bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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: almost 12 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: over 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: about 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: about 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: over 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: over 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: about 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: over 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: about 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: almost 7 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: over 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: about 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: almost 10 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: about 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: about 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: about 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: about 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: over 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: almost 11 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: over 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: about 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: almost 6 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: about 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: over 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: over 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: over 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: about 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: about 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: about 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: over 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: about 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: about 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: about 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: almost 12 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: over 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: about 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: almost 15 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: over 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: about 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: about 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: almost 13 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: over 8 years ago

10.1038/s41420-021-00649-z

Long noncoding RNA DLGAP1-AS2 facilitates Wnt1 transcription through physically interacting with Six3 and drives the malignancy of gastric cancer
Cited by: 12
Author(s): Jiawei Lu, Ying Xü, Wenjie Xie, Yinbing Tang, Heteng Zhang, Beibei Wang, Ji Mao, Rui Tao, Pengcheng Jiang, Wenbo Zhang
Software Mentions: 2
Published: about 5 years ago

10.1111/cmi.12722

Vps13F links bacterial recognition and intracellular killing inDictyostelium
Cited by: 26
Author(s): Jade Leiba, Ayman Sabra, Romain Bodinier, Anna Marchetti, Wanessa Cristina Lima, Astrid Melotti, Jackie Perrin, Frédéric Burdet, Marco Pagni, Thierry Soldati, Emmanuelle Lelong, Pierre Cosson
Software Mentions: 2
Published: over 9 years ago

10.1007/s00018-018-2842-8

Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells
Cited by: 49
Author(s): Tom A.P. Driedonks, Susanne G. van der Grein, Yavuz Ariyürek, Henk P.J. Buermans, Henrike Jekel, Wang Ngai Chow, Marca H. M. Wauben, Amy H. Buck, Peter A.C. ’t Hoen, Esther N. M. Nolte‐‘t Hoen
Software Mentions: 2
Published: over 8 years ago

10.1111/cpr.12564

Suppression of long non‐coding RNA TNRC6C‐AS1 protects against thyroid carcinoma through DNA demethylation of STK4 via the Hippo signalling pathway
Cited by: 29
Author(s): Linjie Yang, Jing Wu, Manli Guo, Yong Zhang, Shao-Gang Ma
Software Mentions: 2
Published: over 7 years ago

10.1016/j.celrep.2021.109542

Gli1+ progenitors mediate bone anabolic function of teriparatide via Hh and Igf signaling
Cited by: 12
Author(s): Yu Shi, Xueyang Liao, James Y. Long, Lutian Yao, Jianquan Chen, Bin Yin, Feng Lou, Guangxu He, Ling Ye, Ling Qin, Fanxin Long
Software Mentions: 2
Published: over 5 years ago

10.1007/s12192-018-0910-5

Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata
Cited by: 18
Author(s): Victoria A. Sleight, Lloyd S. Peck, Elisabeth A. Dyrynda, Valerie J. Smith, Melody S. Clark
Software Mentions: 2
Published: over 8 years ago

10.3390/cells9061371

Intrinsic Abnormalities of Cystic Fibrosis Airway Connective Tissue Revealed by an In Vitro 3D Stromal Model
Cited by: 5
Author(s): Claudia Mazio, Laura S Scognamiglio, Rossella De Cegli, Luis J V Galietta, Diego di Bernardo, Costantino Casale, Francesco Urciuolo, Giorgia Imparato, Paolo Antonio Netti
Software Mentions: 2
Published: over 6 years ago

10.3390/cells10092439

Sexually Dimorphic Transcriptomic Changes of Developing Fetal Brain Reveal Signaling Pathways and Marker Genes of Brain Cells in Domestic Pigs
Cited by: 8
Author(s): Monica Strawn, J.G.N. Moraes, Timothy J. Safranski, Susanta K. Behura
Software Mentions: 2
Published: about 5 years ago

