Tong Li, Xinyu Jia, Lei Lei
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0219976

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes
Cited by: 8
Author(s): Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-89948-0

The chemical defensome of five model teleost fish
Cited by: 15
Author(s): Marta Eide, Xiaokang Zhang, Odd André Karlsen, Jeffrey Goldstone, John J. Stegeman, Inge Jonassen, Anders Goksøyr
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22115959

Nuclear Magnetic Resonance Therapy Modulates the miRNA Profile in Human Primary OA Chondrocytes and Antagonizes Inflammation in Tc28/2a Cells
Cited by: 4
Author(s): Bibiane Steinecker-Frohnwieser, Birgit Lohberger, Nicole Eck, Anda Mann, Cornelia Kratschmann, Andreas Leithner, W. Kullich, Lukas Weigl
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0154156

Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis
Cited by: 11
Author(s): Elaine C. Lee, Heejung Kim, Jennifer Ditano, Dacie Manion, Benjamin L. King, Kevin Strange
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms22116013

Epithelial Regeneration Ability of Crohn’s Disease Assessed Using Patient-Derived Intestinal Organoids
Cited by: 12
Author(s): Chansu Lee, Sung Noh Hong, Eun Ran Kim, Dong Kyung Chang, Young‐Ho Kim
Software Mentions: 1
Published: over 5 years ago

10.1186/s12881-019-0936-2

POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction
Cited by: 19
Author(s): Yiran Li, Yiding Bian, Kai Wang, Xiaoping Wan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0116935

Transcriptional Regulation and Adaptation to a High-Fiber Environment in Bacillus subtilis HH2 Isolated from Feces of the Giant Panda
Cited by: 11
Author(s): Ziyao Zhou, Xiaoxiao Zhou, Li Jin, Zhijun Zhong, Wei Li, Xuehan Liu, Furui Liu, Huaiyi Su, Yongjiu Luo, Wuyang Gu, Chengdong Wang, Hemin Zhang, Desheng Li, Tiantian He, Hualin Fu, Suizhong Cao, Jinjiang Shi, Guangneng Peng
Software Mentions: 1
Published: over 11 years ago

10.1186/s12865-019-0292-1

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells
Cited by: 25
Author(s): Yue Tu, Xiongfei Wu, Fengyun Yu, Jianzhong Dang, Juan Wang, Yaxun Wei, Zhitao Cai, Zhipeng Zhou, Wenbiao Liao, Lian Li, Yi Zhang
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22126218

Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy
Cited by: 8
Author(s): Canan Kuscu, Manjari Kiran, Akram Mohammed, Cem Kuscu, Sarthak Satpathy, Aaron R. Wolen, Elissa Bardhi, Amandeep Bajwa, James D. Eason, Daniel G. Maluf, Valeria R. Mas, Enver Akalin
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0084311

The MicroRNA Expression Signature of Bladder Cancer by Deep Sequencing: The Functional Significance of the miR-195/497 Cluster
Cited by: 130
Author(s): Toshihiko Iwamoto, Naohiko Seki, Hirofumi Yoshino, Takeshi Chiyomaru, Takahiro Yamasaki, Hideo Hidaka, Tomokazu Yonezawa, Nijiro Nohata, Takashi Kinoshita, Masayuki Nakagawa, Hideki Enokida
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0169595

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis
Cited by: 33
Author(s): Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protásio Pereira
Software Mentions: 1
Published: almost 10 years ago

10.1155/2021/8810517

miR-301b-3p Regulates Breast Cancer Cell Proliferation, Migration, and Invasion by Targeting NR3C2
Cited by: 14
Author(s): Yun Fan, Yan Li, Yuzhang Zhu, Gui-Ping Dai, Debo Wu, Zhenzhen Gao, Lei Zhang, Danying Xu
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-90982-1

