bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1111/1751-7915.12713

Transcriptional response ofEscherichia colito ammonia and glucose fluctuations
Cited by: 39
Author(s): Joana Danica Simen, Michael Löffler, Günter Jäger, Karin Schäferhoff, Andreas Freund, Jakob Matthes, Jan Müller, Ralf Takors, RecogNice-Team
Software Mentions: 2
Published: over 9 years ago

10.15698/mic2018.05.630

Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK
Cited by: 11
Author(s): Nazif Maqani, Ryan D. Fine, Mehreen Shahid, Mingguang Li, Elisa Enriquez-Hesles, Jeffrey S. Smith
Software Mentions: 2
Published: over 8 years ago

10.1186/s12934-021-01626-y

Alternative oxidase gene induced by nitric oxide is involved in the regulation of ROS and enhances the resistance of Pleurotus ostreatus to heat stress
Cited by: 14
Author(s): Ludan Hou, Ming Zhao, Chenyang Huang, Qi He, Lijiao Zhang, Jinxia Zhang
Software Mentions: 2
Published: about 5 years ago

10.1099/mgen.0.000246

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii
Cited by: 27
Author(s): Christine J. Boinett, Amy K. Cain, Jane Hawkey, Nhu Tran Do Hoang, Nhu Nguyen Thi Khanh, Duy Pham Thanh, Janina Dordel, James I. Campbell, Nguyen Phu Huong Lan, Matthew Mayho, Gemma Langridge, James Hadfield, Nguyễn Văn Vĩnh Châu, Guy Thwaites, Julian Parkhill, Nicholas R. Thomson, Kathryn E. Holt, Stephen Baker
Software Mentions: 2
Published: over 7 years ago

10.1099/mgen.0.000194

Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Cited by: 28
Author(s): Erin P. Price, Linda T. Viberg, Timothy J. Kidd, Scott C. Bell, Bart J. Currie, Derek S. Sarovich
Software Mentions: 2
Published: about 8 years ago

10.1099/mgen.0.000374

Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex
Cited by: 13
Author(s): Osiel Silva Gonçalves, Kiara França Campos, Jéssica Catarine Silva de Assis, Alexia Suellen Fernandes, Thamires Santos Souza, Luiz Guilherme do Carmo Rodrigues, Marisa Vieira de Queiroz, Mateus Ferreira Santana
Software Mentions: 2
Published: over 6 years ago

10.1099/mgen.0.000148

Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli
Cited by: 6
Author(s): Hélène Gingras, Bédis Dridi, Philippe Leprohon, Marc Ouellette
Software Mentions: 2
Published: over 8 years ago

10.1002/mbo3.768

Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments
Cited by: 17
Author(s): Luis J Perez Calderon, Evangelia Gontikaki, Lloyd D. Potts, Sophie Shaw, Alejandro Gallego, James A. Anderson, Ursula Witte
Software Mentions: 2
Published: almost 8 years ago

10.1002/mbo3.1153

Microbiota succession during aerobic stability of maize silage inoculated with Lentilactobacillus buchneri NCIMB 40788 and Lentilactobacillus hilgardii CNCM‐I‐4785
Cited by: 22
Author(s): Pascal Drouin, Julien Tremblay, Justin B. Renaud, Emmanuelle Apper
Software Mentions: 2
Published: over 5 years ago

10.1002/mbo3.608

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free‐living bacteria in the water column
Cited by: 6
Author(s): Limei Shi, Huang Yin-hui, Min Zhang, Xiaoli Shi, Yuanfeng Cai, Shengling Gao, Xiangming Tang, Feizhou Chen, Yaping Lü, Fanxiang Kong
Software Mentions: 2
Published: over 8 years ago

10.1002/mbo3.510

A1S_2811, a CheA/Y-like hybrid two-component regulator fromAcinetobacter baumanniiATCC17978, is involved in surface motility and biofilm formation in this bacterium
Cited by: 27
Author(s): Rong Chen, Ruichen Lv, Xiao Jun Lin, Min Wang, Zongmin Du, Yafang Tan, Yu‐Jun Cui, Yanfeng Yan, Yanping Luo, Ruifu Yang, Yajun Song
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-019-0780-9