10.3390/cells8111395

Hepatitis C Virus Enhances the Invasiveness of Hepatocellular Carcinoma via EGFR-Mediated Invadopodia Formation and Activation
Cited by: 18
Author(s): Liat Ninio, Abraham Nissani, Tomer Meirson, Tom Domovitz, Alessandro Genna, Shams Twafra, Kannan Srikanth, Roba Dabour, Erez Avraham, Ateret Davidovich, Hava Gil-Henn, Meital Gal-Tanamy
Software Mentions: 2
Published: almost 7 years ago

10.3390/cells10082119

High-Fat Diet Alters the Retinal Transcriptome in the Absence of Gut Microbiota
Cited by: 11
Author(s): David Dao, Bingqing Xie, Urooba Nadeem, Jason Xiao, Asad Movahedan, Mark D’Souza, Vanessa Leone, Seenu M. Hariprasad, Eugene B. Chang, Dinanath Sulakhe, Dimitra Skondra
Software Mentions: 2
Published: about 5 years ago

10.3390/cells9071579

Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments
Cited by: 6
Author(s): Cankut Çubuk, Fatma Ezgi Can, María Peña‐Chilet, Joaquı́n Dopazo
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9092026

Chemical Genetics Approach Identifies Abnormal Inflorescence Meristem 1 as a Putative Target of a Novel Sulfonamide That Protects Catalase2-Deficient Arabidopsis against Photorespiratory Stress
Cited by: 2
Author(s): Tom van der Meer, Arno Verlee, Patrick J. Willems, Francis Impens, Kris Gevaert, Christa Testerink, Christian V. Stevens, Frank Van Breusegem, Pavel Kerchev
Software Mentions: 2
Published: about 6 years ago

10.3390/cells10020200

Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death
Cited by: 8
Author(s): Anna Rusaczonek, Weronika Czarnocka, Patrick J. Willems, Marzena Sujkowska‐Rybkowska, Frank Van Breusegem, Stanisław Karpiński
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9030680

Exosomes from Human Adipose Tissue-Derived Mesenchymal Stem Cells Promote Epidermal Barrier Repair by Inducing de Novo Synthesis of Ceramides in Atopic Dermatitis
Cited by: 81
Author(s): Kyong‐Oh Shin, Dong-Soo Ha, Jin Ock Kim, Debra Crumrine, Jason M. Meyer, Joan S. Wakefield, Yerin Lee, Bogyeong Kim, Sungeun Kim, Hyun-Keun Kim, Joon Lee, Hyuck Hoon Kwon, Gyeong-Hun Park, Jun Ho Lee, Jihye Lim, Sejeong Park, Peter M. Elias, Kyungho Park, Yong Weon Yi, Byong Seung Cho
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9040969

Integrative Analysis of Methylome and Transcriptome Reveals the Regulatory Mechanisms of Hair Follicle Morphogenesis in Cashmere Goat
Cited by: 23
Author(s): Shanhe Wang, Fang Li, Jinwang Liu, Yuelang Zhang, Yujie Zheng, Wei Ge, Qu Liu, Xin Wang
Software Mentions: 2
Published: over 6 years ago

10.3390/cells9122690

The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry
Cited by: 5
Author(s): Mónica Fernández-Cortés, Eduardo Andrés-León, F. Javier Oliver
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9061476

RIG-I Plays a Dominant Role in the Induction of Transcriptional Changes in Zika Virus-Infected Cells, which Protect from Virus-Induced Cell Death
Cited by: 28
Author(s): Mirjam Schilling, Anne Bridgeman, Nicki Gray, Jonny Hertzog, Philip Hublitz, Alain Kohl, Jan Rehwinkel
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-020-00892-8

Ten-eleven translocation methyl-cytosine dioxygenase 2 deficiency exacerbates renal ischemia-reperfusion injury
Cited by: 5
Author(s): Yan Huang, Li Tan, Yuqi Liu, Ning Huang, Jing Cang, Hao Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-019-0628-y

Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer
Cited by: 23
Author(s): Simeng Gu, Shujuan Lin, Yichun Ding, Sangni Qian, Danjie Jiang, Xiaocong Zhang, Qilong Li, Jing Yang, Xiaojiang Ying, Zhenjun Li, Mengling Tang, Jianbing Wang, Mingjuan Jin, Kun Chen
Software Mentions: 2
Published: over 7 years ago

