bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/plants10061204

Identification and Expression Profiling of Nonphosphorus Glycerolipid Synthase Genes in Response to Abiotic Stresses in Dendrobium catenatum
Cited by: 3
Author(s): Xinqiao Zhan, Yichun Qian, Bizeng Mao
Software Mentions: 1
Published: over 5 years ago

10.3390/plants9070891

RNAseq Analysis Reveals Altered Expression of Key Ion Transporters Causing Differential Uptake of Selective Ions in Canola (Brassica napus L.) Grown under NaCl Stress
Cited by: 16
Author(s): Mobina Ulfat, Habib‐ur‐Rehman Athar, Zaheer-Ud-Din Khan, Hazem M. Kalaji
Software Mentions: 1
Published: over 6 years ago

10.1007/s00497-021-00413-4

Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development
Cited by: 20
Author(s): Zhaodong Hao, Zhongjuan Zhang, Daoquan Xiang, Prakash Venglat, Jinhui Chen, Peng Gao, Raju Datla, Dolf Weijers
Software Mentions: 1
Published: over 5 years ago

10.1534/g3.119.400456

Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics
Cited by: 19
Author(s): Silvia Madritsch, Elisabeth Wischnitzki, Peter Kotrade, Ahmed Ashoub, Agnes Burg, Silvia Fluch, Wolfgang Brüggemann, Eva Maria Sehr
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-37422-9

Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa
Cited by: 51
Author(s): Won Ju Hwang, Sang Sun Yoon
Software Mentions: 1
Published: almost 8 years ago

10.1007/s11103-017-0594-8

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene
Cited by: 35
Author(s): Larissa Arrais Guimarães, Ana Paula Zotta Mota, Ana Cláudia Guerra Araújo, Lúcio Flávio de Alencar Figueiredo, Bruna Medeiros Pereira, Mario Alfredo de Passos Saraiva, Raquel Bispo Silva, Etienne G. J. Danchin, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-2957-y

Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves
Cited by: 55
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Hua Bao, Paul Stothard, Philip Griebel, Le Luo Guan
Software Mentions: 1
Published: about 10 years ago

10.1002/pld3.74

Developmental dynamics of stem starch accumulation in Sorghum bicolor
Cited by: 19
Author(s): Brian McKinley, Anna L. Casto, William L. Rooney, John E. Mullet
Software Mentions: 1
Published: about 8 years ago

10.1016/j.xplc.2021.100164

The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen
Cited by: 25
Author(s): Dangping Luo, José C. Huguet‐Tapia, R. Taylor Raborn, Frank F. White, Volker Brendel, Bing Yang
Software Mentions: 1
Published: over 5 years ago

10.1534/g3.119.400852

Maternal Priming of Offspring Immune System inDrosophila
Cited by: 16
Author(s): Julianna Bozler, B. Kacsóh, Giovanni Bosco
Software Mentions: 1
Published: almost 7 years ago

10.1534/g3.119.400875

Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages
Cited by: 6
Author(s): Chang Liu, Cornelius Tlotliso Sello, Yuanyuan Sui, Jingtao Hu, Shaokang Chen, Petunia Msuthwana, Yifang Zhou, Sulleyman Kassim Wachiebine, Yue Sun, Jing Liu, Shengyi Li, Wei Yang, Yupu Song, Yunpeng Xu, Chanying Guo, Qihui Sui, Yanbo Sun
Software Mentions: 1
Published: over 6 years ago

10.1534/g3.119.400963

The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions
Cited by: 13
Author(s): Nicole R. Newell, Surjyendu Ray, Justin E. Dalton, Julia C Fortier, Joyce Y. Kao, Peter L. Chang, Sergey V. Nuzhdin, Michelle N. Arbeitman
Software Mentions: 1
Published: over 6 years ago

10.1007/s00299-015-1822-9

Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize
Cited by: 20
Author(s): Qiuyue Chen, Zhipeng Liu, Baobao Wang, Xufeng Wang, Jinsheng Lai, Feng Tian
Software Mentions: 1
Published: over 11 years ago