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem
Cited by: 76
Author(s): Xinyu Zhu, Stefano Campanaro, Laura Treu, Rekha Seshadri, Natalia Ivanova, Panagiotis Kougias, Nikos C. Kyrpides, Irini Angelidaki
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-018-0583-4

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics
Cited by: 31
Author(s): Alessandra Fontana, Panagiotis Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, L. Morelli, Irini Angelidaki, Stefano Campanaro
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-018-0606-1

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages
Cited by: 25
Author(s): Samuel Jacquiod, Inês Nunes, Asker Brejnrod, Mette Sif Hansen, Peter E. Holm, Anders Johansen, Kristian K. Brandt, Anders Priemé, Søren J. Sørensen
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-017-0311-5

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism
Cited by: 48
Author(s): Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-018-0589-y

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential
Cited by: 16
Author(s): Celso Martins, Adélia Varela, Céline C. Leclercq, Óscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrián, Cristina Silva Pereira
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-020-00833-w

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions
Cited by: 55
Author(s): Stien Beirinckx, Tom Viaene, Annelies Haegeman, Jane Debode, Fien Amery, Sophie Vandenabeele, Hilde Nelissen, Dirk Inzé, Raúl Y. Tito, Jeroen Raes, Caroline De Tender, Sofie Goormachtig
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms8020271

Regulatory Patterns of Crp on Monensin Biosynthesis in Streptomyces cinnamonensis
Cited by: 7
Author(s): Cai‐Xia Lin, Yue Zhang, Jun Wu, Rong-hui Xie, Jianjun Qiao, Guang‐Rong Zhao
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9050991

Global Changes in Asexual Epichloë Transcriptomes during the Early Stages, from Seed to Seedling, of Symbiotum Establishment
Cited by: 6
Author(s): Inoka K Hettiarachchige, Christy J. Vander Jagt, Ross Mann, Tim Sawbridge, Germán Spangenberg, Kathryn M. Guthridge
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms9081680

A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites
Cited by: 7
Author(s): Domenico Davolos, Fabiana Russo, Loredana Canfora, Eligio Malusà, Małgorzata Tartanus, Ewa M. Furmanczyk, Andrea Ceci, Oriana Maggi, Anna Maria Persiani
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms7090358

A Discovery of Relevant Hepatoprotective Effects and Underlying Mechanisms of Dietary Clostridium butyricum Against Corticosterone-Induced Liver Injury in Pekin Ducks
Cited by: 8
Author(s): Yanhan Liu, Cun Liu, Liqing Huang, Zhaofei Xia
Software Mentions: 2
Published: almost 7 years ago

10.3390/microorganisms8091443

Transcriptome Profiling of Potato (Solanum tuberosum L.) Responses to Root-Knot Nematode (Meloidogyne javanica) Infestation during A Compatible Interaction
Cited by: 8
Author(s): Teresia Nyambura Macharia, Daniel Bellieny-Rabelo, Lucy N. Moleleki
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms9071445

Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Cited by: 1
Author(s): Dung Minh Ha-Tran, Trinh Thi My Nguyen, Shou-Chen Lo, Chieh-Chen Huang
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms9071417

Acinetobacter tandoii ZM06 Assists Glutamicibacter nicotianae ZM05 in Resisting Cadmium Pressure to Preserve Dipropyl Phthalate Biodegradation
Cited by: 10
Author(s): Xuejun Wang, Si Shen, Hao Wu, Haixia Wang, Lvjing Wang, Zhenmei Lü
Software Mentions: 2
Published: about 5 years ago

10.3390/microorganisms9020391

Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found
Cited by: 18
Author(s): Souvik Paul, R. N. Chatterjee, M.V.L.N. Raju, B. Prakash, S.V. Rama Rao, Sandeep Yadav, A. Kannan
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms8111759

