bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7554/eLife.48718

Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons
Cited by: 40
Author(s): Max Koppers, Roberta Cagnetta, Toshiaki Shigeoka, Lucia Cs Wunderlich, Pedro P. Vallejo Ramirez, Julie Qiaojin Lin, Sixian Zhao, Maximilian Ah Jakobs, Asha Dwivedy, Michael S. Minett, Anaïs Bellon, Clemens F. Kaminski, William A. Harris, John G. Flanagan, Christine E. Holt
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pntd.0008351

Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and Zika virus infection
Cited by: 17
Author(s): Azali Azlan, Sattam M. Obeidat, Kumitaa Theva Das, Muhammad Amir Yunus, Ghows Azzam
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.53403

Zebrafish macrophage developmental arrest underlies depletion of microglia and reveals Csf1r-independent metaphocytes
Cited by: 36
Author(s): Laura E. Kuil, Nynke Oosterhof, Giuliano Ferrero, Tereza Mikulášová, Martina Hason, Jordy Dekker, Mireia Rovira, Herma C. van der Linde, Paulina Mh van Strien, Emma de Pater, Gerben Schaaf, Erik Mj Bindels, Valérie Wittamer, Tjakko J. van Ham
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0009334

Aedes aegypti dyspepsia encodes a novel member of the SLC16 family of transporters and is critical for reproductive fitness
Cited by: 6
Author(s): Hitoshi Tsujimoto, Michelle A. E. Anderson, Heather Eggleston, K.M. Myles, Zach N. Adelman
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0002616

Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development
Cited by: 62
Author(s): Jatin Shrinet, Shanu Jain, Jaspreet Jain, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 3
Published: almost 13 years ago

10.7554/eLife.58836

Gene autoregulation by 3’ UTR-derived bacterial small RNAs
Cited by: 32
Author(s): Mona Hoyos, Michaela Huber, Konrad U. Förstner, Kai Papenfort
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pntd.0004406

Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host
Cited by: 18
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Patrick Tan, Libor Mikeš, Martin Kašný, Petr Horák, Robin B. Gasser
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2020.00482

Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs
Cited by: 15
Author(s): Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.34970

SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity
Cited by: 17
Author(s): Wenke Wang, Amaresh Chaturbedi, Minghui Wang, Serim An, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.04775

Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns
Cited by: 77
Author(s): Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0171694

An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology
Cited by: 2
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: over 9 years ago

10.3390/medicines6030071

Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth
Cited by: 5
Author(s): Tung-Chin Chiang, Brian Koss, L. Joseph Su, Charity L. Washam, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.43352

Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF
Cited by: 39
Author(s): Manju Sharma, Anuj Srivastava, Heather Fairfield, David E. Bergstrom, William F. Flynn, Robert E. Braun
Software Mentions: 3
Published: over 7 years ago

10.1590/0074-02760190378

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium
Cited by: 3
Author(s): Thaís Cunha de Sousa Cardoso, Carlos Bruno de Araújo, Laysa Gomes Portilho, Luiz Guilherme Alves Mendes, Tamires Caixeta Alves, Gustavo Caetano Silva, Thales Henrique Cherubino Ribeiro, Peterson Elizandro Gandolfi, Enyara Rezende Morais, Laurence Rodrigues do Amaral, Matheus de Souza Gomes
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-43075-z

A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories
Cited by: 35
Author(s): Andrei E. Tarkhov, Ramani Alla, Srinivas Ayyadevara, Mikhail A. Pyatnitskiy, L. I. Men’shikov, Robert J. Shmookler Reis, П. О. Федичев
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-015-0627-x

Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes
Cited by: 19
Author(s): Wei Zhang, Wei Xiang, Meng Heng-lin, Chunhua Ma, Ni-Hao Jiang, Guanghui Zhang, Shengchao Yang
Software Mentions: 3
Published: about 11 years ago

10.1186/s12967-020-02509-3

LTBP1 plays a potential bridge between depressive disorder and glioblastoma
Cited by: 7
Author(s): Xiaojun Fu, Pei Zhang, Hongwang Song, Chenxing Wu, Shengzhen Li, Shouwei Li, Yan Chen
Software Mentions: 2
Published: about 6 years ago

10.1186/s12920-020-00825-7

RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta
Cited by: 4
Author(s): Lidiia Zhytnik, Katre Maasalu, Ene Reimann, Aare Märtson, Sulev Kõks
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12920-018-0376-4

Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis
Cited by: 13
Author(s): Elisabeth De Smit, Samuel W. Lukowski, Lisa K. Anderson, Anne Senabouth, Kaisar Dauyey, Sharon Song, Bruce D. Wyse, Lawrie Wheeler, Christine Y. Chen, Kun Cao, Amy Yuen, Neil Shuey, Linda Clarke, M Isabel G Lopez Sanchez, Stevephen Hung, Alice Pébay, David A. Mackey, Matthew A. Brown, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 2
Published: over 8 years ago

10.1186/s12920-018-0463-6

Selecting precise reference normal tissue samples for cancer research using a deep learning approach
Cited by: 33
Author(s): William Z. D. Zeng, Benjamin S. Glicksberg, Yangyan Li, Bin Chen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12920-018-0379-1

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis
Cited by: 37
Author(s): Madhusudan Grover, Simon J. Gibbons, Asha Nair, Cheryl E. Bernard, Adeel S. Zubair, Seth T. Eisenman, Laura Wilson, Laura Miriel, Pankaj J. Pasricha, Henry P. Parkman, Irene Sarosiek, Richard W. McCallum, Kenneth L. Koch, Thomas L. Abell, William J. Snape, Braden Kuo, Robert J. Shulman, Travis J. McKenzie, Todd A. Kellogg, Michael L. Kendrick, James Tonascia, Frank A. Hamilton, Gianrico Farrugia
Software Mentions: 2
Published: about 8 years ago

10.1186/s12920-019-0498-3

Transcriptomic analysis of fetal membranes reveals pathways involved in preterm birth
Cited by: 18
Author(s): Silvana Pereyra, Claudio Sosa, Bernardo Bertoni, Rossana Sapiro
Software Mentions: 2
Published: over 7 years ago

10.1186/s12920-018-0370-x

Blood pressure signature genes and blood pressure response to thiazide diuretics: results from the PEAR and PEAR-2 studies
Cited by: 6
Author(s): Ana Caroline Costa Sá, Amy Webb, Yan Gong, Caitrin W. McDonough, Mohamed H. Shahin, Somnath Datta, Taimour Langaee, Stephen T. Turner, Amber L. Beitelshees, Arlene B. Chapman, Eric Boerwinkle, John G. Gums, Steven E. Scherer, Rhonda M. Cooper‐DeHoff, Wolfgang Sadée, Julie A. Johnson
Software Mentions: 2
Published: over 8 years ago

10.1186/s12920-019-0550-3

Transcriptome profiling reveals significant changes in the gastric muscularis externa with obesity that partially overlap those that occur with idiopathic gastroparesis
Cited by: 10
Author(s): B. Paul Herring, Meng Chen, Plamen Mihaylov, April M. Hoggatt, Anita Gupta, Attila Nakeeb, Jennifer Choi, John M. Wo
Software Mentions: 2
Published: over 7 years ago

10.1186/s12866-020-02039-4

Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress
Cited by: 7
Author(s): Lei Zhao, Yanjun Zhou, Jianbei Li, Yucheng Xia, Weiyun Wang, Xiuqi Luo, Juan Yin, Jun Zhong
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12866-020-01853-0

Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress
Cited by: 2
Author(s): Xiaorong Gu, Shuai Yang, Xiaoxue Yang, Liangliang Yao, Xuedong Gao, Maoming Zhang, Wei Liu, Haiming Zhao, Qingsheng Wang, Zengjie Li, Zhimin Li, Junjie Ding
Software Mentions: 2
Published: over 6 years ago

10.1186/s12866-015-0513-6

Deep sequencing analysis of transcriptomes in Aspergillus flavus in response to resveratrol
Cited by: 40
Author(s): Houmiao Wang, Yong Lei, Liying Yan, Ke Cheng, Xiaofeng Dai, Ling‐Shu Wan, Wanshou Guo, Cheng Ling, Boshou Liao
Software Mentions: 2
Published: about 11 years ago

10.1186/s12866-018-1158-z

Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth
Cited by: 21
Author(s): Bin He, Zhìhóng Hú, Ling Ma, Haoran Li, Mingqiang Ai, Jizhong Han
Software Mentions: 2
Published: over 8 years ago

10.1186/s12866-016-0761-0

Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanses and polygalacturonases of Fusarium virguliforme
Cited by: 44
Author(s): Hao‐Xun Chang, Craig R. Yendrek, Gustavo Caetano‐Anollés, G. L. Hartman
Software Mentions: 2
Published: over 10 years ago

