bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1186/s12870-020-02555-5

Heat-response patterns of the heat shock transcription factor family in advanced development stages of wheat (Triticum aestivum L.) and thermotolerance-regulation by TaHsfA2–10
Cited by: 18
Author(s): Xiulin Guo, Shuo Yuan, Huaning Zhang, Yuanyuan Zhang, Yujie Zhang, Guiyan Wang, Yaqing Li, Guoliang Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-2267-z

Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools
Cited by: 16
Author(s): Lucía de la Rosa Fernández, E. Zambrana, Elena Ramírez-Parra
Software Mentions: 1
Published: almost 7 years ago

10.3390/antib8040050

NR4A Expression by Human Marginal Zone B-Cells
Cited by: 8
Author(s): Kim Doyon-Laliberté, Josiane Chagnon-Choquet, Michelle Byrns, Matheus Aranguren, Meriam Memmi, Pavel Chrobák, John Stagg, Johanne Poudrier, Michel Roger
Software Mentions: 1
Published: about 7 years ago

10.3390/antibiotics9090619

Amidochelocardin Overcomes Resistance Mechanisms Exerted on Tetracyclines and Natural Chelocardin
Cited by: 8
Author(s): Fabienne Hennessen, Marcus Miethke, Nestor Zaburannyi, Maria Loose, Tadeja Lukežič, Steffen Bernecker, Stephan Hüttel, Rolf Jansen, Judith Schmiedel, Moritz Fritzenwanker, Can Imirzalioglu, Jörg Vogel, Alexander J. Westermann, Thomas Hesterkamp, Marc Stadler, Florian Wagenlehner, Hrvoje Petković, Jennifer Herrmann, Rolf Müller
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.42068

Analysis of the genomic architecture of a complex trait locus in hypertensive rat models links Tmem63c to kidney damage
Cited by: 18
Author(s): Angela Schulz, Nicola Victoria Müller, Nina A. van de Lest, Andreas Eisenreich, Martina Schmidbauer, Andrei Barysenka, Bettina Purfürst, Anje Sporbert, Theodor Lorenzen, Alexander M Meyer, Laura Herlan, Anika Witten, Frank Rühle, Weibin Zhou, Emile de Heer, Marion Scharpfenecker, Daniela Panáková, Monika Stoll, Reinhold Kreutz
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-019-1709-y

Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves
Cited by: 17
Author(s): Luis Alejandro de Haro, Sofía Maité Arellano, Ondřej Novák, Regina Feil, Analía Delina Dumón, María Fernanda Mattio, Danuše Tarkowská, Gabriela Llauger, Miroslav Strnad, John E. Lunn, Stephen Pearce, Carlos María Figueroa, Mariana del Vas
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-2284-y

Transcriptome profiling of differentially expressed genes in cytoplasmic male-sterile line and its fertility restorer line in pigeon pea (Cajanus cajan L.)
Cited by: 11
Author(s): Swati Saxena, Sarika Sahu, Tanvi Kaila, Deepti Nigam, Pavan K. Chaduvla, A. Ramachandra Rao, Sankaran Sandhya, Nagendra Singh, Kishor Gaikwad
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.43570

Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression
Cited by: 14
Author(s): Yumin Qi, Yang Wu, Randy Saunders, Xiaoguang Chen, Chunhong Mao, James K. Biedler, Zhijian Tu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-019-1731-0

RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
Cited by: 55
Author(s): Tingting Dong, Mingku Zhu, Jiawen Yu, Rongpeng Han, Cheng Tang, Tao Xu, Jingran Liu, Zongyun Li
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-02342-2

Overexpression of PpSnRK1α in tomato enhanced salt tolerance by regulating ABA signaling pathway and reactive oxygen metabolism
Cited by: 36
Author(s): Wenru Wang, Jiahui Liang, Guifang Wang, Maoxiang Sun, Futian Peng, Yuansong Xiao
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.40448

H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes
Cited by: 33
Author(s): Itamar Lev, Hila Gingold, Oded Rechavi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12870-020-02448-7

A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]
Cited by: 33
Author(s): Shunkai Hu, Mi Zhang, Yiqing Yang, Wei Xuan, Zhongwei Zou, Emmanuel Arkorful, Yi Chen, Qingping Ma, Anburaj Jeyaraj, Xuan Chen, Xinghui Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-021-03032-3