Response of Coral Reef Dinoflagellates to Nanoplastics under Experimental Conditions Suggests Downregulation of Cellular Metabolism
Cited by: 24
Author(s): Christina Ripken, Konstantin Khalturin, Eiichi Shoguchi
Software Mentions: 2
Published: almost 6 years ago

10.17912/micropub.biology.000397

Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans.
Cited by: 3
Author(s): Sarah M Cohen, Jessica J. Sun, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 2
Published: over 5 years ago

10.1093/molbev/msaa071

Rampant Misexpression in a Mimulus (Monkeyflower) Introgression Line Caused by Hybrid Sterility, Not Regulatory Divergence
Cited by: 7
Author(s): Rachel E. Kerwin, Andrea L. Sweigart
Software Mentions: 2
Published: over 6 years ago

10.1093/molbev/msx123

Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers
Cited by: 47
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 2
Published: over 9 years ago

10.1093/molbev/msw119

Sex, Scavengers, and Chaperones: Transcriptome Secrets of DivergentSymbiodiniumThermal Tolerances
Cited by: 110
Author(s): Rachel A. Levin, Victor H. Beltran, Ross Hill, Staffan Kjelleberg, Diane McDougald, Peter D. Steinberg, Madeleine J. H. van Oppen
Software Mentions: 2
Published: about 10 years ago

10.1186/s13041-020-00715-0

The novel multiple sclerosis susceptibility gene ATXN1 regulates B cell receptor signaling in B-1a cells
Cited by: 5
Author(s): Qin Ma, Alessandro Didonna
Software Mentions: 2
Published: over 5 years ago

10.12688/wellcomeopenres.14645.4

Probing Plasmodium falciparum sexual commitment at the single-cell level
Cited by: 44
Author(s): Nicolas M. B. Brancucci, Mariana De Niz, Timothy J. Straub, Deepali Ravel, Lauriane Sollelis, Bruce W. Birren, Till S. Voss, Daniel E. Neafsey, Matthias Marti
Software Mentions: 2
Published: almost 8 years ago

10.12688/wellcomeopenres.14797.2

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern
Cited by: 10
Author(s): Jing-wen Lin, Adam J. Reid, Deirdre Cunningham, Ulrike Böhme, Irene Tumwine, Sara Keller-Mclaughlin, Mandy Sanders, Matthew Berriman, Jean Langhorne
Software Mentions: 2
Published: over 7 years ago

10.12688/wellcomeopenres.15059.1

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313
Cited by: 8
Author(s): Edna Ondari, Elizabeth J. Klemm, Chisomo Msefula, Moataz Abd El Ghany, Jennifer N. Heath, Derek Pickard, Lars Barquist, Gordon Dougan, Robert A. Kingsley, Calman A. MacLennan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12957-020-01909-5

Combining texture features of whole slide images improves prognostic prediction of recurrence-free survival for cutaneous melanoma patients
Cited by: 7
Author(s): Yanbin Peng, Yunfeng Chu, Zhong Chen, Wen Zhou, Shengxiang Wan, Yingfeng Xiao, Youlong Zhang, Jialu Li
Software Mentions: 2
Published: about 6 years ago

10.1186/s13071-019-3506-8

Anopheles aquasalis transcriptome reveals autophagic responses to Plasmodium vivax midgut invasion
Cited by: 7
Author(s): Rosa Amélia Gonçalves Santana, Maurício Oliveira, Iria Cabral, Rubens Celso Andrade Silva, Débora Raysa Teixeira de Sousa, L. S. Ferreira, Marcus Vinícius Guimarães Lacerda, Wuelton Marcelo Monteiro, Patrícia Abrantes, Maria das Graças Vale Barbosa Guerra, Henrique Silveira
Software Mentions: 2
Published: over 7 years ago

