bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0162390

Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer
Cited by: 16
Author(s): Jonas Stenløkke Madsen, Leise Riber, Witold Kot, Alrun Basfeld, Mette Burmølle, Lars Hestbjerg Hansen, Søren J. Sørensen
Software Mentions: 1
Published: about 8 years ago

10.1186/s12967-019-1987-z

Frequent genetic aberrations in the cell cycle related genes in mucosal melanoma indicate the potential for targeted therapy
Cited by: 18
Author(s): Lina Xu, Zhiyuan Cheng, Chuanliang Cui, Xiaowen Wu, Huan Yu, Jun Guo, Yan Kong
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-98323-y

Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress
Cited by: 2
Author(s): А. Г. Степченко, Т. Н. Порцева, И. А. Глухов, А. П. Котнова, B. M. Lyanova, С. Г. Георгиева, Е. В. Панкратова
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0200732

Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq.
Cited by: 7
Author(s): E. Armstrong, Andrés Iriarte, P. Nicolini, Jorge De los Santos, J. Ithurralde, Alejandro Bielli, G. Bianchi, Francisco Peñagaricano
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0247888

Transcriptional analysis of islets of Langerhans from organ donors of different ages
Cited by: 8
Author(s): Peter Seiron, Anton Stenwall, A. Hedin, Louise Granlund, Jonathan L.S. Esguerra, Petr Volkov, Erik Renström, Olle Korsgren, Marcus Lundberg, Oskar Skog
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0100839

Tissue-Specific Expressed Antibody Variable Gene Repertoires
Cited by: 34
Author(s): Bryan Briney, Jordan R. Willis, Jessica A. Finn, Brett A. McKinney, James E. Crowe
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4723-9

Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential
Cited by: 19
Author(s): Nicky‐Lee Willson, R. E. A. Forder, Rick Tearle, J. L. Williams, Robert J. Hughes, G. S. Nattrass, P. I. Hynd
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0215122

Calcium-induced differentiation in normal human colonoid cultures: Cell-cell / cell-matrix adhesion, barrier formation and tissue integrity
Cited by: 24
Author(s): Durga Attili, Shannon D. McClintock, Areeba H. Rizvi, Shailja Pandya, Humza Rehman, Daniyal M. Nadeem, Aliah Richter, Dafydd G. Thomas, Michael K. Dame, D. Kim Turgeon, James Varani, Muhammad N. Aslam
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2546-0

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
Cited by: 20
Author(s): María Fernanda Torres, Noushin Ghaffari, Ester Alvarenga Santos Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson, Lisa J. Vaillancourt
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-017-4177-5

Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types
Cited by: 29
Author(s): Guillem Ylla, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-016-2454-3

Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors
Cited by: 75
Author(s): Troy J. Huth, Sean P. Place
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0170085

Differential DNA Methylation Regions in Adult Human Sperm following Adolescent Chemotherapy: Potential for Epigenetic Inheritance
Cited by: 39
Author(s): Margarett Shnorhavorian, Stephen M. Schwartz, Barbara Stansfeld, Ingrid Sadler‐Riggleman, Daniel Beck, Michael K. Skinner
Software Mentions: 1
Published: almost 8 years ago

10.3390/s21061938

Gated Graph Attention Network for Cancer Prediction
Cited by: 2
Author(s): Linling Qiu, Li Han, Meihong Wang, Xiaoli Wang
Software Mentions: 1
Published: over 3 years ago

10.1038/s41392-020-0170-6

p190A inactivating mutations cause aberrant RhoA activation and promote malignant transformation via the Hippo-YAP pathway in endometrial cancer
Cited by: 12
Author(s): Wen Xu, Jing Wan, Qizhi He, Mengfei Wang, Shuangdi Li, Mei Jiang, Zhen Qian, Binya Liu, Wen Lu, Kai Wang, Kun Gao, Xiaoping Wan
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-6149-4

Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis
Cited by: 7
Author(s): Humaira Rasheed, Chenxu Ye, Yufeng Meng, Yuehua Ran, Jing Li, Xiaoqing Su
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.26071

Intratumor heterogeneity ofHMCN1mutant alleles associated with poor prognosis in patients with breast cancer
Cited by: 16
Author(s): Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0193665

Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica
Cited by: 9
Author(s): Tokuko Ujino‐Ihara, S. Ueno, Kentaro Uchiyama, Norihiro Futamura
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-3059-6

RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response
Cited by: 6
Author(s): Andrea Prunotto, Brian J. Stevenson, Corinne Berthonneche, Fanny Schüpfer, Jacques S. Beckmann, Fabienne Maurer, Sven Bergmann
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0160517

Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq
Cited by: 26
Author(s): Mandy J. Peffers, Katarzyna Goljanek‐Whysall, John A. Collins, Yongxiang Fang, Michael D. Rushton, John Loughlin, Carole J. Proctor, Peter Clegg
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0217507

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing
Cited by: 17
Author(s): Anson T. Ku, Naveen Ravi, Minjun Yang, Mikael Evander, Thomas Laurell, Hans Lilja, Yvonne Ceder
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5310-9

Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis
Cited by: 5
Author(s): Ken Kraaijeveld, Vicencio Oostra, Maartje Liefting, Bregje Wertheim, Emile de Meijer, Jacintha Ellers
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-017-4151-2

Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization
Cited by: 39
Author(s): Audrey M. V. Ah‐Fong, Jolly Shrivastava, Howard S. Judelson
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0035961

Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens
Cited by: 38
Author(s): Li Xiao, Liechi Zhang, Yang Ge, Honglin Zhu, Yulong He
Software Mentions: 1
Published: over 12 years ago

10.1186/s13287-016-0389-x

Adipose-derived mesenchymal stem cells from patients with atherosclerotic renovascular disease have increased DNA damage and reduced angiogenesis that can be modified by hypoxia
Cited by: 24
Author(s): Ahmed Saad, Xiang Yang Zhu, Joerg Herrmann, La Tonya J. Hickson, Hui Tang, Allan B. Dietz, André J. van Wijnen, Lilach O. Lerman, Stephen C. Textor
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.26401

Exploiting the transcriptional specificity of the alpha-methylacyl-CoA racemase AMACR promoter for the molecular imaging of prostate cancer
Cited by: 4
Author(s): Mariya Shapovalova, Julia Davydova, Christine Henzler, Mark Daniel, Scott M. Dehm, Christopher A. Warlick, Aaron M. LeBeau
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0038298

Genome-Wide MicroRNA Expression Analysis of Clear Cell Renal Cell Carcinoma by Next Generation Deep Sequencing
Cited by: 104
Author(s): Susanne Osanto, Yongjun Qin, Henk P.J. Buermans, Joost Berkers, Evelyne Lerut, Jelle J. Goeman, Hendrik Van Poppel
Software Mentions: 1
Published: over 12 years ago

10.1186/s13287-018-1120-x

OCT4 maintains self-renewal and reverses senescence in human hair follicle mesenchymal stem cells through the downregulation of p21 by DNA methyltransferases
Cited by: 32
Author(s): Yan Lü, Huinan Qu, Da Qi, Wenhong Xu, Shutong Liu, Xiangshu Jin, Peiye Song, Yantong Guo, Yiyang Jia, Xinqi Wang, Hairi Li, Yulin Li, Chengshi Quan
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0185595

De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes
Cited by: 15
Author(s): Ingrid Garbus, José R. Romero, Juan Pablo Selva, María Cielo Pasten, Carolina Chinestra, José Luís Carballo, Diego Zappacosta, Viviana Echenique
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.26377

Targeting the Wnt/β-catenin pathway in human osteosarcoma cells
Cited by: 43
Author(s): Fang Fang, Ashley M. VanCleave, Ralph Helmuth, Haydee M. Torres, Kirby Rickel, Hannah Wollenzien, Hongli Sun, Erliang Zeng, Jing Zhao, Jianning Tao
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0231206

Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113
Cited by: 30
Author(s): Mukesh Kumar Malviya, Changning Li, Manoj Kumar Solanki, Rajesh Kumar Singh, Reemon Htun, Pratiksha Singh, Krishan K. Verma, Li‐Tao Yang, Yang–Rui Li
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0186382

Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions
Cited by: 14
Author(s): Boon Huat Cheah, Sudhir Jadhao, Madavan Vasudevan, R Wickneswari V Ratnam, Kalaivani K. Nadarajah
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-017-4144-1

Deciphering the olfactory repertoire of the tiger mosquito Aedes albopictus
Cited by: 29
Author(s): Fabrizio Lombardo, Marco Salvemini, Carmine Fiorillo, Tony Nolan, Laurence J. Zwiebel, José M. C. Ribeiro, Bruno Arcà
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-016-2470-3

Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear
Cited by: 30
Author(s): Mao-Song Pei, Jianxin Niu, Chenjing Li, Fuliang Cao, Shaowen Quan
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.27493

DOT1L inhibition is lethal for multiple myeloma due to perturbation of the endoplasmic reticulum stress pathway
Cited by: 10
Author(s): Caroline Dafflon, Swann Gaulis, Louise Barys, Karen Kapur, Vanessa Cornacchione, Lina Schukur, Sebastian Bergling, Elisabetta Traggiai, Selina Jansky, Leon Hellmann, Barbara Schacher Engstler, Gráinne Kerr, Antoine DeWeck, David A. Ruddy, Ulrike Naumann, Frédéric Stauffer, Christoph Gaul, Ying Lin, Éric Billy, Andreas Weiss, Francesco Hofmann, Moriko Ito, Ralph Tiedt
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0200826

BRD4 amplification facilitates an oncogenic gene expression program in high-grade serous ovarian cancer and confers sensitivity to BET inhibitors
Cited by: 43
Author(s): Garrett W. Rhyasen, Yi Yao, Jingwen Zhang, Austin Dulak, Lillian Castriotta, Kelly Jacques, Wei Zhao, Farzin Gharahdaghi, Maureen M. Hattersley, Paul Lyne, Edwin Clark, Michael Zinda, Stephen E. Fawell, Gordon B. Mills, Huawei Chen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1707-x

Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition
Cited by: 74
Author(s): Bing Tian, Xueling Li, Mridul Kalita, Steven G. Widen, Jun Yang, Suresh K. Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanlei Kong, Thomas G. Wood, Bruce A. Luxon, Allan R. Brasier
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0194765

IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs
Cited by: 17
Author(s): Louise Brogaard, Lars Erik Larsen, Peter M. H. Heegaard, Christian Anthon, Jan Gorodkin, Ralf Dürrwald, Kerstin Skovgaard
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0159372

Antennal and Abdominal Transcriptomes Reveal Chemosensory Genes in the Asian Citrus Psyllid, Diaphorina citri
Cited by: 39
Author(s): Zhongzhen Wu, Zuyong He, Shuying Bin, Lei Chen, Qunxin Han, Jintian Lin
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-6037-y

Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites
Cited by: 15
Author(s): Chenxu Ye, Humaira Rasheed, Yuehua Ran, Yang Xiao, Lianxi Xing, Xiaoqing Su
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0200558

FAK auto-phosphorylation site tyrosine 397 is required for development but dispensable for normal skin homeostasis
Cited by: 8
Author(s): Joel B. Heim, Cera A. McDonald, Saranya P. Wyles, Sindhuja Sominidi‐Damodaran, Edwin J. Squirewell, Ming Li, Catherine Motsonelidze, Ralph T. Böttcher, Jan van Deursen, Alexander Meves
Software Mentions: 1
Published: over 6 years ago

10.1155/2020/3296192

TRAF6 Promotes Gastric Cancer Cell Self-Renewal, Proliferation, and Migration
Cited by: 12
Author(s): Mengting Yang, Meng Jin, Kailong Li, Haifeng Liu, Xiaonan Yang, Xiaobei Zhang, Bin Zhang, Aihua Gong, Qingli Bie
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0187351

Kojic acid-mediated damage responses induce mycelial regeneration in the basidiomycete Hypsizygus marmoreus
Cited by: 10
Author(s): Jinjing Zhang, Hui Chen, Mingjie Chen, Hong Wang, Qian Wang, Xiaoxia Song, Haibo Hao, Zhen Feng
Software Mentions: 1
Published: about 7 years ago

10.5966/sctm.2015-0429

Direct Isolation and Characterization of Human Nephron Progenitors
Cited by: 22
Author(s): Stefano Da Sacco, Matthew E. Thornton, Astgik Petrosyan, Maria Lavarreda-Pearce, Sargis Sedrakyan, Brendan H. Grubbs, Roger E. De Filippo, Laura Perin
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-020-06968-2

Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach
Cited by: 5
Author(s): José Ricardo Parreira, Lorenzo E. Hernández-Castellano, A. Argüello, J. Capote, N. Castro, Susana de Sousa Araújo, André M. Almeida
Software Mentions: 1
Published: about 4 years ago

