10.3390/genes11070787

Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Cited by: 11
Author(s): Cécile Fruchard, Hélène Badouin, David Latrasse, Ravi Suresh Devani, Aline Muyle, Bénédicte Rhoné, Susanne S. Renner, Anjan K. Banerjee, Abdelhafid Bendahmane, Gabriel Marais
Software Mentions: 3
Published: about 6 years ago

10.1038/s41420-021-00588-9

Integrated analysis of high-throughput sequencing data reveals the key role of LINC00467 in the invasion and metastasis of testicular germ cell tumors
Cited by: 21
Author(s): Hao Bo, Fang Zhu, Zhizhong Liu, Qi Deng, Guangmin Liu, Ruixue Li, Wenbing Zhu, Yue‐Qiu Tan, Gang Liu, Jingyu Fan, Liqing Fan
Software Mentions: 3
Published: about 5 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of <i>Paeonia lactiflora</i> Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-29759-y

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis
Cited by: 36
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Terence McGonigle, D. Mok, Angela Baird, Borut Klopcic, Lavinia Gordon, Shelley Gorman, Cynthia Forest, Roger Bouillon, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: about 8 years ago

10.1155/2021/5589101

Weighted Gene Coexpression Network Analysis to Construct Competitive Endogenous RNA Network in Chromogenic Renal Cell Carcinoma
Cited by: 1
Author(s): Yon-Bo Chen, Liang Gao, Jindong Zhang, Jiang Guo, Ping-Hong You, Liang-you Tang, Ying-Wen Liu
Software Mentions: 3
Published: about 5 years ago

10.1155/2018/4767328

Digital Gene Expression Profiling Analysis of Aged Mice under Moxibustion Treatment
Cited by: 6
Author(s): Nan Liu, Yunyao Jiang, Min Xing, Baixiao Zhao, Jincai Hou, Minyee Lim, Jian Huang, Xue Li, Li Han
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms19082300

Transcriptomic Analyses of Root Restriction Effects on Phytohormone Content and Signal Transduction during Grape Berry Development and Ripening
Cited by: 12
Author(s): Lu Feng, Ji Cao, Shiping Wang, Ling Jiang, Xian Li, Chongde Sun
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30640-1

PyMT-1099, a versatile murine cell model for EMT in breast cancer
Cited by: 14
Author(s): Mohit Saxena, Ravi Kiran Reddy Kalathur, Melanie Neutzner, Gerhard Christofori
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.586658

Cardiac Regeneration and Tumor Growth—What Do They Have in Common?
Cited by: 1
Author(s): Severin Dicks, Lonny Jürgensen, Florian Leuschner, David Hassel, Geoffroy Andrieux, Melanie Boerries
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-87955-9

Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Cited by: 5
Author(s): Diane Sutcliffe, Ashok R. Dinasarapu, Jasper E. Visser, Joery den Hoed, Fatemeh Seifar, Piyush Joshi, Irène Ceballos-Picot, Tejas Sardar, Ellen J. Hess, Yan V. Sun, Zhexing Wen, Michael E. Zwick, Hyder A. Jinnah
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn &amp; Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-019-40016-8

Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas
Cited by: 10
Author(s): Greta Alì, Rossella Bruno, Anello Marcello Poma, Ornella Affinito, Antonella Monticelli, Paolo Piaggi, Sara Ricciardi, Marco Lucchi, Franca Melfi, Antonio Chella, Sérgio Cocozza, Gabriella Fontanini
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-018-1601-1

Transcriptomic signature reveals mechanism of flower bud distortion in witches’-broom disease of soybean (Glycine max)
Cited by: 10
Author(s): Sarika Jaiswal, P. V. Jadhav, Rahul Singh Jasrotia, P. B. Kale, Snehal Krishna Kad, M. P. Moharil, M. S. Dudhare, Jashminkumar Kheni, A. G. Deshmukh, S. S. Mane, R. S. Nandanwar, Suprasanna Penna, J. G. Manjaya, Mir Asif Iquebal, R. S. Tomar, Prashant G. Kawar, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btv209

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Cited by: 39
Author(s): Emmanuel Dimont, Jiantao Shi, Rory Kirchner, Winston Hide
Software Mentions: 3
Published: over 11 years ago

10.14814/phy2.13019

Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
Cited by: 19
Author(s): Sindre Lee, Frode Norheim, Torgrim M. Langleite, Hans Jørgen Noreng, Trygve H. Storås, Lydia A. Afman, Gary Frost, Jimmy D. Bell, E. Louise Thomas, Kristoffer Jensen Kolnes, Daniel S. Tangen, Hans Kristian Stadheim, Gregor D. Gilfillan, Hanne Løvdal Gulseth, Kåre I. Birkeland, Jørgen Jensen, Christian A. Drevon, Torgeir Holen
Software Mentions: 3
Published: almost 10 years ago