Analysis of the role of Purα in the pathogenesis of Alzheimer's disease based on RNA-seq and ChIP-seq
Cited by: 4
Author(s): Xiaoguang Shi, Shuanglai Ren, Bingying Zhang, Shanshan Guo, Wenxin He, Chengmin Yuan, Xiaofan Yang, Kevin Ig-lzevbekhai, Tao Sun, Qinwen Wang, Jianqi Cui
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22126430

Null cyp1b1 Activity in Zebrafish Leads to Variable Craniofacial Defects Associated with Altered Expression of Extracellular Matrix and Lipid Metabolism Genes
Cited by: 5
Author(s): Susana Alexandre-Moreno, Juan-Manuel Bonet-Fernández, Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar, Julio Escribano
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0159295

Transcriptome Profiling Reveals Disruption of Innate Immunity in Chronic Heavy Ethanol Consuming Female Rhesus Macaques
Cited by: 29
Author(s): Suhas Sureshchandra, Maham Rais, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0090895

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]
Cited by: 9
Author(s): Yan Ling, Yinghong Gu, Tao Xiang, Xianjun Lai, Yizheng Zhang, Xuemei Tan, Haiyan Wang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0208459

Gene landscape and correlation between B-cell infiltration and programmed death ligand 1 expression in lung adenocarcinoma patients from The Cancer Genome Atlas data set
Cited by: 18
Author(s): Kuo‐Hao Ho, Chih‐Ju Chang, Tsung-Hui Huang, Chwen‐Ming Shih, Ann‐Jeng Liu, Peng-Hsu Chen, Kur‐Ta Cheng, Ku‐Chung Chen
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-92489-1

Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis
Cited by: 2
Author(s): Xinyi Gu, Bo Jin, Zhidan Qi, Xiaofeng Yin
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-93128-5

Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)
Cited by: 5
Author(s): Michaël Pierrelée, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, Bianca Habermann
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0226338

Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development
Cited by: 10
Author(s): Safoora Amini, Khadijah Rosli, Mohd-Faizal Abu-Bakar, Hamidah Alias, Mohd-Noor Mat-Isa, Mohd-Afiq-Aizat Juhari, Jumaat Haji-Adam, Hoe-Han Goh, Kiew Lian Wan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0147527

Use of De Novo Transcriptome Libraries to Characterize a Novel Oleaginous Marine Chlorella Species during the Accumulation of Triacylglycerols
Cited by: 16
Author(s): Cresten Mansfeldt, Lubna V. Richter, Beth A. Ahner, William P. Cochlan, Ruth Richardson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0175622

Correlation of EGFR or KRAS mutation status with 18F-FDG uptake on PET-CT scan in lung adenocarcinoma
Cited by: 19
Author(s): Kazuya Takamochi, Kaoru Mogushi, Hideya Kawaji, Kota Imashimizu, Manabu Fukui, Shiaki Oh, Masayoshi Itoh, Yoshihide Hayashizaki, Weijey Ko, Masao Akeboshi, Kenji Suzuki
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0179881

Loss of prion protein induces a primed state of type I interferon-responsive genes
Cited by: 15
Author(s): Giulia Malachin, Malin Rokseth Reiten, Øyvind Salvesen, Håvard Aanes, Jorke H. Kamstra, Kerstin Skovgaard, Peter M. H. Heegaard, Cecilie Ersdal, Arild Espenes, Michael A. Tranulis, Maren Bakkebø
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0213149

Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission
Cited by: 7
Author(s): Md. Shamimuzzaman, Daniel K. Hasegawa, Wenbo Chen, Alvin M. Simmons, Zhangjun Fei, Kai-Shu Ling
Software Mentions: 1
Published: over 7 years ago

10.1186/s12865-021-00439-3

Differential long non-coding RNA expression profile and function analysis in primary Sjogren’s syndrome
Cited by: 7
Author(s): Xiaochan Chen, Qi Cheng, Yan Du, Lei Liu, Huaxiang Wu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0120388