10.1007/s00299-017-2177-1

Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae
Cited by: 11
Author(s): Vasja Progar, Jernej Jakše, Nataša Štajner, Sebastjan Radišek, Branka Javornik, Sabina Berne
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-08026-x

Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome
Cited by: 1
Author(s): Po-Shun Chuang, Satoshi Mitarai
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-5517-4

Gene regulation of Sclerotinia sclerotiorum during infection of Glycine max: on the road to pathogenesis
Cited by: 33
Author(s): Nathaniel M. Westrick, Ashish Ranjan, Sachin Jain, C. R. Grau, Damon Smith, Mehdi Kabbage
Software Mentions: 1
Published: over 7 years ago

10.1111/pbi.13484

GhARF16‐1 modulates leaf development by transcriptionally regulating theGhKNOX2‐1gene in cotton
Cited by: 13
Author(s): Guanghui Xiao, Yuzhou Zhang, Hongbin Li, Xuan Fu, Hǎihóng Shāng, Changsong Zou, Jiřı́ Friml, Gao Xiao
Software Mentions: 1
Published: about 6 years ago

10.1111/pbi.13058

Os<scp>ACL</scp>‐A2 negatively regulates cell death and disease resistance in rice
Cited by: 43
Author(s): Banpu Ruan, Zhihua Hua, Juan Zhao, Bin Zhang, Deyong Ren, Chaolei Liu, Shenglong Yang, Anpeng Zhang, Hongzhen Jiang, Haiping Yu, Jiang Hu, Li Zhu, Guang Chen, Lan Shen, Guojun Dong, Guangheng Zhang, Dali Zeng, Longbiao Guo, Qian Qian, Zhenyu Gao
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37763-5

Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy
Cited by: 2
Author(s): Ryan Sprissler, Robert W. Bina, Willard S. Kasoff, Marlys H. Witte, Michael Bernas, C. Walter, David M. Labiner, Branden Lau, Michael F. Hammer, Martin E. Weinand
Software Mentions: 1
Published: over 7 years ago

10.1111/pbi.12960

Transgenic creeping bentgrass overexpressing Osa‐miR393a exhibits altered plant development and improved multiple stress tolerance
Cited by: 63
Author(s): Junlong Zhao, Shuangrong Yuan, Man Zhou, Nannan Yuan, Zhigang Li, Qian Hu, Frank Bethea, Haibo Liu, Shigui Li, Hong Luo
Software Mentions: 1
Published: over 8 years ago

10.1111/pbi.12754

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth
Cited by: 40
Author(s): Qiang Lu, Fenjuan Shao, Colleen MacMillan, Iain W. Wilson, Karen Van der Merwe, Steven G. Hussey, Alexander Andrew Myburg, Xiaomei Dong, Deyou Qiu
Software Mentions: 1
Published: over 9 years ago

10.1534/g3.120.401348

Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera
Cited by: 6
Author(s): Kira Treibergs, Gonzalo Giribet
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-37609-0

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone
Cited by: 20
Author(s): Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Jennifer Tickner, Nathan J. Pavlos, Frank Dudbridge, Jiake Xu, John P. Walsh, Scott G. Wilson
Software Mentions: 1
Published: over 7 years ago

10.1093/g3journal/jkab020

Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes
Cited by: 22
Author(s): Caitlin E. McDonough-Goldstein, Kirill Borziak, Scott Pitnick, Steve Dorus
Software Mentions: 1
Published: over 5 years ago

10.1111/pbi.12913

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat
Cited by: 27
Author(s): Elodie Rey, Michaël Abrouk, Gabriel Keeble‐Gagnère, Miroslava Karafiátová, Jan Vrána, Sandrine Balzergue, Ludivine Soubigou‐Taconnat, Véronique Brunaud, Marie‐Laure Martin‐Magniette, Takashi R. Endo, Jan Bartoš, R. Appels, Jaroslav Doležel
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-5522-7

Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2
Cited by: 9
Author(s): Allison R. Kolbe, Anthony J. Studer, Omar E. Cornejo, Asaph B. Cousins
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-15-492

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development
Cited by: 63
Author(s): David Fernando Plaza, Chi Feng Lin, Niels Sebastiaan Johannes van der Velden, Markus Aebi, Markus Künzler
Software Mentions: 1
Published: over 12 years ago

10.1155/2021/5552324

TMEM100 Modulates TGF-β Signaling Pathway to Inhibit Colorectal Cancer Progression
Cited by: 3
Author(s): Huixia Li, C. Yan Cheng, Weibo You, Jiujian Zheng, Jie Xu, Peng Gao, Jianping Wang
Software Mentions: 1
Published: about 5 years ago

10.1155/2021/2894117

MiR-490-5p Restrains Progression of Gastric cancer through DTL Repression
Cited by: 5
Author(s): Jianjie Li, Xiaoyue Xu, Chunhui Liu, Xiaoxue Xi, Yang Wang, Xiaotang Wu, Hua Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3664-z

Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
Cited by: 16
Author(s): Antanas Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-37755-5

Reference assembly and gene expression analysis of Apostichopus japonicus larval development
Cited by: 9
Author(s): Alexey V. Boyko, Alexander S. Girich, М. Г. Елисейкина, С. И. Масленников, Igor Yu. Dolmatov
Software Mentions: 1
Published: over 7 years ago

10.3390/genes6030901

Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress
Cited by: 30
Author(s): Cai‐Hua Zhang, Tao Ma, Wei Luo, Jieting Xu, Jianquan Liu, Dongshi Wan
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-018-38368-8

Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Cited by: 31
Author(s): Ki Wook Kim, Jessica L. Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A. Bull, Fabio Luciani, Marc R. Wilkins, Jacki Catteau, W. Ian Lipkin, William D. Rawlinson, Thomas Briese, Maria E. Craig
Software Mentions: 1
Published: over 7 years ago

10.1007/s00425-020-03424-z

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach
Cited by: 3
Author(s): Izabela Sierocka, Sylwia Alaba, Artur Jarmołowski, Wojciech M. Karłowski, Zofia Szweykowska-Kulińska
Software Mentions: 1
Published: over 6 years ago

10.3390/genes8040119

Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing
Cited by: 40
Author(s): Yue Li, Liqiang Wan, Shuyi Bi, Xiu-Fu Wan, Zhenyi Li, Jiang Cao, Zongyong Tong, Hongyu Xu, Feng He, Xianglin Li
Software Mentions: 1
Published: over 9 years ago

10.3390/genes8060156

Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)
Cited by: 31
Author(s): Kewei Feng, Xiaojun Nie, Licao Cui, Pingchuan Deng, Mengxing Wang, Weining Song
Software Mentions: 1
Published: over 9 years ago

10.3390/genes8080195

Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell
Cited by: 4
Author(s): Gonzalo H. Villarino, Qiwen Hu, Michael J. Scanlon, Lukas A. Mueller, Aureliano Bombarely, Neil S. Mattson
Software Mentions: 1
Published: about 9 years ago

10.3390/ani11061563

Expression Characteristics of microRNA in Pig Umbilical Venous Blood and Umbilical Arterial Blood
Cited by: 5
Author(s): Mailin Gan, Lin Liu, Shunhua Zhang, Zhanbao Guo, Yimin Tan, Jia Luo, Qiong Yang, Hongmei Pan, Xuewei Li, Jinyong Wang, Linyuan Shen, Li Zhu
Software Mentions: 1
Published: over 5 years ago

10.14814/phy2.14344

Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia
Cited by: 9
Author(s): Matthew W. Gorr, Krishna Sriram, Amy M. Chinn, Abinaya Muthusamy, Paul A. Insel
Software Mentions: 1
Published: almost 7 years ago