10.1186/s13148-021-01109-2

Genome‑wide profiling of DNA methylation and gene expression unravel the epigenetic landscape in diabetes-related hypothyroidism
Cited by: 3
Author(s): Jingyi Luo, Xiaoxia Wang, Yuan Li, Lixin Guo
Software Mentions: 2
Published: over 5 years ago

10.1002/cti2.1082

Immunological observations and transcriptomic analysis of trimester‐specific full‐term placentas from three Zika virus‐infected women
Cited by: 19
Author(s): Fok‐Moon Lum, Vipin Narang, Susan Swee-Shan Hue, Jie Chen, Naomi McGovern, Ravisankar Rajarethinam, Jeslin J. L. Tan, Siti Naqiah Amrun, Yi‐Hao Chan, Cheryl Yi‐Pin Lee, Tze-Kwang Chua, Wearn‐Xin Yee, Nicholas Kim‐Wah Yeo, T. Y. T. Tan, Xuan Liu, Sam Haldenby, Yee‐Sin Leo, Florent Ginhoux, Jerry Ky Chan, Julian A. Hiscox, Chia-Yin Chong, Lisa F. P. Ng
Software Mentions: 2
Published: almost 8 years ago

10.1002/cti2.1334

Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity
Cited by: 4
Author(s): Harshi Weerakoon, Jasmin Straube, Katie E. Lineburg, Leanne Cooper, Steven Lane, Corey Smith, Saleh Alabbas, Jakob Begun, John J. Miles, Michelle M. Hill, Ailin Lepletier
Software Mentions: 2
Published: almost 6 years ago

10.1002/ctm2.399

Identification of biomarkers complementary to homologous recombination deficiency for improving the clinical outcome of ovarian serous cystadenocarcinoma
Cited by: 18
Author(s): Zhiwen Shi, Qingguo Zhao, Bin Lv, Xinyu Qu, Xiao Han, Hongyan Wang, Junjun Qiu, Keqin Hua
Software Mentions: 2
Published: over 5 years ago

10.1002/ctm2.328

Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma
Cited by: 20
Author(s): Chuanjie Zhang, Xuan Lu, Jingyi Huang, Hongchao He, Li Chen, Yihan Liu, Haofei Wang, Yu Xu, Siwei Xing, Xiaohao Ruan, Xiaoqun Yang, Lu Chen, Danfeng Xu
Software Mentions: 2
Published: almost 6 years ago

10.1007/s12094-021-02621-w

Aberrantly low STAT3 and STAT5 responses are associated with poor outcome and an inflammatory gene expression signature in pediatric acute myeloid leukemia
Cited by: 5
Author(s): Priya Narayanan, Tsz-Kwong Man, Robert B. Gerbing, Rhonda E. Ries, Alexandra M. Stevens, Y.-C. Wang, Xin Long, Alan S. Gamis, Todd M. Cooper, Soheil Meshinchi, Todd A. Alonzo, Michele S. Redell
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-02384-8

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina
Cited by: 18
Author(s): Purushothaman Natarajan, Ashok Kumar Murugesan, Ganesan Govindan, Ayyaru Gopalakrishnan, Ravichandiran Kumar, Purushothaman Duraisamy, Raju Balaji, Tanuja Tanuja, P. Sushree Shyamli, Ajay Parida, Madasamy Parani
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-019-0334-5

Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment
Cited by: 16
Author(s): Nagahiro Ochiai, Yutaka Nakachi, Tomotaka Yokoo, Takahiro Ichihara, Tore Eriksson, Yuki Yonemoto, Takumi Kato, Hitoshi Ogata, Natsuko Fujimoto, Yasuhiro Kobayashi, Nobuyuki Udagawa, Shinsuke Kaku, Tomokazu Ueki, Yasushi Okazaki, Naoyuki Takahashi, Toshio Suda
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-021-01743-9