10.1186/s13071-014-0622-3

Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery
Cited by: 11
Author(s): Nicholas J. Wheeler, Prince N Agbedanu, Michael J. Kimber, Paula Ribeiro, Tim A. Day, Mostafa Zamanian
Software Mentions: 2
Published: over 11 years ago

10.1186/s13071-016-1642-y

CAP protein superfamily members in Toxocara canis
Cited by: 6
Author(s): Andreas J. Stroehlein, Neil D. Young, Ross S. Hall, Pasi K. Korhonen, Andreas Hofmann, Paul W. Sternberg, Abdul Jabbar, Robin B. Gasser
Software Mentions: 2
Published: about 10 years ago

10.1186/s13071-018-3086-z

Transcriptomic analysis of male and female Schistosoma mekongi adult worms
Cited by: 25
Author(s): Orawan Phuphisut, Pravech Ajawatanawong, Yanin Limpanont, Onrapak Reamtong, Supaporn Nuamtanong, Sumate Ampawong, Salisa Chaimon, Paron Dekumyoy, Dorn Watthanakulpanich, Brett E. Swierczewski, Poom Adisakwattana
Software Mentions: 2
Published: almost 8 years ago

10.3390/pathogens9020145

Comparative Transcriptome Analysis of Two Cucumber Cultivars with Different Sensitivity to Cucumber Mosaic Virus Infection
Cited by: 10
Author(s): Z Šubr, Lukáš Predajňa, Katarína Šoltýs, Boris Bokor, Jaroslav Budiš, Miroslav Glasa
Software Mentions: 2
Published: over 6 years ago

10.3390/pathogens3040875

Comparison of Potato and Asian Citrus Psyllid Adult and Nymph Transcriptomes Identified Vector Transcripts with Potential Involvement in Circulative, Propagative Liberibacter Transmission
Cited by: 35
Author(s): Tonja W. Fisher, Meenal Vyas, Rong He, William M. Nelson, 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: 2
Published: almost 12 years ago

10.1186/s12969-019-0347-0

Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells
Cited by: 10
Author(s): Kaiyu Jiang, Rie Karasawa, Zihua Hu, Yanmin Chen, Lucy C Holmes, Kathleen M. O’Neil, James N. Jarvis
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.6949

Comprehensive transcriptional profiling of aging porcine liver
Cited by: 6
Author(s): Jianning Chen, Qin Zou, Daojun Lv, Muhammad Ali Raza, Xue Wang, Chen Yan, Xiaoyu Xi, Peilin Li, Anxiang Wen, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.11714

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
Cited by: 1
Author(s): Alex E. Mohr, Rebecca A. Reiss, Monique Beaudet, Johnny A. Sena, Jay S. Naik, Benjimen R. Walker, Karen L. Sweazea
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.3696

RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
Cited by: 4
Author(s): V. Katelyn Chandler, John P. Wares
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.8684

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity inC. elegans
Cited by: 10
Author(s): Charles Viau, Orçun Haçarız, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10204

Transcriptome analysis of diploid and triploid Populus tomentosa
Cited by: 3
Author(s): Bin Wen, Xiaozhen Liu, Zhiming Zhang, Hanyao Zhang
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.6991

Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
Cited by: 18
Author(s): Yidan Song, Yihua Pan, Jun Li
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.7360

A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
Cited by: 22
Author(s): Ruoyan Cao, Qiqi Wu, Qiulan Li, Meiling Yao, Hongbo Zhou
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.7946

High expression of HSP90 is associated with poor prognosis in patients with colorectal cancer
Cited by: 22
Author(s): Shuming Zhang, Shichao Guo, Zhangfu Li, Dan Li, Qimin Zhan
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.11875

Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing
Cited by: 1
Author(s): Tomoko Matsuda
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.8277

Biomarker potential of repetitive-element transcriptome in lung cancer
Cited by: 10
Author(s): María Castellano Arroyo, Rocío Bautista, Rafael Larrosa, Manuel Cobo, M. Gonzalo Claros
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.7353