Transcriptome and metabolite profiling analyses provide insight into volatile compounds of the apple cultivar ‘Ruixue’ and its parents during fruit development
Cited by: 30
Author(s): Xiaojie Liu, Nini Hao, Feng Ran, Zhipeng Meng, Yanan Li, Zhengyang Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-02846-5

Molecular cloning and characterization of GhERF105, a gene contributing to the regulation of gland formation in upland cotton (Gossypium hirsutum L.)
Cited by: 10
Author(s): Chaofeng Wu, Hongyan Cheng, Shuyan Li, Dongyun Zuo, Zhongxu Lin, Youping Zhang, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03131-1

Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis
Cited by: 13
Author(s): Jianhua Zhao, Chengzhen Sun, Fu-Ming Shi, Shanshan Ma, Jinshuang Zheng, Xin Du, Liping Zhang
Software Mentions: 1
Published: over 5 years ago

10.3390/ani9121141

Liver Transcriptome Changes of Hyla Rabbit in Response to Chronic Heat Stress
Cited by: 6
Author(s): Zhoulin Wu, Xue Yang, Shiyi Chen, Feilong Deng, Xianbo Jia, Shiyan Hu, Jie Wang, Songjia Lai
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-021-02944-4

Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach
Cited by: 11
Author(s): Mahpara Fatima, Xiaokai Ma, Ping Zhou, Madiha Zaynab, Ray Ming
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-019-1654-9

Comparative transcriptome analysis reveals gene network regulating cadmium uptake and translocation in peanut roots under iron deficiency
Cited by: 33
Author(s): Chen Chu, Qiqi Cao, Qing Jiang, Li Jin, Rugang Yu, Gangrong Shi
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12870-021-02872-3

Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar
Cited by: 14
Author(s): Zihao Cheng, Xuemei Zhang, Wenjing Yao, Kai Zhao, Lin Liu, Guisheng Fan, Boru Zhou, Tongmin Jiang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-03128-w

Transcriptome analysis of resistant and susceptible mulberry responses to Meloidogyne enterolobii infection
Cited by: 4
Author(s): Hanjuan Shao, Yu Fu, Pan Zhang, Chunping You, Chuanren Li, Huan Peng
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms17081324

Genes Expressed Differentially in Hessian Fly Larvae Feeding in Resistant and Susceptible Plants
Cited by: 7
Author(s): Ming‐Shun Chen, Sanzhen Liu, Haiyan Wang, Xiaoyan Cheng, Mustapha El Bouhssini, R. Jeff Whitworth
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms17101758

Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita
Cited by: 12
Author(s): Parthiban Subramanian, Inchan Choi, Vimalraj Mani, Jun Hyung Park, Sathiyamoorthy Subramaniyam, Kang-Hyun Choi, Ji Hyun Sim, Chang-Muk Lee, Jun Mo Koo, Bum-Soo Hahn
Software Mentions: 1
Published: about 10 years ago

10.1186/s12870-021-03063-w

Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses
Cited by: 20
Author(s): Jiaojiao Lu, Qing Zhang, Lixin Lang, Chuang Jiang, Xiaofeng Wang, Hao Sun
Software Mentions: 1
Published: over 5 years ago

10.1038/s41597-019-0210-7

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress
Cited by: 13
Author(s): Zhibo Li, Zeng XiaoYan, Jianwei Xu, Ruihai Zhao, Wei Yinong
Software Mentions: 1
Published: about 7 years ago

10.1038/s41597-019-0101-y

Transcriptome profiles of three Muscat table grape cultivars to dissect the mechanism of terpene biosynthesis
Cited by: 5
Author(s): Lina Sun, Baoqing Zhu, Xuanyin Zhang, Guojun Zhang, Ailing Yan, Huiling Wang, Xiaoyue Wang, Huini Xu
Software Mentions: 1
Published: over 7 years ago

10.1038/sdata.2018.170

Transcriptomic analyses of murine ventricular cardiomyocytes
Cited by: 14
Author(s): Morgan Yoann Edwin Chevalier, Sarah H. Vermij, Kurt Wyler, Ludovic Gillet, Irene Keller, Hugues Abriel
Software Mentions: 1
Published: about 8 years ago

10.1038/sdata.2018.123

Transcriptional profiling of stellate ganglia from normotensive and spontaneously hypertensive rat strains
Cited by: 9
Author(s): Harvey Davis, Emma N. Bardsley, David J. Paterson
Software Mentions: 1
Published: over 8 years ago