10.1186/s12866-018-1289-2

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans
Cited by: 8
Author(s): Francesca Scolari, Geoffrey M. Attardo, Emre Aksoy, Brian L. Weiss, Grazia Savini, Peter Takáč, Adly M. M. Abd-Alla, Andrew G. Parker, Serap Aksoy, Anna R. Malacrida
Software Mentions: 2
Published: about 8 years ago

10.1186/s12870-019-1933-5

De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress
Cited by: 38
Author(s): Shixin Deng, Jun Ma, Lili Zhang, Faju Chen, Ziyang Sang, Zhongkui Jia, Ma Li
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-015-0521-6

A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites
Cited by: 74
Author(s): Hongyu Chen, Xiuling Chen, Dong Chen, Jin-Fu Li, Yi Zhang, Aoxue Wang
Software Mentions: 2
Published: over 11 years ago

10.1186/s12870-016-0962-6

Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents
Cited by: 12
Author(s): Yongbin Zhuang, Erin A. Tripp
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12870-017-1032-4

Transcriptomic analysis links gene expression to unilateral pollen-pistil reproductive barriers
Cited by: 6
Author(s): Amanda K. Broz, Rafael F. Guerrero, April M. Randle, You Soon Baek, Matthew W. Hahn, Patricia A. Bedinger
Software Mentions: 2
Published: over 9 years ago

10.1186/s12870-014-0368-2

Regulation of Zn and Fe transporters by the GPC1gene during early wheat monocarpic senescence
Cited by: 101
Author(s): Stephen Pearce, Facundo Tabbita, Dario Cantu, Vince Buffalo, Raz Avni, Hans Vazquez-Gross, Rongrong Zhao, Christopher J. Conley, Assaf Distelfeld, Jorge Dubcovksy
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12870-014-0356-6

Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis
Cited by: 17
Author(s): R. Petersen, Haris Djozgic, Benjamin Rieger, Steffen Rapp, Erwin R. Schmidt
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12870-017-1192-2

Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.)
Cited by: 37
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Roman O. Novakovskiy, Anastasiya V. Snezhkina, Maria S. Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12870-020-02709-5

Heterologous expression of heat stress-responsive AtPLC9 confers heat tolerance in transgenic rice
Cited by: 14
Author(s): Yuliang Liu, Xinye Liu, Xue Wang, Guolian Kang, Weiwei Qi, Hua-Liang Ren, Haorui Hu, Dan Sun, Jiaoteng Bai, Shuzhi Zheng
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-019-2073-7

Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations
Cited by: 18
Author(s): Xiaofeng Qi, Elizabeth L. Ogden, José V. Die, Mark K. Ehlenfeldt, James J. Polashock, Omar Darwish, Nadim W. Alkharouf, Lisa J. Rowland
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-019-1935-3

Rpv3–1 mediated resistance to grapevine downy mildew is associated with specific host transcriptional responses and the accumulation of stilbenes
Cited by: 35
Author(s): Birgit Eisenmann, Stefan Czemmel, Tobias Ziegler, Günther Buchholz, A. Kortekamp, Oliver Trapp, Thomas Rausch, Ian B. Dry, Jochen Bogs
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-019-2081-7

Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis
Cited by: 7
Author(s): Guiliang Xin, Jia-Qian Liu, Jia Liu, Xiaolong Ren, Xiaomin Du, Wenzhe Liu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-020-02643-6

Interaction of zinc and IAA alleviate aluminum-induced damage on photosystems via promoting proton motive force and reducing proton gradient in alfalfa
Cited by: 10
Author(s): Liantai Su, Jianming Xie, Wuwu Wen, Jiaojiao Li, Peng Zhou, Yuan An
Software Mentions: 2
Published: about 6 years ago

10.1186/s12870-020-02487-0

Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana
Cited by: 13
Author(s): Andras Bittner, Jörn van Buer, Margarete Baier
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2229-14-46

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement
Cited by: 35
Author(s): Rong He, Fernanda Salvato, Park Jeong-Jin, Minjeong Kim, William M. Nelson, Tiago Santana Balbuena, Mark R. Willer, John A. Crow, Greg May, Carol Soderlund, Jay J. Thelen, David R. Gang
Software Mentions: 2
Published: over 12 years ago