A six-microRNA signature can better predict overall survival of patients with esophagus adenocarcinoma
Cited by: 7
Author(s): Tian Lan, Yunyan Lu, Zunqiang Xiao, Huiling Xu, Jinlan He, Zujian Hu, Weimin Mao
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.6397

Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma
Cited by: 26
Author(s): Shusen Zhang, Ruoyan Cao, Qiulan Li, Meiling Yao, Yu Chen, Hongbo Zhou
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.3275

Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fishXiphophorus multilineatus
Cited by: 4
Author(s): Yuan Lu, Charlotte Marie Klimovich, Kalen Z Robeson, William Boswell, Oscar Ríos-Cardenas, Ronald B. Walter, Molly R. Morris
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.10770

Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.
Cited by: 8
Author(s): Yudong Ren, Ning Zhang, Ru Li, Xiaomin Ma, Lugang Zhang
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.7785

Warm seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea
Cited by: 11
Author(s): Christine Guzman, Michael P. Atrigenio, Chuya Shinzato, Porfirio M. Aliño, Cecilia Conaco
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.2945

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
Cited by: 71
Author(s): William J. Brazelton, Christopher N Thornton, Alex Hyer, Katrina I. Twing, August Longino, Susan Q. Lang, Marvin D. Lilley, Gretchen L. Früh-Green, M. O. Schrenk
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.10159

Transcriptome-wide identification of MAPKKK genes in bermudagrass (Cynodon dactylon L.) and their potential roles in low temperature stress responses
Cited by: 3
Author(s): Wei Wang, Anwen Shao, Erick Amombo, Shugao Fan, Xiao Xu, Jinmin Fu
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.7732

Liver slice culture as a model for lipid metabolism in fish
Cited by: 7
Author(s): Thomas Nelson Harvey, Simen Rød Sandve, Yang Jin, Jon Olav Vik, Jacob Torgersen
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.9704

miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2
Cited by: 12
Author(s): Yan Wang, Shengtao Shang, Kun Yu, Hongbin Sun, Wenrui Ma, Wei Zhao
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.12114

Expression and prognosis of CDC45 in cervical cancer based on the GEO database
Cited by: 7
Author(s): Zikang He, Xiaojin Wang, Zhiming Yang, Ying Jiang, Luhui Li, Zheyao Song, Jiahui Wan, Jiangbo Shu, Naiwen Zhang, Rongjun Cui
Software Mentions: 2
Published: almost 5 years ago

10.7717/peerj.10762

A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing
Cited by: 8
Author(s): Alison Noble, John Pearson, Joseph M. Boden, L. John Horwood, Neil J. Gemmell, Martin A. Kennedy, Amy J. Osborne
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.7602

Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer
Cited by: 36
Author(s): Wenliang Yuan, Syd S. Peng, Jingyu Wang, Wei Cai, Zhen Ye, Ye Wang, Meiliang Wang, Hao Xu, Shouwen Jiang, Dan Sun, Chaoxu Dai, Linhua Jiang, Xiaobo Li
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.5389

Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
Cited by: 17
Author(s): Yeyu Chen, Liu Ya, Quan Gong, Jiansheng Lai, Mingjiang Song, Jun Du, Xiaochuan Deng
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pntd.0004311

The Effect of In Vitro Cultivation on the Transcriptome of Adult Brugia malayi
Cited by: 21
Author(s): Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew R. Moorhead, Steven A. Williams, Timothy G. Geary
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pntd.0008341

Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly
Cited by: 8
Author(s): Joy M. Kabaka, Benson M. Wachira, Clarence M. Mang’era, Martin K. Rono, Ahmed Hassanali, Sylvance Okoth, Vincent O. Oduol, Rosaline W. Macharia, Grace Murilla, Paul O. Mireji
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pntd.0005826

The microbiome in urogenital schistosomiasis and induced bladder pathologies
Cited by: 36
Author(s): Adewale Adebayo, Mangesh V. Suryavanshi, Shrikant Bhute, Atinuke M Agunloye, Raphael D. Isokpehi, Chiaka I. Anumudu, Yogesh S. Shouche
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0187147