10.3390/genes8100287

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes
Cited by: 18
Author(s): Étienne Danchin, Laetitia Perfus‐Barbeoch, Corinne Rancurel, Peter Thorpe, Martine Da Rocha, Simon Bajew, Roy Neilson, Elena Sokolova Guzeeva, Corinne Da Silva, Julie Guy, Karine Labadie, Daniel Esmenjaud, J. Helder, John T. Jones, Sebastian Eves‐van den Akker
Software Mentions: 1
Published: about 9 years ago

10.3390/genes8110291

RNA-Seq Analysis of Plant Maturity in Crested Wheatgrass (Agropyron cristatum L.)
Cited by: 6
Author(s): Fangqin Zeng, Bill Biligetu, Bruce Coulman, Michael P. Schellenberg, Yong‐Bi Fu
Software Mentions: 1
Published: about 9 years ago

10.3390/genes8110317

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome
Cited by: 19
Author(s): Alexandra J. Weisberg, Gunjune Kim, James H. Westwood, John G. Jelesko
Software Mentions: 1
Published: almost 9 years ago

10.3390/genes8110330

The HMGA1 Pseudogene 7 Induces miR-483 and miR-675 Upregulation by Activating Egr1 through a ceRNA Mechanism
Cited by: 21
Author(s): Marco De Martino, Giuseppe Palma, Amalia Azzariti, Claudio Arra, Alfredo Fusco, Francesco Esposito
Software Mentions: 1
Published: almost 9 years ago

10.14814/phy2.12473

The effect of acute and long-term physical activity on extracellular matrix and serglycin in human skeletal muscle
Cited by: 43
Author(s): Marit Hjorth, Frode Norheim, Astri Jeanette Meen, Shirin Pourteymour, Sindre Lee, Torgeir Holen, Jørgen Jensen, Kåre I. Birkeland, Vladimir Martinov, Torgrim M. Langleite, Kristin Eckardt, Christian A. Drevon, Svein Olav Kolset
Software Mentions: 1
Published: about 11 years ago

10.14814/phy2.14289

Prostaglandin D2signaling is not involved in the recovery of rat hind limb tendons from injury
Cited by: 3
Author(s): Dylan C. Sarver, Kristoffer B. Sugg, Jeffrey R Talarek, Jacob B. Swanson, David J. Oliver, Aaron C. Hinken, Henning F. Kramer, Christopher L. Mendias
Software Mentions: 1
Published: almost 7 years ago

10.14814/phy2.12750

RNA-sequencing of WFS1-deficient pancreatic islets
Cited by: 17
Author(s): Marilin Ivask, Alison Hugill, Sulev Kõks
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-019-38628-1

Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Cited by: 38
Author(s): Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.9849

Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat
Cited by: 0
Author(s): Junhao Huang, Lesha Zhang, Yang Fang, Wan Jiang, Juan Du, Jiaquan Zhu, Min Hu, Bing Shen
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.4140

Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
Cited by: 18
Author(s): Jinge Ma, Linmiao Li, Haiying Jiang, Xiujuan Zhang, Juan Li, Guanyu Li, Lihong Yuan, Jun Wu, Jinping Chen
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.5681

De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis
Cited by: 19
Author(s): Li Li, Mimi Li, Xiwu Qi, Tang Xingli, Yunshan Zhou
Software Mentions: 1
Published: about 8 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 6 years ago

10.1038/s41398-021-01270-5

Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape
Cited by: 10
Author(s): Divya Mehta, Karen Grewen, Brenda Pearson, Shivangi Wani, Leanne Wallace, Anjali K. Henders, Elisabeth B. Binder, Vibe G. Frøkjær, Samantha Meltzer‐Brody, Naomi R. Wray, Alison M. Stuebe
Software Mentions: 1
Published: over 5 years ago

10.3906/biy-2101-61

Identification of differentially expressed microRNAs in primary esophageal achalasia by next-generation sequencing
Cited by: 2
Author(s): Mahin Gholipour, Javad Mikaeli, Seyed Javad Mowla, Mohammad Reza Bakhtiarizadeh, Marie Saghaeian Jazi, Naeme Javid, Narges Fazlollahi, Masoud Khoshnia, Nasser Behnampour, Abdolvahab Moradi
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.02383-14