10.1002/sctm.19-0231

SOX9+/PTF1A+ Cells Define the Tip Progenitor Cells of the Human Fetal Pancreas of the Second Trimester
Cited by: 16
Author(s): Valentina Villani, Matthew E. Thornton, Heather N. Zook, Christiana Crook, Brendan H. Grubbs, Giuseppe Orlando, Roger E. De Filippo, Hsun Teresa Ku, Laura Perin
Software Mentions: 1
Published: about 5 years ago

10.1186/s13018-021-02508-0

Cornuside I promoted osteogenic differentiation of bone mesenchymal stem cells through PI3K/Akt signaling pathway
Cited by: 5
Author(s): Feng Gao, Shuhua Xia, Xiuhui Wang, Xiaoxiao Zhou, Jun Wang
Software Mentions: 1
Published: over 3 years ago

10.1002/path.5551

Large‐scale analysis of <scp>BAP1</scp> expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma
Cited by: 22
Author(s): Assunta De Rienzo, Lucian R. Chirieac, Yin P. Hung, David T. Severson, Samuel Freyaldenhoven, Corinne E. Gustafson, Nhien Dao, Claire Meyerovitz, Michela E Oster, Roderick V. Jensen, Beow Y. Yeap, Raphael Bueno, William G. Richards
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0130902

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
Cited by: 23
Author(s): Yuanhao Zhang, Leahana Rowehl, Julia M. Krumsiek, Erika P. Orner, Nurmohammad Shaikh, Phillip I. Tarr, Erica Sodergren, George M. Weinstock, Edgar C. Boedeker, Xuejian Xiong, John Parkinson, Daniel N. Frank, Ellen Li, Grace Gathungu
Software Mentions: 1
Published: over 9 years ago

10.1007/s00122-018-3070-1

Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines
Cited by: 16
Author(s): Paola Barba, Jacquelyn Lillis, R. Stephen Luce, Renaud Travadon, Michael V. Osier, Kendra Baumgartner, Wayne F. Wilcox, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 1
Published: almost 7 years ago

10.1007/s00122-020-03561-9

Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank
Cited by: 15
Author(s): Anna Gordon, Curt A. McCartney, Ron Knox, Nelzo C. Ereful, Colin W. Hiebert, David Konkin, Ya-Chih Hsueh, Vijai Bhadauria, Mara Sgroi, Donal M. O’Sullivan, Caroline Hadley, Lesley A. Boyd, J. I. Menzies
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0237744

Transcriptome analysis and comparison reveal divergence between the Mediterranean and the greenhouse whiteflies
Cited by: 1
Author(s): Yujun Wang, Hua-Ling Wang, Xiaowei Wang, Shu‐Sheng Liu
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0100477

Transcriptomic Analysis of Prunus domestica Undergoing Hypersensitive Response to Plum Pox Virus Infection
Cited by: 35
Author(s): Bernardo Rodamilans, David San León, Louisa Mühlberger, Thierry Candresse, M. Neumüller, Juan Carlos Oliveros, Juan Antonio Garcı́a
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0165268

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells
Cited by: 19
Author(s): Sarita Panula, Ahmed Reda, Jan-Bernd Stukenborg, Cyril Ramathal, Meena Sukhwani, Halima Albalushi, Daniel Edsgärd, Michiko Nakamura, Olle Söder, Kyle E. Orwig, Shinya Yamanaka, Renee A. Reijo Pera, Outi Hovatta
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-017-3689-3

An evolutionarily conserved transcriptional response to viral infection in Caenorhabditis nematodes
Cited by: 53
Author(s): Kevin Chen, Carl Franz, Hongbing Jiang, Yanfang Jiang, David Wang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0200210

Transcription factor induced conversion of human fibroblasts towards the hair cell lineage
Cited by: 23
Author(s): Maria B Duran Alonso, Iris Lopez Hernandez, Miguel A. de la Fuente, Javier García‐Sancho, Fernando Giráldez, Thomas Schimmang
Software Mentions: 1
Published: over 6 years ago

10.7150/thno.42423

Circular RNA circFBXW4 suppresses hepatic fibrosis via targeting the miR-18b-3p/FBXW7 axis
Cited by: 46
Author(s): Xin Chen, Hai-Di Li, Fang-tian Bu, Xiaofeng Li, Yu Chen, Sai Zhu, Jianan Wang, Siyu Chen, Ying‐Yin Sun, Xue‐Yin Pan, Na-Na Yin, Jiejie Xu, Cheng Huang, Jun Li
Software Mentions: 1
Published: almost 5 years ago