De novo-based transcriptome profiling of male-sterile and fertile watermelon lines
Cited by: 5
Author(s): Sun-Ju Rhee, Tae-Hyung Kwon, Minseok Seo, Yoon Jeong Jang, Tae Yong Sim, Seoae Cho, Sang-Wook Han, Gung Pyo Lee
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0244558

DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden
Cited by: 8
Author(s): McKayla J. Riggs, Nan Lin, Chi Wang, Dava W. Piecoro, Rachel W. Miller, Oliver A. Hampton, Mahadev Rao, Frederick R. Ueland, Jill Kolesar
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0258090

Activation of fibroblast growth factor-inducible 14 in the early phase of childhood IgA nephropathy
Cited by: 1
Author(s): Yuko Tezuka, Minenori Eguchi‐Ishimae, Erina Ozaki, Toshiyuki Ito, Eiichi Ishii, Mariko Eguchi
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0180323

Seasonal differences in the testicular transcriptome profile of free-living European beavers (Castor fiber L.) determined by the RNA-Seq method
Cited by: 12
Author(s): Iwona Bogacka, Łukasz Paukszto, J Jastrzebski, Joanna Czerwińśka, Katarzyna Chojnowska, Barbara Kamińska, Aleksandra Kurzyńska, Nina Smolińska, Zygmunt Giżejewski, Tadeusz Kamiński
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0133468

Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica ‘Fuji’
Cited by: 24
Author(s): Nan Wang, Yi Zheng, Naibin Duan, Zongying Zhang, Xiaohao Ji, Shenghui Jiang, Shasha Sun, Long Yang, Yang Bai, Zhangjun Fei, Xuesen Chen
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0068191

Transient Exposure to Low Levels of Insecticide Affects Metabolic Networks of Honeybee Larvae
Cited by: 110
Author(s): K. Derecka, Martin Blythe, Sunir Malla, Diane P. Genereux, Alessandro Guffanti, Paolo Pavan, Anna Moles, Charles J.P. Snart, Thomas B. Ryder, Catharine A. Ortori, David A. Barrett, Eugene F. Schuster, Reinhard Stöger
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0239771

Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts
Cited by: 9
Author(s): Laurynne C. Coates, Jaclyn Mahoney, John S. Ramsey, EricaRose Warwick, Richard S. Johnson, Michael J. MacCoss, Stuart B. Krasnoff, Kevin J. Howe, Kathy Moulton, Surya Saha, Lukas A. Mueller, David G. Hall, Robert G. Shatters, Michelle Heck, Carolyn M. Slupsky
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0138162

Transcriptome Analysis of Poplar during Leaf Spot Infection with Sphaerulina spp.
Cited by: 29
Author(s): Adam Foster, G. Pelletier, Philippe Tanguay, Armand Séguin
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0240149

In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm
Cited by: 52
Author(s): Laura Artigas, Mireia Coma, Pedro Matos-Filipe, Joaquim Aguirre‐Plans, Judith Farrés, Raquel Valls, Narcís Fernández-Fuentes, Juan de la Haba-Rodríguez, Àlex Olvera, José Luis Barberá, Rafael Morales, Baldo Oliva, José Manuel Mas
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0220118

Molecular network-based identification of competing endogenous RNAs in bladder cancer
Cited by: 15
Author(s): Weidong Jiang, Pingcheng Yuan
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0165368

Gene Expression Dynamics Accompanying the Sponge Thermal Stress Response
Cited by: 35
Author(s): Christine Guzman, Cecilia Conaco
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0223554

An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma
Cited by: 7
Author(s): Imlimaong Aier, Rahul Semwal, Aiindrila Dhara, Nirmalya Sen, Pritish Kumar Varadwaj
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0108200

Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp
Cited by: 72
Author(s): Yanliang Jiang, Songhao Zhang, Jian Xu, Jianxin Feng, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Peng Xu
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0241698

Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation
Cited by: 25
Author(s): Bo Yu, Naresh Doni Jayavelu, Stephanie L. Battle, Jessica C. Mar, Timothy Schimmel, Jacques Cohen, R. David Hawkins
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0114376

Transcriptome Sequencing Reveals the Virulence and Environmental Genetic Programs of Vibrio vulnificus Exposed to Host and Estuarine Conditions
Cited by: 41
Author(s): Tiffany C. Williams, Eric G. Blackman, Shatavia S. Morrison, Cynthia Gibas, James D. Oliver
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0179531

Combining 'omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut
Cited by: 96
Author(s): Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard S. Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas A. Mueller, Michael J. MacCoss, Robert G. Shatters, Michelle Heck
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0186681

Transcriptome analysis of sheep oral mucosa response to Orf virus infection
Cited by: 12
Author(s): Huaijie Jia, Leilei Zhan, Xiaoxia Wang, Xu He, Guohua Chen, Yu Zhang, Feng Yuan, Yaxun Wei, Yi Zhang, Zhizhong Jing
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0029002

Deep Sequencing Whole Transcriptome Exploration of the σE Regulon in Neisseria meningitidis
Cited by: 25
Author(s): Robert Antonius Gerhardus Huis in ‘t Veld, Antonius Marcellinus Willemsen, A. H. C. van Kampen, Edward J. Bradley, Frank Baas, Yvonne Pannekoek, Arie van der Ende
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0068352

Detecting Splicing Variants in Idiopathic Pulmonary Fibrosis from Non-Differentially Expressed Genes
Cited by: 24
Author(s): Nan Deng, Cecilia G. Sánchez, Joseph A. Lasky, Dongxiao Zhu
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0106100

Differential Expression of Meis2, Mab21l2 and Tbx3 during Limb Development Associated with Diversification of Limb Morphology in Mammals
Cited by: 15
Author(s): Mengyao Dai, Yao Wang, Fang Lü, David M. Irwin, Tengteng Zhu, Junpeng Zhang, Zhe Wang
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0175417

Caste-, sex-, and age-dependent expression of immune-related genes in a Japanese subterranean termite, Reticulitermes speratus
Cited by: 31
Author(s): Yuki Mitaka, Keiko Kobayashi, Kenji Matsuura
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0121104

Lessons Learned from Whole Exome Sequencing in Multiplex Families Affected by a Complex Genetic Disorder, Intracranial Aneurysm
Cited by: 32
Author(s): Janice L. Farlow, Hai Lin, Laura Sauerbeck, Dongbing Lai, Daniel L. Koller, Elizabeth Pugh, Kurt N. Hetrick, Hua Ling, Rachel Kleinloog, Pieter van der Vlies, Patrick Deelen, Morris A. Swertz, Bon H. Verweij, Luca Regli, Gabriël J.E. Rinkel, Ynte M. Ruigrok, Kimberly F. Doheny, Yunlong Liu, Tatiana Foroud, Joseph P. Broderick, Daniel Woo, Brett M. Kissela, Dawn Kleindorfer, Alex Schneider, Mario Zuccarello, Andrew J. Ringer, Ranjan Deka, Robert D. Brown, John Huston, Irene Mesissner, David O. Wiebers, Adnan I. Qureshi, Peter A. Rasmussen, E. Sander Connolly, Ralph L. Sacco, Marc Malkaff, Troy D. Payner, Gary G. Ferguson, E. François Aldrich, Guy A. Rouleau, Craig S. Anderson, Edward Mee, Graeme J. Hankey, Neville W. Knuckey, Peter Reilly, John D. Laidlaw, Paul D’Urso, Jeffrey V. Rosenfeld, M. Morgan, Nicholas W.C. Dorsch, Michael Besser, H. Hunt Batjer, Marie-Claude Richard, Amin Kassam, Gary K. Steinberg, S. Claiborne Johnston, Nerissa Ko, Steven L. Giannotta, Neal F. Kassell, Bradford B. Worrall, Kenneth C. Lui, Aaron S. Dumont, David L. Tirschell, Anthony M. Kaufmann, Winfield S. Fisher, Khaled Aziz, Arthur L. Day, Rose Du, Christopher S. Ogilvy, Stephen B. Lewis, Kieran Murphy, Martin G. Radvany, Dheerah Gandhi, Lynda Lisabeth, Aditya S. Pandey, Lewis B. Morgenstern, Colin P. Derdeyn, Carl D. Langefeld, Joan E. Bailey-Wilson
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0165850