High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile
Cited by: 133
Author(s): Marcin Dembek, Lars Barquist, Christine J. Boinett, Amy K. Cain, Matthew Mayho, Trevor D. Lawley, Neil F. Fairweather, Robert P. Fagan
Software Mentions: 1
Published: over 11 years ago

10.1128/mBio.01384-18

Inhibition of EGFR Signaling Protects from Mucormycosis
Cited by: 42
Author(s): Tonya Watkins, Teclegiorgis Gebremariam, Marc Swidergall, Amol C. Shetty, Karen T. Graf, Abdullah Alqarihi, Sondus Alkhazraji, Abrar I. Alsaadi, Vonetta L. Edwards, Scott G. Filler, Ashraf S. Ibrahim, Vincent M. Bruno
Software Mentions: 1
Published: about 8 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: over 6 years ago

10.1128/mBio.00789-19

A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer
Cited by: 65
Author(s): Dawn E. Holmes, Toshiyuki Ueki, Haiyan Tang, Junhu Zhou, Jessica A. Smith, Gina Chaput, Derek R. Lovley
Software Mentions: 1
Published: about 7 years ago

10.1128/mBio.02176-19

Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers
Cited by: 40
Author(s): Jiwei Zhang, Kevin A.T. Silverstein, Jesús D. Castaño, Melania Figueroa, Jonathan S. Schilling
Software Mentions: 1
Published: almost 7 years ago

10.1128/mBio.02243-19

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis
Cited by: 37
Author(s): Tjorven Hinzke, Manuel Kleiner, Corinna Breusing, Horst Felbeck, Robert Häsler, Stefan M. Sievert, Rabea Schlüter, Philip Rosenstiel, Thorsten B. H. Reusch, Thomas Schweder, Stephanie Markert
Software Mentions: 1
Published: almost 7 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: over 8 years ago

10.7554/eLife.28415

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions
Cited by: 54
Author(s): Jason A. Morrison, Rebecca McLennan, Lauren A. Wolfe, Madelaine Gogol, Samuel R. Meier, Mary Cathleen McKinney, Jessica M. Teddy, Laura Holmes, Craig L. Semerad, Andrew Box, Hua Li, Kathryn Hall, Anoja Perera, Paul M. Kulesa
Software Mentions: 1
Published: almost 9 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 7 years ago

10.1128/mSphere.00283-16

Global Role of Cyclic AMP Signaling in pH-Dependent Responses in Candida albicans
Cited by: 14
Author(s): Jeffrey M. Hollomon, Nora Grahl, Sven D. Willger, Katja Koeppen, Deborah A. Hogan
Software Mentions: 1
Published: almost 10 years ago

10.1128/mSphere.00245-17

Transcriptomic Signatures of Tacaribe Virus-Infected Jamaican Fruit Bats
Cited by: 17
Author(s): Diana L. Gerrard, Ann Hawkinson, Tyler Sherman, Cassandra M. Modahl, Gretchen Hume, Corey L. Campbell, Tony Schountz, Seth Frietze
Software Mentions: 1
Published: about 9 years ago

10.1128/mSphereDirect.00375-17

The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
Cited by: 12
Author(s): Jannik Donner, Michael Reck, Boyke Bunk, Michael Jarek, Constantin Benjamin App, Jan P. Meier‐Kolthoff, Jörg Overmann, Rolf Müller, Andreas Kirschning, Irene Wagner‐Döbler
Software Mentions: 1
Published: about 9 years ago

10.1128/mSphere.00094-17

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea
Cited by: 14
Author(s): Louisi Souza de Oliveira, Diogo A. Tschoeke, Ana Carolina Rubem Magalhães Lopes, Daniela Bueno Sudatti, Pedro Milet Meirelles, Cristiane C. Thompson, Renato Crespo Pereira, Fabiano L. Thompson
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.50346

Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway
Cited by: 2
Author(s): Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kayoko Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Katsuyuki Murata, Masafumi Muratani, Masatsugu Ema, Jun-Dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken‐ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama
Software Mentions: 1
Published: over 5 years ago

10.1128/mSphereDirect.00262-18

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis
Cited by: 58
Author(s): Zhi-Luo Deng, Cornelia Gottschick, Sabin Bhuju, Clarissa Masur, Christoph Abels, Irene Wagner‐Döbler
Software Mentions: 1
Published: over 8 years ago

10.1128/mSphere.00366-18

Glucose Signaling Is Important for Nutrient Adaptation during Differentiation of Pleomorphic African Trypanosomes
Cited by: 33
Author(s): Yijian Qiu, Jillian E. Milanes, Jessica A. Jones, Rooksana E. Noorai, Vijay Shankar, James C. Morris
Software Mentions: 1
Published: almost 8 years ago

10.1128/mSphere.00620-19

Global Transcriptomic Analysis of the Candida albicans Response to Treatment with a Novel Inhibitor of Filamentation
Cited by: 16
Author(s): Jesús A. Romo, Hao Zhang, Hong Cai, David Kadosh, Julia Koehler, Stephen P. Saville, Yufeng Wang, José L. Lopez-Ribot
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSphere.00983-19

20-Hydroxyecdysone Primes Innate Immune Responses That Limit Bacterial and Malarial Parasite Survival in Anopheles gambiae
Cited by: 28
Author(s): Richard A. K. Reynolds, Hyeogsun Kwon, Ryan C. Smith
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.00179-21

The pH-Responsive Transcription Factors YlRim101 and Mhy1 Regulate Alkaline pH-Induced Filamentation in the Dimorphic Yeast Yarrowia lipolytica
Cited by: 8
Author(s): Tao Shu, Xinyu He, Jia-Wen Chen, Yi-Sheng Mao, Xiang-Dong Gao
Software Mentions: 1
Published: over 5 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 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

10.1128/mSystems.00275-18

Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum
Cited by: 3
Author(s): Jake J. Flood, Shelley D. Copley
Software Mentions: 1
Published: almost 8 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 6 years ago

10.1128/mSystems.00819-20

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy
Cited by: 16
Author(s): Jiawei He, Xu‐jie Zhou, Yafeng Li, Yan-Na Wang, Lijun Liu, Sufang Shi, Xu Xin, Rongshan Li, Mario Falchi, Jicheng Lv, Hong Zhang
Software Mentions: 1
Published: over 5 years ago

10.1128/mSystems.01190-20

Juvenile Hormone-Sensitive Ribosomal Activity Enhances Viral Replication in Aedes aegypti
Cited by: 7
Author(s): Zuo-Kun Shi, Dan Wen, Mengmeng Chang, Xiaomei Sun, Yanhong Wang, Chihang Cheng, Liqin Zhang, Ai Zheng, Zhen Zou
Software Mentions: 1
Published: over 5 years ago

10.1186/s40246-021-00308-5

High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis
Cited by: 15
Author(s): Weitong Cui, Huaru Xue, Lei Wei, Jinghua Jin, Xuewen Tian, Qinglu Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41396-020-00797-7

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
Cited by: 14
Author(s): Gust Bilcke, Koen Van Den Berge, Sam De Decker, Eli Bonneure, Nicole Poulsen, Petra Bulánková, Cristina Maria Osuna-Cruz, Jack Dickenson, Koen Sabbe, Georg Pohnert, Klaas Vandepoele, Sven Mangelinckx, Lieven De Veylder, Wim Vyverman
Software Mentions: 1
Published: about 6 years ago

10.1038/s41396-019-0393-0

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide
Cited by: 101
Author(s): Zahra F. Islam, Paul R. F. Cordero, Joanna Feng, Ya-Jou Chen, Sean K. Bay, Thanavit Jirapanjawat, Roslyn M. Gleadow, Carlo R. Carere, Matthew B. Stott, Eleonora Chiri, Chris Greening
Software Mentions: 1
Published: over 7 years ago