Immunoreactive peptide maps of SARS-CoV-2
Cited by: 35
Author(s): Nischay Mishra, Xi Huang, Saurabh Joshi, Cheng Guo, James Ng, Riddhi Thakkar, Yongjian Wu, Dong Xiao, Qianlin Li, Richard S. Pinapati, Eric Sullivan, Adrian Caciula, Rafal Tokarz, Thomas Briese, Jiahai Lu, W. Ian Lipkin
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-02295-8

FUT6 deficiency compromises basophil function by selectively abrogating their sialyl-Lewis x expression
Cited by: 6
Author(s): Kia Joo Puan, Boris San Luis, Nurhashikin Yusof, Dilip Kumar, Anand Kumar Andiappan, Wendy Lee, Samanta Cajic, Dragana Vuckovic, Jing De Chan, Tobias Döllner, Han Wei Hou, Yunxuan Jiang, Chao Tian, Erdmann Rapp, Michael Poidinger, De Yun Wang, Nicole Soranzo, Bernett Lee, Olaf Rötzschke
Software Mentions: 2
Published: over 5 years ago

10.14252/foodsafetyfscj.D-20-00032

Effect of Transgenic Rootstock Grafting on the Omics Profiles in Tomato
Cited by: 9
Author(s): Hiroaki Kodama, Taira Miyahara, Taichi Oguchi, Takashi Tsujimoto, Yoshihiro Ozeki, Toshiki Ogawa, Yube Yamaguchi, Daisaku Ohta
Software Mentions: 2
Published: almost 6 years ago

10.3390/foods10050936

Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity
Cited by: 16
Author(s): Ioannis Kafantaris, Christina Tsadila, Marios Nikolaidis, Eleni Tsavea, Tilemachos G. Dimitriou, Ioannis Iliopoulos, Grigoris D. Amoutzias, Dimitris Mossialos
Software Mentions: 2
Published: over 5 years ago

10.3389/fnagi.2021.645649

Transcriptome Analysis of Microglia Reveals That the TLR2/IRF7 Signaling Axis Mediates Neuroinflammation After Subarachnoid Hemorrhage
Cited by: 5
Author(s): Shenbin Xu, Shuhao Mei, Jianing Lu, Haijian Wu, Xiao Dong, Ligen Shi, Jingyi Zhou, Jianmin Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fbioe.2018.00019

Phosphoproteome of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395, under Nitrogen-Replete and -Deplete Conditions
Cited by: 1
Author(s): Michael T. Guarnieri, Alida T. Gerritsen, Calvin A. Henard, Eric P. Knoshaug
Software Mentions: 2
Published: over 8 years ago

10.3389/fbioe.2021.701039

Identification of Key mRNAs as Prediction Models for Early Metastasis of Pancreatic Cancer Based on LASSO
Cited by: 7
Author(s): Ke Xue, Huilin Zheng, Xiaowen Qian, Zheng Chen, Yangjun Gu, Zhenhua Hu, Lei Zhang, Jian Wan
Software Mentions: 2
Published: about 5 years ago

10.3389/fbioe.2020.00668

Identification and Analysis of p53-Regulated Enhancers in Hepatic Carcinoma
Cited by: 5
Author(s): Yin Zhang, Mingming Qian, Fei Tang, Qingqing Huang, Wenzhu Wang, Yanjing Li, Zhi Xue Li, Bei-Ping Li, Zheng-Liang Qiu, Junjie Yue, Zhiyun Guo
Software Mentions: 2
Published: over 6 years ago

10.3389/fcvm.2020.581362

Identification of Transcriptional Variation in Aortic Remodeling Using a Murine Transverse Aortic Constriction (TAC) Model
Cited by: 3
Author(s): Xinlu Zhang, Ting Feng, Xin-Xin I. Zeng, Hongbin Liang, Bo Situ, Qiuxia Zhang, Fengyun Zhou, Yejia Chen, Tao Wang, Du Cai, Xinxin Lin, Jiancheng Xiu, Lei Zheng
Software Mentions: 2
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568