A Genome-Wide Scan Reveals Important Roles of DNA Methylation in Human Longevity by Regulating Age-Related Disease Genes
Cited by: 37
Author(s): Fu-Hui Xiao, Yonghan He, Qi-Gang Li, Huan Wu, Longhai Luo, Qing‐Peng Kong
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0175315

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus
Cited by: 26
Author(s): Jianjian Lv, Longtao Zhang, Ping Liu, Jian Li
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5823-x

Understanding the liver under heat stress with statistical learning: an integrated metabolomics and transcriptomics computational approach
Cited by: 15
Author(s): Allen Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh, Carl J. Schmidt
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0228078

Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation
Cited by: 8
Author(s): Sang Hoon Kim, Se Won Kim, Gah‐Hyun Lim, Jae Il Lyu, Hong‐Il Choi, Yeong Deuk Jo, Si-Yong Kang, Byoung-Cheorl Kang, Jin-Baek Kim
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0113091

Comparative Transcriptomic Analysis of the Response to Cold Acclimation in Eucalyptus dunnii
Cited by: 18
Author(s): Yiqing Liu, Yi Jiang, Jianbin Lan, Yong Zou, Junping Gao
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-021-07825-6

Maternal cold exposure induces distinct transcriptome changes in the placenta and fetal brown adipose tissue in mice
Cited by: 3
Author(s): Sujoy Ghosh, Chul‐Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jenny L. Sones, Heike Münzberg, Leanne M. Redman, Jason Y. Chang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0116437

Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
Cited by: 19
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-021-93381-8

The coordination of major events in C4 photosynthesis evolution in the genus Flaveria
Cited by: 12
Author(s): Ming‐Ju Amy Lyu, Udo Gowik, Steven Kelly, Sarah Covshoff, Julian M. Hibberd, Rowan F. Sage, Martha Ludwig, Gane Ka Shu Wong, Peter Westhoff, Xin Guang Zhu
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22137025

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development
Cited by: 7
Author(s): Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragón-Palomino, Serena Aceto
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0158711

Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis
Cited by: 14
Author(s): Joachim von Wulffen, RecogNice-Team, Oliver Sawodny, Ronny Feuer
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0073783

Inducible Knockdown of Plasmodium Gene Expression Using the glmS Ribozyme
Cited by: 190
Author(s): Parichat Prommana, Chairat Uthaipibull, Chayaphat Wongsombat, Sumalee Kamchonwongpaisan, Yongyuth Yuthavong, Ellen Knuepfer, Anthony A. Holder, Philip Shaw
Software Mentions: 1
Published: about 13 years ago

10.1038/s41598-021-95403-x

Identification of intima-to-media signals for flow-induced vascular remodeling using correlative gene expression analysis
Cited by: 4
Author(s): John Kolega, Kerry E. Poppenberg, Hee‐Woong Lim, Liza Gutierrez, Sricharan S. Veeturi, Adnan H. Siddiqui, Hamidreza Rajabzadeh-Oghaz, Vincent M. Tutino
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-96046-8

Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator
Cited by: 4
Author(s): Shukria Akbar, D. Cole Stevens
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0174892

Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle
Cited by: 29
Author(s): Jason Ioannidis, F.X. Donadeu
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-95938-z

Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells
Cited by: 3
Author(s): Hongyu Chen, Xi Chen, Yifei Shen, Xinxin Yin, FangJie Liu, Lu Liu, Jie Yao, Qinjie Chu, Yaqin Wang, Hongyan Qi, Michael P. Timko, Weijia Fang, Longjiang Fan
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0182866

IFNAR2-dependent gene expression profile induced by IFN-α in Pteropus alecto bat cells and impact of IFNAR2 knockout on virus infection
Cited by: 25
Author(s): Qian Zhang, Leiping Zeng, Peng Zhou, Aaron T. Irving, Shang Li, Shi Z, Lin‐Fa Wang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0214526

Bacterial translocation in acute lymphocytic leukemia
Cited by: 7
Author(s): Yajing Song, Péter Gyarmati
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568