10.1038/s41396-017-0034-4

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise
Cited by: 27
Author(s): Songjun Hou, Mario López‐Pérez, Ulrike Pfreundt, Natalia Belkin, Kurt Stüber, Bruno Huettel, Richard Reinhardt, Ilana Berman‐Frank, Francisco Rodrı́guez-Valera, Wolfgang R. Hess
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41396-017-0005-9

Deciphering the nature of the coral–Chromera association
Cited by: 31
Author(s): Amin R. Mohamed, Vivian R. Cumbo, Saki Harii, Chuya Shinzato, Cheong Xin Chan, Mark A. Ragan, Nori Satoh, Eldon E. Ball, David J. Miller
Software Mentions: 1
Published: almost 9 years ago

10.1038/ismej.2017.18

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects
Cited by: 27
Author(s): Beatriz Sabater-Muñoz, Christina Toft, David Alvarez‐Ponce, Mario A. Fares
Software Mentions: 1
Published: over 9 years ago

10.1038/s41396-020-0718-z

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms
Cited by: 12
Author(s): Rebecca E. Cooper, Carl‐Eric Wegner, Stefan Kügler, Remington X. Poulin, Nico Ueberschaar, Jens D. Wurlitzer, Daniel Stettin, Thomas Wichard, Georg Pohnert, Kirsten Küsel
Software Mentions: 1
Published: over 6 years ago

10.7150/ijbs.55559

Generation of VEGF knock-in Cashmere goat via the CRISPR/Cas9 system
Cited by: 12
Author(s): Xiao Hu, Hao Fei, Xiaocong Li, Zhiyuan Xun, Yuan Gao, Bo Ren, Ming Cang, Hao Liang, Dongjun Liu
Software Mentions: 1
Published: almost 6 years ago

10.7150/ijbs.63430

CCNB2/SASP/Cathepsin B & PGE2 Axis Induce Cell Senescence Mediated Malignant Transformation
Cited by: 5
Author(s): Ying Wang, Hanbing Zhang, Minglei Wang, Jing He, Hui Guo, Lihua Li, Jie Wang
Software Mentions: 1
Published: almost 6 years ago

10.7150/ijbs.57871

Characteristics of the PI3K/AKT and MAPK/ERK pathways involved in the maintenance of self-renewal in lung cancer stem-like cells
Cited by: 14
Author(s): Jingyuan Li, Yunlong Wang, Dan Xie, Pei Qin, Xue Wan, H. Rosie Xing, Ting Ye
Software Mentions: 1
Published: almost 6 years ago

10.7150/ijbs.59581

The effect of mitochondrial transplantation therapy from different gender on inhibiting cell proliferation of malignant melanoma
Cited by: 8
Author(s): Zhenyao Yu, Yixue Hou, Wei Zhou, Zizhen Zhao, Zesheng Liu, Ailing Fu
Software Mentions: 1
Published: almost 6 years ago

10.7150/ijbs.62471

Rutin attenuates Sorafenib-induced Chemoresistance and Autophagy in Hepatocellular Carcinoma by regulating BANCR/miRNA-590-5P/OLR1 Axis
Cited by: 28
Author(s): Meng Zhou, Gan Zhang, Jun Hu, Yanzhi Zhu, Haoming Lan, Xianfeng Shen, Yi Lv, Lei Huang
Software Mentions: 1
Published: almost 6 years ago

10.7150/ijbs.36412

Circular RNA profiling identified an abundant circular RNA circTMTC1 that inhibits chicken skeletal muscle satellite cell differentiation by sponging miR-128-3p
Cited by: 56
Author(s): Xiaoxu Shen, Zihao Liu, Xinao Cao, Haorong He, Shunshun Han, Yuqi Chen, Can Cui, Jing Zhao, Diyan Li, Yan Wang, Qing Zhu, Huadong Yin
Software Mentions: 1
Published: almost 8 years ago