10.1038/sdata.2017.172

Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints
Cited by: 6
Author(s): Dominika A. Rudzka, William Clark, Ann Hedley, Gabriela Kalna, Michael F. Olson
Software Mentions: 1
Published: about 9 years ago

10.1038/sdata.2016.101

ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells
Cited by: 7
Author(s): Nicola Rath, Gabriela Kalna, William Clark, Michael F. Olson
Software Mentions: 1
Published: about 10 years ago

10.1126/sciadv.abc8145

NSG-Pro mouse model for uncovering resistance mechanisms and unique vulnerabilities in human luminal breast cancers
Cited by: 9
Author(s): Yunguang Sun, Ning Yang, Fransiscus E. Utama, Sameer S. Udhane, Junling Zhang, Amy R. Peck, Alicia F Yanac, Katherine E. Duffey, John F. Langenheim, Vindhya Udhane, Guanjun Xia, Jess F. Peterson, Julie M. Jorns, Marja T. Nevalainen, Romain Rouet, Peter Schofield, Daniel Christ, Christopher J. Ormandy, Anne Rosenberg, Inna Chervoneva, Shirng‐Wern Tsaih, Michael J. Flister, Serge Y. Fuchs, Kay Uwe Wagner, Hallgeir Rui
Software Mentions: 1
Published: about 5 years ago

10.1126/sciadv.abg5283

Human tumor microenvironment chip evaluates the consequences of platelet extravasation and combinatorial antitumor-antiplatelet therapy in ovarian cancer
Cited by: 35
Author(s): Biswajit Saha, Tanmay Mathur, James J. Tronolone, Mithil Chokshi, Giriraj Lokhande, Amirali Selahi, Akhilesh K. Gaharwar, Vahid Afshar-Kharghan, Anil K. Sood, Gang Bao, Abhishek Jain
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.aba0353

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community
Cited by: 23
Author(s): Tahmineh Khazaei, Rory L. Williams, Said R. Bogatyrev, John C. Doyle, Christopher S. Henry, Rustem F. Ismagilov
Software Mentions: 1
Published: over 6 years ago

10.1186/s12870-020-02526-w

Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses
Cited by: 30
Author(s): Qinbin Zhang, Hui Liu, Xiaolin Wu, Wei Wang
Software Mentions: 1
Published: over 6 years ago

10.1038/srep11126

Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71
Cited by: 38
Author(s): Sibylle Mitschka, Thomas Ulas, Tobias Goller, Karin Schneider, Angela Egert, Jérôme Mertens, Oliver Brüstle, Hubert Schorle, Marc Beyer, Kathrin Klee, Jia Xue, Patrick Günther, Kevin Baßler, Joachim L. Schultze, Waldemar Kolanus
Software Mentions: 1
Published: over 11 years ago

10.3390/ani10010075

The Overexpression of Tβ4 in the Hair Follicle Tissue of Alpas Cashmere Goats Increases Cashmere Yield and Promotes Hair Follicle Development
Cited by: 13
Author(s): Bai Dai, Hao Liang, Dongdong Guo, Zhao-Wei Bi, Jiangzi Yuan, Yifeng Jin, Huan Yao Lei, Xudong Guo, Ming Cang, Dongjun Liu
Software Mentions: 1
Published: almost 7 years ago

10.1126/sciadv.abb3713

GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production
Cited by: 23
Author(s): Elaheh Mahootchi, Selina Cannon Homaei, Rune Kleppe, Ingeborg Winge, Tor‐Arne Hegvik, Ricardo Pérez, Christian Totland, Floriana Mogavero, Anne Baumann, Jeffrey Glennon, Hrvoje Miletić, Petri Kursula, Jan Haavik
Software Mentions: 1
Published: over 6 years ago

10.1038/srep13443

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data
Cited by: 7
Author(s): Praveen Kumar, Thanh Hoang, Michael L. Robinson, Panagiotis A. Tsonis, Chun Liang
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms18091977

Deep Circular RNA Sequencing Provides Insights into the Mechanism Underlying Grass Carp Reovirus Infection
Cited by: 44
Author(s): Libo He, Aidi Zhang, Lv Xiong, Yongming Li, Rong Huang, Lanjie Liao, Zhu Zhang, And Yaping Wang
Software Mentions: 1
Published: about 9 years ago

10.1126/sciadv.aau7314

Improving the metabolic fidelity of cancer models with a physiological cell culture medium
Cited by: 226
Author(s): Johan Vande Voorde, Tobias Ackermann, Nadja Pfetzer, David Sumpton, Gillian Mackay, Gabriela Kalna, Colin Nixon, Karen Blyth, Eyal Gottlieb, Saverio Tardito
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep14976