10.1186/s12870-021-02921-x

Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall
Cited by: 1
Author(s): Wenquan Bao, Dun Ao, Lin Wang, Zhihao Ling, Maoshan Chen, Yue Bai, Tana Wuyun, Junxing Chen, Shuning Zhang, Fengming Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-017-1055-x

Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation
Cited by: 14
Author(s): Hongjun Liu, Langlang Ma, Xuerong Yang, Lin Zhang, Xing Zeng, Shupeng Xie, Huanwei Peng, Shibin Gao, Hung-Ching Lin, Guangtang Pan, Yongrui Wu, Yaou Shen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12944-017-0424-7

The effects of short-term high-fat feeding on exercise capacity: multi-tissue transcriptome changes by RNA sequencing analysis
Cited by: 6
Author(s): Xiao Ye, Wanshan Wang, Liguo Chen, Jieyu Chen, Pingping Jiang, Xiu‐Qiong Fu, Xin Nie, Hiu Yee Kwan, Yanyan Liu, Xiaoshan Zhao
Software Mentions: 2
Published: almost 10 years ago

10.3390/md11030830

The CHROMEVALOA Database: A Resource for the Evaluation of Okadaic Acid Contamination in the Marine Environment Based on the Chromatin-Associated Transcriptome of the Mussel Mytilus galloprovincialis
Cited by: 22
Author(s): Victoria Suárez-Ulloa, Juan Fernández‐Tajes, Vanessa Aguiar‐Pulido, Ciro Rivera-Casas, Rodrigo González-Romero, Juan Ausió, Josefina Méndez, Julián Dorado, José M. Eirín‐López
Software Mentions: 2
Published: over 13 years ago

10.1155/2018/6808934

RIG-I Signaling via MAVS Is Dispensable for Survival in Lethal Influenza Infection In Vivo
Cited by: 10
Author(s): Wenxin Wu, Xiaoqiu Wang, Wei Zhang, Lili Tian, J. Leland Booth, Elizabeth S. Duggan, Sunil S. More, Lin Liu, Mikhail G. Dozmorov, Jordan P. Metcalf
Software Mentions: 2
Published: almost 8 years ago

10.3390/medicina57060515

TBX2, a Novel Regulator of Labour
Cited by: 1
Author(s): Febilla Fernando, G. J. M. Veenboer, Martijn A. Oudijk, M. A. M. Kampman, Karst Y. Heida, Louise J M Lagendijk, Joris A. M. van der Post, Aldo Jongejan, Gijs B. Afink, Carrie Ris‐Stalpers
Software Mentions: 2
Published: over 5 years ago

10.1097/MD.0000000000027248

Construction and comprehensive analysis of a competitive endogenous RNA network to reveal potential biomarkers for the malignant differentiation of glioma
Cited by: 0
Author(s): Xin Li, Jingwen Zhang, Min Zhang, Xianghua Qi, Shiyuan Wang, Jing Teng
Software Mentions: 2
Published: about 5 years ago

10.1097/MD.0000000000016437

Analysis of the long non-coding RNA LINC01614 in non-small cell lung cancer
Cited by: 13
Author(s): Yan Sun, Chunhua Ling
Software Mentions: 2
Published: over 7 years ago

10.1590/0074-02760180053

Follow up of a robust meta-signature to identify Zika virus infection in Aedes aegypti: another brick in the wall
Cited by: 2
Author(s): Eduardo R. Fukutani, Moreno S. Rodrigues, José Irahe Kasprzykowski, Cintia Figueiredo de Araújo, Alexandre Rossi Paschoal, Pablo Ivan Pereira Ramos, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 2
Published: over 8 years ago

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: over 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: almost 8 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: over 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: almost 9 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: almost 6 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: over 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: about 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: almost 8 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: about 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: about 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: over 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: over 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: over 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: almost 6 years ago

10.1371/journal.pgen.1008317

RNA Polymerase II CTD phosphatase Rtr1 fine-tunes transcription termination
Cited by: 11
Author(s): José Victorino, Melanie J. Fox, Whitney R. Smith-Kinnaman, Sarah A. Peck Justice, Katlyn Hughes Burriss, Asha K. Boyd, Megan A. Zimmerly, Rachel R. Chan, Gerald O. Hunter, Yunlong Liu, Amber L. Mosley
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1004549

Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture
Cited by: 48
Author(s): Martin Ar, Helio A. Costa, Tuuli Lappalainen, Brenna M. Henn, Jeffrey M. Kidd, Muh Ching Yee, Fabian Grubert, Howard M. Cann, M Snyder, Stephen B. Montgomery, Carlos D. Bustamante
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1005634

EGFR/Ras Signaling Controls Drosophila Intestinal Stem Cell Proliferation via Capicua-Regulated Genes
Cited by: 108
Author(s): Yinhua Jin, Nati Ha, Marta Forés, Jun Xiang, Christine Gläßer, Julieta Antonella Maldera, Gerardo Jiménez, Bruce A. Edgar
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1006129

Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome
Cited by: 43
Author(s): Ronghui Li, Qiaoxiang Dong, Xinni Yuan, Xin Zeng, Yu Gao, Cassandra Chiao, Hongda Li, Xinyu Zhao, Sündüz Keleş, Zefeng Wang, Qiang Chang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1008606

A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans
Cited by: 8
Author(s): Yuehui Zhao, Lijiang Long, Jason Wan, Shweta Biliya, Shannon C. Brady, Daehan Lee, Akinade Ojemakinde, Erik C. Andersen, Fredrik Vannberg, Hang Lu, Patrick T. McGrath
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1005722

Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation
Cited by: 44
Author(s): Reed M. Stubbendieck, Paul D. Straight
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1007258

The long-range interaction map of ribosomal DNA arrays
Cited by: 32
Author(s): Shui Yu, Bernardo Lemos
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005531

A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary
Cited by: 84
Author(s): Y. Q. Shirleen Soh, Jan Philipp Junker, Mark E. Gill, Jacob L. Mueller, Alexander van Oudenaarden, David C. Page
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1008588

Loss of androgen signaling in mesenchymal sonic hedgehog responsive cells diminishes prostate development, growth, and regeneration
Cited by: 17
Author(s): Vien Le, Yongfeng He, Joseph Aldahl, Erika Hooker, Yu E, Adam Olson, Won Kyung Kim, Dong-Hoon Lee, Monica Wong, Rory R Sheng, Jiaqi Mi, Joseph Geradts, Gerald R. Cunha, Zijie Sun
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1008676

Germ cell-intrinsic effects of sex chromosomes on early oocyte differentiation in mice
Cited by: 17
Author(s): Norio Hamada, Nobuhiko Hamazaki, So Shimamoto, Orie Hikabe, Go Nagamatsu, Yuki Takada, Kiyoko Kato, Kozaburo Hayashi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1004655

The Nuclear Immune Receptor RPS4 Is Required for RRS1SLH1-Dependent Constitutive Defense Activation in Arabidopsis thaliana
Cited by: 95
Author(s): Kee Hoon Sohn, Cécile Segonzac, Ghanasyam Rallapalli, Panagiotis F. Sarris, Joo Yong Woo, Simon J. Williams, Toby E. Newman, Kyung Hee Paek, Boštjan Kobe, Jonathan D. G. Jones
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1009404

Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates
Cited by: 8
Author(s): Pedro Andrade, Małgorzata Anna Gazda, Pedro M. Araújo, Sandra Afonso, Jacob Agerbo Rasmussen, C Marques, Ricardo J. Lopes, M. Thomas P. Gilbert, Miguel Carneiro
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1004362

Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies
Cited by: 34
Author(s): Josephine A. Reinhardt, Cara L. Brand, Kimberly A. Paczolt, Philip M. Johns, Richard H. Baker, Gerald S. Wilkinson
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1003006

New Partners in Regulation of Gene Expression: The Enhancer of Trithorax and Polycomb Corto Interacts with Methylated Ribosomal Protein L12 Via Its Chromodomain
Cited by: 18
Author(s): Anne Coléno-Costes, Suk Min Jang, Augustin de Vanssay, Julien Rougeot, Tahar Bouceba, Neel B. Randsholt, Jean‐Michel Gibert, Stéphane Le Crom, Emmanuèle Mouchel‐Vielh, Sébastien Bloyer, Frédérique Peronnet
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pgen.1008338

Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development
Cited by: 4
Author(s): Angelina Zheleva, Eva Gómez-Orte, Beatriz Sáenz-Narciso, Begoña Ezcurra, Henok Kassahun, María de Toro, Antonio Miranda‐Vizuete, Ralf Schnabel, Hilde Nilsen, Juan Cabello
Software Mentions: 2
Published: about 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568