10.7150/thno.42010

Skipping of exon 10 in Axl pre-mRNA regulated by PTBP1 mediates invasion and metastasis process of liver cancer cells
Cited by: 27
Author(s): Lianghua Shen, Sijia Lei, Bin Zhang, Shuaiguang Li, Luyuan Huang, Alexander Czachor, Mason Breitzig, Yuman Gao, Meiyan Huang, Xuemei Mo, Qi Zheng, Han Sun, Feng Wang
Software Mentions: 1
Published: almost 5 years ago

10.7150/thno.45971

KRAS Mutation-Responsive miR-139-5p inhibits Colorectal Cancer Progression and is repressed by Wnt Signaling
Cited by: 35
Author(s): Feng Du, Tianyu Cao, Hui Xie, Ting Li, Lina Sun, Hao Líu, Hao Guo, Xin Wang, Qi Liu, Taewan Kim, Jeffrey L. Franklin, Ramona Graves‐Deal, Wei Han, Zuhong Tian, Minghui Ge, Yongzhan Nie, Daiming Fan, Robert J. Coffey, Yuanyuan Lu, Xiaodi Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0216294

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus
Cited by: 8
Author(s): Anna Abramova, Magnus Alm Rosenblad, Anders Blomberg, Tomas Larsson
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0178189

Systematic genomic and translational efficiency studies of uveal melanoma
Cited by: 27
Author(s): Chelsea Place Johnson, Ivana K. Kim, Bita Esmaeli, Ali Amin‐Mansour, Daniel J. Treacy, Scott L. Carter, Eran Hodis, Nikhil Wagle, Sara Seepo, Xiaoxing Yu, Anne Marie Lane, Evangelos S. Gragoudas, Francisca Vázquez, Elizabeth Nickerson, Kristian Cibulskis, Aaron McKenna, Stacey Gabriel, Gad Getz, Eliezer M. Van Allen, Peter A.C. ’t Hoen, Levi A. Garraway, Scott E. Woodman
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0002402

Sex-Biased Expression of MicroRNAs in Schistosoma mansoni
Cited by: 59
Author(s): A. De Marco, Ana Kozomara, Jerome H. L. Hui, Aidan M. Emery, David Rollinson, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0003975

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
Cited by: 31
Author(s): Andrew P. Jackson, Sophie Goyard, Dong Xia, Bernardo J. Foth, Mandy Sanders, Jonathan M. Wastling, Paola Minóprio, Matthew Berriman
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0009377

Combined gene deletion of dihydrofolate reductase-thymidylate synthase and pteridine reductase in Leishmania infantum
Cited by: 5
Author(s): Arijit Bhattacharya, Philippe Leprohon, Marc Ouellette
Software Mentions: 1
Published: over 3 years ago

10.7150/thno.48028

IL-33/ST2 induces neutrophil-dependent reactive oxygen species production and mediates gout pain
Cited by: 31
Author(s): Chengyu Yin, Boyu Liu, Yuanyuan Li, Xiaojie Li, Jie Wang, Ruixiang Chen, Yan Tai, Qiyang Shou, Ping Wang, Xiaomei Shao, Yi Liang, Hong Zhou, Wen-Li Mi, Jianqiao Fang
Software Mentions: 1
Published: almost 5 years ago

10.7150/thno.49186

Discovery of extracellular vesicles derived miR-181a-5p in patient's serum as an indicator for bone-metastatic prostate cancer
Cited by: 28
Author(s): Yanqing Wang, Yuxiang Fang, Baijun Dong, Xin Du, Jialin Wang, Xiao Wang, Wei‐Qiang Gao, Wei Xue
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-016-2665-7

Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum
Cited by: 33
Author(s): Shiri Barad, Noa Sela, Dilip Kumar, Amit Kumar-Dubey, Nofar Glam-Matana, Amir Sherman, Dov Prusky
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.09594

A robust transcriptional program in newts undergoing multiple events of lens regeneration throughout their lifespan
Cited by: 28
Author(s): Konstantinos Sousounis, Feng Qi, Manisha Yadav, José Luis Millán, Fubito Toyama, Chikafumi Chiba, Yukiko Eguchi, Goro Eguchi, Panagiotis A. Tsonis
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-017-4250-0

Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla)
Cited by: 50
Author(s): Wenjia Wang, Lianfeng Gu, Shanwen Ye, Hangxiao Zhang, Changyang Cai, Mengqi Xiang, Yanfeng Gao, Qin Wang, Chentao Lin, Qiang Zhu
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.68054

SMA-miRs (miR-181a-5p, -324-5p, and -451a) are overexpressed in spinal muscular atrophy skeletal muscle and serum samples
Cited by: 9
Author(s): Emanuela Abiusi, Paola Infante, Cinzia Cagnoli, Ludovica Lospinoso Severini, Marika Pane, Giorgia Coratti, Maria Carmela Pera, Adele D’Amico, F Diano, Agnese Novelli, Serena Spartano, Stefania Fiori, Giovanni Baranello, Isabella Moroni, Marina Mora, Maria Barbara Pasanisi, Krizia Pocino, Loredana Le Pera, Davide D’Amico, Lorena Travaglini, Francesco Ria, Claudio Bruno, Denise Locatelli, Enrico Bertini, Lucia Morandi, Eugenio Mercuri, Lucia Di Marcotullio, Francesco Danilo Tiziano
Software Mentions: 1
Published: about 3 years ago

10.7554/eLife.08833

Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality
Cited by: 68
Author(s): Sunitha Rangaraju, Gregory M. Solis, Ryan Thompson, Rafael L. Gomez‐Amaro, Leo Kurian, Sandra E. Encalada, Alexander B. Niculescu, Daniel R. Salomon, Michael Petrascheck
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pntd.0006186

Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti
Cited by: 10
Author(s): Matthew W. Eng, Anthony Clemons, Casey Hill, Roberta Engel, David W. Severson, Susanta K. Behura
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0004634

Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis
Cited by: 28
Author(s): Fuqiang Huang, Zhisheng Dang, Yutaka Suzuki, T Horiuchi, Kinpei Yagi, Hirokazu Kouguchi, Takao Irie, Kyeong-Soon Kim, Yuzaburo Oku
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.59177

A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm
Cited by: 291
Author(s): Michael R. Garvin, Christiane Alvarez, J Izaak Miller, Érica T. Prates, Angelica M. Walker, B. Kirtley Amos, Alan E. Mast, Amy C. Justice, Bruce J. Aronow, Daniel Jacobson
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.9021

Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing
Cited by: 14
Author(s): Yue Zhang, Di Wang, Di Shen, Yang Luo, Yi‐Qun Che
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.11781

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris
Cited by: 5
Author(s): Sandra Cervantes, Jaana Vuosku, Tanja Pyhäjärvi
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.10976

Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots
Cited by: 2
Author(s): Liangchen Su, Shuai Liu, Xing Liu, Baihong Zhang, Meijuan Li, Lidan Zeng, Ling Li
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-020-6755-1

Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells
Cited by: 9
Author(s): Hanna Helgeland, Ingvild Gabrielsen, Helle Akselsen, Arvind Sundaram, Siri Tennebø Flåm, Benedicte A. Lie
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.10249

Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes
Cited by: 2
Author(s): Xiaoping Li, Qihe Yu, Jishang Chen, Hui Huang, Zhuangsheng Liu, Chengxing Wang, Yuan He, Xin Zhang, Weiwen Li, Chao Li, Jinglin Zhao, Wansheng Long
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-15-183

Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilissymbionts
Cited by: 57
Author(s): Yuuki Kodama, Haruo Suzuki, Hideo Dohra, Manabu Sugii, Tatsuya Kitazume, Katsushi Yamaguchi, Shuji Shigenobu, Masahiro Fujishima
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.4276

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A
Cited by: 17
Author(s): Shelby Calkins, Nicole C. Elledge, Katherine E. Mueller, Stephen M. Marek, Matthew Brian Couger, Mostafa S. Elshahed, Noha H. Youssef
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.9262

Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas
Cited by: 8
Author(s): Wenjing Zeng, Yang Yi, Zhipeng Wen, Peng Chen, Xiaoping Chen, Zhicheng Gong
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.2520

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
Cited by: 26
Author(s): Moshtaghi Azam, Md. Lifat Rahi, Tuan Viet Nguyen, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.47262