A high-throughput RNA-seq approach to profile transcriptional responses
Cited by: 23
Author(s): Gregory A Moyerbrailean, Gordon O Davis, Chris T. Harvey, Donovan Watza, Xiaoquan Wen, Roger Piqué-Regi, Francesca Luca
Software Mentions: 1
Published: about 11 years ago

10.1093/schbul/sby017.541

F10. DIFFERENTIAL EXPRESSION OF MICRORNAS IN CEREBROSPINAL FLUID AND PLASMA SAMPLES IN SCHIZOPHRENIA
Cited by: 5
Author(s): Juan Gallego, Eric Alsop, Todd Lencz, Kendall Van Keuren‐Jensen, Anil K. Malhotra
Software Mentions: 1
Published: over 8 years ago

10.1016/j.xpro.2021.100716

Protocol to generate and characterize biofouling transformants of a model marine diatom
Cited by: 0
Author(s): Weiqi Fu, Bushra Dohai, Diana Charles El Assal, Sarah Daakour, Amnah Alzahmi, David R. Nelson, Ashish Jaiswal, Alexandra Mystikou, Mehar Sultana, James Weston, Kourosh Salehi‐Ashtiani
Software Mentions: 1
Published: about 5 years ago

10.1038/srep20316

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention
Cited by: 21
Author(s): Samantha N. McNulty, Christina Strübe, Bruce A. Rosa, John Martin, Rahul Tyagi, Young Jun Choi, Qi Wang, Kymberlie H. Pepin, Xu Zhang, Philip Ozersky, Richard K. Wilson, Paul W. Sternberg, Robin B. Gasser, Makedonka Mitreva
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep21962

Improved lipids, diastolic pressure and kidney function are potential contributors to familial longevity: a study on 60 Chinese centenarian families
Cited by: 13
Author(s): Yonghan He, Shao-Yan Pu, Fu-Hui Xiao, Xiao‐Qiong Chen, Dongjing Yan, Yaowen Liu, Rong Lin, Xiaoping Liao, Qin Yu, Libin Yang, Xiaoxi Yang, Ming-Xia Ge, Ying Liu, Jianjun Jiang, Wei Cai, Qing‐Peng Kong
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22416

RNA sequencing reveals region-specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis
Cited by: 18
Author(s): André Schwambach Vieira, A. H. de Matos, Amanda Morato do Canto, Cristiane S. Rocha, Benilton Carvalho, Vinícius D'Ávila Bitencourt Pascoal, Braxton A. Norwood, Sebastian Bauer, Felix Rosenow, Rovílson Gilioli, Fernando Cendes, Íscia Lopes‐Cendes
Software Mentions: 1
Published: over 10 years ago

10.1038/srep22611

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions
Cited by: 53
Author(s): Feng Wei, Xiaoping Hu, Xiangming Xu
Software Mentions: 1
Published: over 10 years ago

10.1016/j.xpro.2021.100447

Application of high-throughput 5′P sequencing for the study of co-translational mRNA decay
Cited by: 4
Author(s): Yujie Zhang, Vicent Pelechano
Software Mentions: 1
Published: over 5 years ago

10.1186/s12870-021-02954-2

Cold acclimation can specifically inhibit chlorophyll biosynthesis in young leaves of Pakchoi
Cited by: 7
Author(s): Wang Hui-yu, Zhubo Li, Lingyun Yuan, Haihong Zhou, Xilin Hou, Xilin Hou
Software Mentions: 1
Published: over 5 years ago

10.1186/s12284-021-00512-w

Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54
Cited by: 8
Author(s): Peng Ma, Lin X, Xingjia Xiang, Haiyan Ren, Xiaoqin Fan, Kegui Chen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.ppat.1008270

New 2-Ethylthio-4-methylaminoquinazoline derivatives inhibiting two subunits of cytochrome bc1 in Mycobacterium tuberculosis
Cited by: 36
Author(s): Andréanne Lupien, Caroline S. Foo, Svetlana Savina, Anthony Vocat, Jérémie Piton, Natalia Monakhova, Andrej Benjak, Dirk A. Lamprecht, Adrie J. C. Steyn, Kévin Pethe, Vadim Makarov, Stewart T. Cole
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.ppat.1008072

Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
Cited by: 37
Author(s): Ogan K. Kumova, Adam J Fike, Jillian L. Thayer, Linda Nguyen, Joshua Chang Mell, Judy Mae Pascasio, Christopher J. Stairiker, Leticia G. León, Peter D. Katsikis, Alison J. Carey
Software Mentions: 1
Published: about 7 years ago

10.1186/s40795-021-00454-y

Effect of a dietary and exercise intervention in women with overweight and obesity undergoing fertility treatments: protocol for a randomized controlled trial
Cited by: 0
Author(s): Kindann Fawcett, Audrey Martinez, Meghan Crimmins, Clark Sims, Elisabet Børsheim, Aline Andres
Software Mentions: 1
Published: about 5 years ago

10.1186/s12868-021-00661-0

NRXN1α+/- is associated with increased excitability in ASD iPSC-derived neurons
Cited by: 12
Author(s): Sahar Avazzadeh, Leo R. Quinlan, Jamie Reilly, Katya McDonagh, Amirhossein Jalali, Yanqin Wang, Veronica McInerney, Janusz Krawczyk, Yicheng Ding, Jacqueline Fitzgerald, Matthew L. O’Sullivan, Eva Forman, Sally Ann Lynch, Sean Ennis, Niamh Feerick, Richard B. Reilly, Weidong Li, Xu Shen, Guangming Yang, Yin Lu, Hilde Peeters, Peter Dockery, Timothy O’Brien, Sanbing Shen, Louise Gallagher
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.ppat.1008048

Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission
Cited by: 30
Author(s): Mohammad Zeeshan, F. B. Shilliday, Tianyang Liu, Steven Abel, Tobias Mourier, David J. P. Ferguson, Edward Rea, Rebecca R. Stanway, Magali Roques, Desiree Williams, Emilie Daniel, Declan Brady, A. J. Roberts, Anthony A. Holder, Arnab Pain, Karine G. Le Roch, Carolyn A. Moores, Rita Tewari
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.6540

Exosomes from bulk and stem cells from human prostate cancer have a differential microRNA content that contributes cooperatively over local and pre-metastatic niche
Cited by: 173
Author(s): Catherine Sánchez, Eliana Andahur, Rodrigo Valenzuela, Enrique A. Castellón, Juan Fullá, Christian G. Ramos, Juan Carlos Triviño
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.ppat.1007974

Humoral immunity prevents clinical malaria during Plasmodium relapses without eliminating gametocytes
Cited by: 15
Author(s): Chester J. Joyner, Cristiana Ferreira Alves de Brito, Celia L. Saney, Regina Joice Cordy, Maren L. Smith, Stacey A. Lapp, Mónica Cabrera-Mora, Shuya Kyu, Nicolas Lackman, Mustafa V. Nural, Jeremy D. DeBarry, Jessica C. Kissinger, Mark P. Styczynski, F Eun-Hyung Lee, Tracey J. Lamb, Mary R. Galinski
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.ppat.1007164

Plasmodium male gametocyte development and transmission are critically regulated by the two putative deadenylases of the CAF1/CCR4/NOT complex
Cited by: 24
Author(s): Kevin J. Hart, Jenna Oberstaller, Michael P. Walker, Allen M. Minns, Mark Kennedy, Ian Padykula, John Adams, Scott E. Lindner
Software Mentions: 1
Published: almost 8 years ago

10.3390/ani11010080

Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies
Cited by: 3
Author(s): Xin Li, Chenying Duan, Ruyi Li, Dong Wang
Software Mentions: 1
Published: almost 6 years ago

10.3390/ani9121002

Integrative Analysis of Methylation and Transcriptional Profiles to Reveal the Genetic Stability of Cashmere Traits in the Tβ4 Overexpression of Cashmere Goats
Cited by: 7
Author(s): Bai Dai, Meng Zhang, Jiangzi Yuan, Li-qing Ren, Xiaoyu Han, Dongjun Liu
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms19051467

Circulating MicroRNAs in Young Patients with Acute Coronary Syndrome
Cited by: 19
Author(s): Kind-Leng Tong, Ahmad Syadi Mahmood Zuhdi, Wan Azman Wan Ahmad, Paul M. Vanhoutte, João Pedro de Magalhães, Mohd Rais Mustafa, Pooi-Fong Wong
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1007491

EspL is essential for virulence and stabilizes EspE, EspF and EspH levels in Mycobacterium tuberculosis
Cited by: 28
Author(s): Claudia Sala, Nina T. Odermatt, Paloma Soler-Arnedo, Muhammet F. Gülen, Sofia von Schultz, Andrej Benjak, Stewart T. Cole
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.8014

Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers
Cited by: 29
Author(s): James R. Bradford, Mark Wappett, Garry Beran, Armelle Logié, Oona Delpuech, H. Shelton Brown, Joanna Boros, Nicola J. Camp, Robert McEwen, Anne Marie Mazzola, Celina M. D’Cruz, Simon T. Barry
Software Mentions: 1
Published: over 10 years ago

10.1038/srep33660

Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses
Cited by: 36
Author(s): Amira Suriaty Yaakop, Kok‐Gan Chan, Robson Ee, Yan Lue Lim, Siew Kim Lee, Fazilah Abd Manan, Kian Mau Goh
Software Mentions: 1
Published: about 10 years ago

10.18632/aging.202733

Sex-specific differences of humoral immunity and transcriptome diversification in older adults vaccinated with inactivated quadrivalent influenza vaccines
Cited by: 0
Author(s): Jing Yang, Xiaoyuan Huang, Jiayou Zhang, Renfeng Fan, Wei Zhao, Han Tian, Kai Duan, Xinguo Li, Peiyu Zeng, Jinglong Deng, Jikai Zhang, Xiaoming Yang
Software Mentions: 1
Published: over 5 years ago

10.1038/srep35323

Effects of aged garlic extract and FruArg on gene expression and signaling pathways in lipopolysaccharide-activated microglial cells
Cited by: 15
Author(s): Hailong Song, Yuan Lu, Zhe Qu, Valeri V. Mossine, Matthew B. Martin, Jie Hou, Jiankun Cui, Brenda A. Peculis, Thomas P. Mawhinney, Jianlin Cheng, C. Michael Greenlief, Kevin L. Fritsche, Francis J. Schmidt, Ronald B. Walter, Dennis B. Lubahn, Grace Y. Sun
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.ppat.1007465

Specificity and functional interplay between influenza virus PA-X and NS1 shutoff activity
Cited by: 34
Author(s): Chutikarn Chaimayo, Megan M Dunagan, Tsuyoshi Hayashi, Netty Santoso, Toru Takimoto
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep35852

Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment
Cited by: 38
Author(s): Christian Weber, Mikael Koutero, Marie‐Agnès Dillies, Hugo Varet, César López‐Camarillo, Jean Yves Coppée, Chung-Chau Hon, Nancy Guillén
Software Mentions: 1
Published: about 10 years ago

10.1038/srep35830

Establishment of a translational endothelial cell model using directed differentiation of induced pluripotent stem cells from Cynomolgus monkey
Cited by: 8
Author(s): Eva C. Thoma, Tobias Heckel, David M. Keller, Nicolas Giroud, Brian C. Leonard, Klaus Christensen, Adrian Roth, Cristina Bertinetti-Lapatki, Martin Gräf, Christoph Patsch
Software Mentions: 1
Published: about 10 years ago

10.1038/srep36007

Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana
Cited by: 16
Author(s): Chao Wu, Xinyue Li, Song Guo, Sek‐Man Wong
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.ppat.1007246

Type I IFN signaling blockade by a PASylated antagonist during chronic SIV infection suppresses specific inflammatory pathways but does not alter T cell activation or virus replication
Cited by: 29
Author(s): Krystelle Nganou-Makamdop, James M. Billingsley, Zak A. Yaffe, Gregory O’Connor, Gregory K. Tharp, Amy Ransier, Farida Laboune, Rodrigo Matus‐Nicodemos, Andrea M Lerner, Lavina Gharu, Jennifer Rosenstein, Mandy L. Ford, Martin Schlapschy, Nadine Kuhn, Alexandra Lensch, Jeffrey D. Lifson, Martha Nason, Arne Skerra, Gideon Schreiber, Steven E. Bosinger, Daniel C. Douek
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19092631

Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-acyl-l-homoserine Lactone Accumulation
Cited by: 8
Author(s): Haijun Lu, Yili Huang
Software Mentions: 1
Published: about 8 years ago

10.1038/srep37110

The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis
Cited by: 104
Author(s): Karl M. Glastad, Kaustubh Gokhale, Jürgen Liebig, Michael A. D. Goodisman
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms19102924

Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules
Cited by: 47
Author(s): Yingbin Xue, Q. J. Zhuang, Shengnan Zhu, Bi-Xian Xiao, Chaojie Liang, Hong Liao, Jichun Tian
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms19103158