10.7150/ijbs.58916

Circular RNA circBCBM1 promotes breast cancer brain metastasis by modulating miR-125a/BRD4 axis
Cited by: 27
Author(s): Bo Fu, Wei Liu, Congshan Zhu, Peng Li, Li Wang, Pan Li, Ké Li, Peiying Cai, Min Meng, Yiting Wang, Anqi Zhang, Wenqiang Tang, Meng An
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13046-018-0833-0

Overexpression of the Kininogen-1 inhibits proliferation and induces apoptosis of glioma cells
Cited by: 41
Author(s): Jinfang Xu, Jun Fang, Zhonghao Cheng, Longlong Fan, Weiwei Hu, Feng Zhou, Hong Shen
Software Mentions: 1
Published: about 8 years ago

10.1186/s13046-019-1315-8

Long non-coding RNA LUCAT1/miR-5582-3p/TCF7L2 axis regulates breast cancer stemness via Wnt/β-catenin pathway
Cited by: 93
Author(s): Aiping Zheng, Xinyue Song, Lin Zhang, Lin Zhao, Xiaoyun Mao, Minjie Wei, Feng Jin
Software Mentions: 1
Published: over 7 years ago

10.1186/s13046-020-01763-z

Therapeutic evaluation of palbociclib and its compatibility with other chemotherapies for primary and recurrent nasopharyngeal carcinoma
Cited by: 11
Author(s): Zhichao Xue, Vivian Wai Yan Lui, Yongshu Li, Lin Jia, Chanping You, Xin Li, Wenying Piao, Hui Yuan, Pek Lan Khong, Kwok Wai Lo, Lydia W.T. Cheung, Victor Ho Fan Lee, Anne W.M. Lee, Sai Wah Tsao, Chi Man Tsang
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.40969

Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites
Cited by: 41
Author(s): Juliane Fischer, Sebastian Müller, Tina Netzker, Nils Jäger, Agnieszka Gacek‐Matthews, Kirstin Scherlach, Maria C. Stroe, María García‐Altares, Francesco Pezzini, Hanno Schoeler, Michael Reichelt, Jonathan Gershenzon, Mario K. C. Krespach, Ekaterina Shelest, Volker Schroeckh, Vito Valiante, Thorsten Heinzel, Christian Hertweck, Joseph Strauss, Axel A. Brakhage
Software Mentions: 1
Published: about 8 years ago

10.1084/jem.20190450

Tumor-derived IL-6 and trans-signaling among tumor, fat, and muscle mediate pancreatic cancer cachexia
Cited by: 76
Author(s): Joseph E. Rupert, Ashok Narasimhan, Daenique H. Jengelley, Yanlin Jiang, Jianguo Liu, Ernie D. Au, Libbie M Silverman, George E. Sandusky, Andrea Bonetto, Sha Cao, Xiaoyu Lu, Thomas M. O’Connell, Yunlong Liu, Leonidas G. Koniaris, Teresa A. Zimmers
Software Mentions: 1
Published: over 5 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 8 years ago

10.7554/eLife.63502

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Cited by: 88
Author(s): Anastasia A. Minervina, Ekaterina A. Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z. Mamedov, André Franke, Grigory A. Efimov, Dmitriy M. Chudakov, Thierry Mora, Aleksandra M. Walczak, Yuri B Lebedev, Mikhail V. Pogorelyy
Software Mentions: 1
Published: almost 6 years ago

10.3390/jof7050373

Transcriptome Analysis of the Japanese Pine Sawyer Beetle, Monochamus alternatus, Infected with the Entomopathogenic Fungus Metarhizium anisopliae JEF-197
Cited by: 4
Author(s): Jong-Cheol Kim, Mi-Rong Lee, Sihyeon Kim, So-Eun Park, Se-Jin Lee, Tae‐Young Shin, Woo Jin Kim, Jaesu Kim
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568