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand
Cited by: 20
Author(s): Marian Morales, Vladimir Sentchilo, Claire Bertelli, Andrea Komljenović, Nadezda Kryuchkova-Mostacci, Audrey Bourdilloud, Burkhard Linke, Alexander Goesmann, Keith Harshman, Francisca H. I. D. Segers, Fabien Delapierre, Damien Fiorucci, Mathieu Seppey, Evgeniya Trofimenco, Pauline Berra, Athimed El Taher, Chloé Loiseau, Dejan Roggero, Madeleine Sulfiotti, Angela Etienne, Gustavo Ruiz Buendia, Loïc Pillard, Angélique Escoriza, Roxane Moritz, Cédric Schneider, Esteban Alfonso, Fatma Ben Jeddou, Oliver Selmoni, Grégory Resch, Gilbert Greub, Olivier Emery, Manupriyam Dubey, Trestan Pillonel, Marc Robinson‐Rechavi, Jan Roelof van der Meer
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0105138

Contrasting Metabolism in Perenniating Structures of Upland and Lowland Switchgrass Plants Late in the Growing Season
Cited by: 22
Author(s): Nathan A. Palmer, Aaron J. Saathoff, Christian M. Tobias, Paul Twigg, Yuannan Xia, Kenneth P. Vogel, M. Soundararajan, Scott E. Sattler, Gautam Sarath
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0251883

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment
Cited by: 5
Author(s): Theodore M. Flynn, Dionysios A. Antonopoulos, Kelly Skinner, Jennifer M. Brulc, Eric R. Johnston, Maxim I. Boyanov, Man Jae Kwon, Kenneth M. Kemner, Edward J. O’Loughlin
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0223273

eQTL mapping of rare variant associations using RNA-seq data: An evaluation of approaches
Cited by: 2
Author(s): Sharon M. Lutz, Annie Thwing, Tasha E. Fingerlin
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0214275

Genetic and epigenetic profiling of the infertile male
Cited by: 38
Author(s): Stephanie Cheung, Alessandra Parrella, Zev Rosenwaks, Gianpiero D. Palermo
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0225062

Unique transcriptomic landscapes identified in idiopathic spontaneous and infection related preterm births compared to normal term births
Cited by: 24
Author(s): Heather Brockway, Suhas G. Kallapur, Irina A. Buhimschi, Catalin S. Buhimschi, William E. Ackerman, Louis J. Muglia, Helen Jones
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0182694

Comparison of alternative approaches for analysing multi-level RNA-seq data
Cited by: 22
Author(s): Irina Mohorianu, Amanda Bretman, Damian T. Smith, Emily K. Fowler, Tamás Dalmay, Tracey Chapman
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0085150

Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures
Cited by: 124
Author(s): Isabella Zwiener, Barbara Frisch, Harald Binder
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0198186

Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development
Cited by: 13
Author(s): Xiaofan Niu, Audrey M. V. Ah‐Fong, Lilianna A Lopez, Howard S. Judelson
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0258194

Identification of differentially expressed long noncoding RNAs and pathways in liver tissues from rats with hepatic fibrosis
Cited by: 0
Author(s): Yan Wang, Xiyuan Xiao, Xiaobo Wang, Feng Guo, Xiaozhong Wang
Software Mentions: 2
Published: almost 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568