Comparative Analysis of the Integument Transcriptomes between stick Mutant and Wild-Type Silkworms
Cited by: 3
Author(s): Tan D, Hai Hu, Xiaoling Tong, Minjin Han, Songyuan Wu, Xin Ding, Fangyin Dai, Cheng Lü
Software Mentions: 1
Published: about 8 years ago

10.1186/s12867-019-0124-0

Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms
Cited by: 20
Author(s): Sara Harðardóttir, Sylke Wohlrab, Ditte Marie Hjort, Bernd Krock, Torkel Gissel Nielsen, Uwe John, Nina Lundholm
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.ppat.1007153

The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37
Cited by: 21
Author(s): Emily Woods, Adrianne N. Edwards, Kevin O. Childress, Joshua B. Jones, Shonna M. McBride
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1007007

Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
Cited by: 92
Author(s): Nuria Trevijano-Contador, Haroldo César de Oliveira, Rocío García-Rodas, Suélen Andreia Rossi, Irene L. Llorente, Ángel Zaballos, Guilhem Janbon, Joaquı́n Ariño, Óscar Zaragoza
Software Mentions: 1
Published: over 8 years ago

10.1038/srep37770

Genome-wide transcriptome analysis revealed organelle specific responses to temperature variations in algae
Cited by: 34
Author(s): HyeonSeok Shin, Seong-Joo Hong, Chan Yul Yoo, Mi-Ae Han, Hookeun Lee, Hyung‐Kyoon Choi, Suhyung Cho, Choul-Gyun Lee, Byung-Kwan Cho
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12866-018-1225-5

Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015
Cited by: 9
Author(s): Liu Cong, Dongying Fan, Yanfang Li, Yue Chen, Lili Huang, Yan Xia
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1006985

Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment
Cited by: 64
Author(s): Arunakumar Gangaplara, Craig Martens, Eric Dahlstrom, Amina Metidji, Ameya Gokhale, Deborah D. Glass, Maria Lopez-Ocasio, Rachel Baur, Kishore Kanakabandi, Stephen F. Porcella, Ethan M. Shevach
Software Mentions: 1
Published: over 8 years ago

10.1038/srep40325

KANK1 inhibits cell growth by inducing apoptosis through regulating CXXC5 in human malignant peripheral nerve sheath tumors
Cited by: 22
Author(s): Zelin Cui, Yingjia Shen, Kenny H Chen, Suresh K. Mittal, Jer-Yen Yang, Guangjun Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006940

Pleiotropic roles of Clostridium difficile sin locus
Cited by: 45
Author(s): Brintha P. Girinathan, Jiangtao Ou, Bruno Dupuy, Revathi Govind
Software Mentions: 1
Published: over 8 years ago

10.1038/srep40618

Identification of misexpressed genetic elements in hybrids between Drosophila-related species
Cited by: 27
Author(s): Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron, Claudia M. A. Carareto, Cristina Vieira
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006917

SpdC, a novel virulence factor, controls histidine kinase activity in Staphylococcus aureus
Cited by: 38
Author(s): Olivier Poupel, Caroline Proux, Bernd Jabla, Tarek Msadek, Sarah Dubrac
Software Mentions: 1
Published: over 8 years ago

10.3390/ani11082273

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression
Cited by: 1
Author(s): Menelaos Kavouras, Emmanouil E. Malandrakis, E. Blom, Kyriaki Tsilika, Theodoros Danis, Panagiota Panagiotaki, Athanasios Exadactylos
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1006868

Interferon regulatory factor 8 regulates caspase-1 expression to facilitate Epstein-Barr virus reactivation in response to B cell receptor stimulation and chemical induction
Cited by: 40
Author(s): Dongwen Lv, Kun Zhang, Renfeng Li
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep41063

Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites
Cited by: 30
Author(s): Simone Pelliciari, Eva Pinatel, Andrea Vannini, Clelia Peano, Simone Puccio, Gianluca De Bellis, Alberto Danielli, Vincenzo Scarlato, Davide Roncarati
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12866-021-02257-4

Regulation of virulence and β-lactamase gene expression in Staphylococcus aureus isolates: cooperation of two-component systems in bloodstream superbugs
Cited by: 7
Author(s): Sanaz Dehbashi, Hamed Tahmasebi, Behrouz Zeyni, Mohammad Reza Arabestani
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1006802

Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis
Cited by: 25
Author(s): Franc Llorens, Katrin Thüne, Eulàlia Martı́, Ειrini Kanata, Dimitra Dafou, Daniela Díaz-Lucena, Ana Vivancos, Orr Shomroni, Saima Zafar, Matthias Schmitz, Uwe Michel, Natalia Fernández‐Borges, Olivier Andréoletti, José Antonio del Río, Juana Díez, André Fischer, Stefan Bonn, Theodoros Sklaviadis, Juan María Torres, Isidre Ferrer, Inga Zerr
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep42225

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis
Cited by: 78
Author(s): Núria Andreu, Jody Phelan, Paola Flórez de Sessions, Jacqueline M. Cliff, Taane G. Clark, Martin L. Hibberd
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006844

RNA-Seq of Kaposi’s sarcoma reveals alterations in glucose and lipid metabolism
Cited by: 40
Author(s): For Yue Tso, Andrew V. Kossenkov, Salum J. Lidenge, Owen Ngalamika, John R. Ngowi, Julius Mwaiselage, Jayamanna Wickramasinghe, Eun Hee Kwon, John T. West, Paul M. Lieberman, Charles Wood
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006524

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs
Cited by: 69
Author(s): Ohad Yogev, Stephen Henderson, Matthew J. Hayes, Sara Marelli, Yifat Ofir-Birin, Neta Regev‐Rudzki, Javier Herrero, Tariq Enver
Software Mentions: 1
Published: about 9 years ago

10.18632/aging.103330

PLK1 Inhibition alleviates transplant-associated obliterative bronchiolitis by suppressing myofibroblast differentiation
Cited by: 7
Author(s): Jizhang Yu, Heng Xu, Jikai Cui, Shanshan Chen, Hao Zhang, Yanqiang Zou, Jing Zhao, Le Shen, Lang Jiang, Zhang Chen, Hao Líu, Dan Zhang, Jiahong Xia, Jie Wu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-021-02304-0

The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response
Cited by: 3
Author(s): Xiaohong Chen, Aiqi Hu, Qian Zou, Sha Luo, Hetao Wu, Chunxiao Yan, Tao Liu, Donglan He, Xiaohua Li, Guyue Cheng
Software Mentions: 1
Published: about 5 years ago

10.1038/srep43850

Dynamics of miRNA transcriptome during gonadal development of zebrafish
Cited by: 58
Author(s): Christopher Presslauer, Teshome Tilahun Bizuayehu, Martina Kopp, Jorge M.O. Fernandes, Igor Babiak
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms19123892

Distinct Patterns of PPARγ Promoter Usage, Lipid Degradation Activity, and Gene Expression in Subcutaneous Adipose Tissue of Lean and Obese Swine
Cited by: 5
Author(s): Bowen Song, Shengwei Di, Shiquan Cui, Na Chen, Huan Wang, Xuan Wang, Qian Gao, Guizhi Tong, Hongbao Wang, Xuankai Huang, Liyan Ding, Ying Gao, Jun Li, Xibiao Wang
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep44546

Novel transcriptome assembly and comparative toxicity pathway analysis in mahi-mahi (Coryphaena hippurus) embryos and larvae exposed to Deepwater Horizon oil
Cited by: 31
Author(s): Elvis Genbo Xu, Edward M. Mager, Martin Grosell, E. Starr Hazard, Gary Hardiman, Daniel Schlenk
Software Mentions: 1
Published: over 9 years ago

10.1038/srep44061

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects
Cited by: 129
Author(s): Ashish Yeri, Amanda Courtright, Rebecca Reiman, Elizabeth Carlson, Taylor Beecroft, Alex Janss, Ashley L. Siniard, Ryan Richholt, Chris Balak, Joel Rozowsky, Robert Kitchen, Elizabeth Hutchins, Joseph Winarta, Roger L. McCoy, Matthew Anastasi, Kim S, Matthew J. Huentelman, Kendall Van Keuren‐Jensen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006560

Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei
Cited by: 78
Author(s): Elisha Mugo, Christine Clayton
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006471

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli
Cited by: 63
Author(s): Luther A. Bartelt, David T. Bolick, Jordi Mayneris‐Perxachs, Glynis L. Kolling, Gregory L. Medlock, Edna I. Zaenker, Jeffery Donowitz, Rose Viguna Thomas-Beckett, Allison R. Rogala, Ian M. Carroll, Steven M. Singer, Jason A. Papin, Jonathan R. Swann, Richard L. Guerrant
Software Mentions: 1
Published: over 9 years ago

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583