Sex-specific transcriptomic responses to changes in the nutritional environment
Cited by: 39
Author(s): M. Florencia Camus, Matthew D. W. Piper, Max Reuter
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.10223

Transcriptome and gene expression analysis ofRhynchophorus ferrugineus(Coleoptera: Curculionidae) during developmental stages
Cited by: 8
Author(s): Hui Yang, Danping Xu, Zhihang Zhuo, Jingjing Hu, Binfeng Lu
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj.8394

LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
Cited by: 11
Author(s): Zhou Wei, Kang Huang, Qiuyan Zhang, Shaojun Ye, Zibiao Zhong, Cheng Zeng, Guizhu Peng, Ling Li, Qifa Ye
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.8379

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis
Cited by: 12
Author(s): Xuhui Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jianbin Guo
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.8776

Physiological parameters and differential expression analysis of N-phenyl-N′-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis
Cited by: 4
Author(s): Lejun Ouyang, Zechen Wang, Limei Li, Baoling Chen
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots
Cited by: 1
Author(s): Wang Wei, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Ye, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.10668

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis
Cited by: 4
Author(s): Juan Wang, Xiongfei Wu, Yue Tu, Jianzhong Dang, Zhitao Cai, Wenjing Liao, Weili Quan, Yaxun Wei
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.8609

Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation
Cited by: 4
Author(s): Wenmin Qiu, Jingen Li, Wei Yi, Fan Feng, Jing Jiang, Mingying Liu, Xiaojiao Han, Chaoguang Tian, Shihong Zhang, Renying Zhuo
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.1591

The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission
Cited by: 54
Author(s): Eugene V. Ryabov, Jessica Fannon, Jonathan D. Moore, Graham R. Wood, David J. Evans
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.10654

Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
Cited by: 9
Author(s): Chelsea Hall, Sara Camilli, Henry Dwaah, Benjamin Kornegay, Christie A. Lacy, Malcolm Hill, Andrew P. Hill
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.11755

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Cited by: 2
Author(s): Mengjun Huang, Haitao Xing, Zhexin Li, Honglei Li, Lin Wu, Yi Jiang
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.5307

A novel long non-coding RNA, AC012456.4, as a valuable and independent prognostic biomarker of survival in oral squamous cell carcinoma
Cited by: 11
Author(s): Xuegang Hu, Zailing Qiu, Jianchai Zeng, Tingting Xiao, Zhihong Ke, Hongbing Lyu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-2052-9

Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum
Cited by: 27
Author(s): Erica Lasek‐Nesselquist, Jennifer H. Wisecaver, Jeremiah D. Hackett, Matthew D. Johnson
Software Mentions: 1
Published: about 9 years ago

10.7717/peerj.10328

Deregulation of lysophosphatidic acid metabolism in oral cancer promotes cell migration via the up-regulation of COX-2
Cited by: 3
Author(s): Mariati Abdul Rahman, Malcolm Tan, Steven P. Johnson, Robert Hollows, Wen Lin Chai, Jason Peter Mansell, Lee Fah Yap, Ian C. Paterson
Software Mentions: 1
Published: about 4 years ago

10.7717/peerj.11135

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem
Cited by: 0
Author(s): Gina A. Garzón-Martínez, Francy Liliana García Arias, Felix E. Enciso-Rodríguez, Mauricio Soto‐Suárez, Carolina González, Aureliano Bombarely, Luz Stella Barrero, Jaime A. Osorio Guarín
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.7442

Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
Cited by: 4
Author(s): Feng Pang, Mengmeng Zhang, Guohua Li, Zhenxing Zhang, Haifeng Huang, Baobao Li, Chengqiang Wang, Xiaohong Yang, Yiying Zheng, Q. An, Luyin Zhang, Lijun Du, Fengyang Wang
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3959

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
Cited by: 37
Author(s): Jiuqiang Guan, Keren Long, Jideng Ma, Jinwei Zhang, Dafang He, Long Jin, Qianzi Tang, Anan Jiang, Xun Wang, Yaodong Hu, Shilin Tian, Zhi Jiang, Mingzhou Li, Xiaolin Luo
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.8368

Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma
Cited by: 12
Author(s): Xun Shi, You Li, Yehuan Sun, Xu Zhao, Xin Sun, Tuotuo Gong, Zhinan Liang, Yuan Ma, Xiaozhi Zhang
Software Mentions: 1
Published: almost 5 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568