10.1186/s40168-018-0606-1

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

10.1186/s13073-015-0183-x

Restoration of mesenchymal retinal pigmented epithelial cells by TGFβ pathway inhibitors: implications for age-related macular degeneration
Cited by: 87
Author(s): Monte J. Radeke, Carolyn M. Radeke, Ying-Hsuan Shih, Jane Hu, Dean Bok, Lincoln V. Johnson, Peter Coffey
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1006256

The Musashi 1 Controls the Splicing of Photoreceptor-Specific Exons in the Vertebrate Retina
Cited by: 58
Author(s): Daniel P. Murphy, Benjamin Cieply, Russ P. Carstens, Visvanathan Ramamurthy, Peter Stoilov
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-016-0381-1

Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia
Cited by: 6
Author(s): Martin I. Sigurdsson, Louis A. Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary F. Aranki, Gregory S. Couper, Stanton K. Shernan, J. G. Seidman, Simon C. Body, Jochen D. Muehlschlegel
Software Mentions: 2
Published: over 9 years ago

10.1186/s13073-017-0407-3

Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance
Cited by: 26
Author(s): David J. Duffy, Aleksandar Krstić, Melinda Halász, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G. Higgins, Walter Kölch
Software Mentions: 2
Published: over 9 years ago

10.1186/s40168-018-0583-4

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

10.3389/fimmu.2015.00023

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq
Cited by: 31
Author(s): Maura E. Casey, Kieran G. Meade, Nicolas C. Nalpas, Maria Taraktsoglou, John A. Browne, Kate E. Killick, Stephen D. E. Park, Eamonn Gormley, Karsten Hokamp, David A. Magee, David E. MacHugh
Software Mentions: 2
Published: over 11 years ago

10.1186/s13073-018-0558-x

Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease
Cited by: 35
Author(s): Angela Mo, Urko M. Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad, Greg Gibson
Software Mentions: 2
Published: about 8 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

10.1002/mbo3.510

A1S_2811, a CheA/Y-like hybrid two-component regulator from<i>Acinetobacter baumannii</i>ATCC17978, is involved in surface motility and biofilm formation in this bacterium
Cited by: 27
Author(s): Rong Chen, Ruichen Lv, Xiao Jun Lin, Min Wang, Zongmin Du, Yafang Tan, Yu‐Jun Cui, Yanfeng Yan, Yanping Luo, Ruifu Yang, Yajun Song
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms18071512

The Prostate Cancer Cells Resistant to Docetaxel as in vitro Model for Discovering MicroRNAs Predictive of the Onset of Docetaxel Resistance
Cited by: 5
Author(s): Lorenzo Bascetta, Arianna Oliviero, Romina D’Aurizio, Monica Evangelista, Alberto Mercatanti, Marco Pellegrini, Francesca Marrocolo, Sergio Bracarda, Milena Rizzo
Software Mentions: 2
Published: about 9 years ago

10.3389/fimmu.2020.607891

MAPKAP Kinase-2 Drives Expression of Angiogenic Factors by Tumor-Associated Macrophages in a Model of Inflammation-Induced Colon Cancer
Cited by: 12
Author(s): Lucia Suárez‐López, Yi Wen Kong, Ganapathy Sriram, Jesse C. Patterson, Samantha G. Rosenberg, Sandra Morandell, Kevin M. Haigis, Michael B. Yaffe
Software Mentions: 2
Published: over 5 years ago

10.5808/GI.2019.17.1.e2

Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease
Cited by: 5
Author(s): Seokjin Ham, Yeon‐Mok Oh, Tae-Young Roh
Software Mentions: 2
Published: over 7 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

10.1016/j.gpb.2020.06.003

m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes
Cited by: 43
Author(s): Yuhuan Li, Qingyang Zhang, Guanshen Cui, Fen Zhao, Xin Tian, Bao‐Fa Sun, Ying Yang, Wei Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.672700

Host-Parasite Interaction of Atlantic salmon (Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease
Cited by: 18
Author(s): Natasha A. Botwright, Amin R. Mohamed, Joel Slinger, Paula C. Lima, James W. Wynne
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms20194900

Exploring the Molecular Crosstalk between Pancreatic Bud and Mesenchyme in Embryogenesis: Novel Signals Involved
Cited by: 3
Author(s): Ilaria Guerriero, Maria Teresa De Angelis, Fulvio D’Angelo, Rita Leveque, Eleonora Savignano, Luca Roberto, Valeria Lucci, P. Mazzone, Simona Laurino, Giovanni Storto, Anna Nardelli, Alessandro Sgambato, Michele Ceccarelli, Mario De Felice, Elena Amendola, Geppino Falco
Software Mentions: 2
Published: almost 7 years ago

10.1093/gigascience/giy045

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis
Cited by: 10
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 2
Published: over 8 years ago

10.1002/mbo3.1153

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

10.1002/mbo3.768

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

10.3389/fimmu.2017.00876

Transcriptional Profiling of Midguts Prepared from Trypanosoma/T. congolense-Positive Glossina palpalis palpalis Collected from Two Distinct Cameroonian Foci: Coordinated Signatures of the Midguts’ Remodeling As T. congolense-Supportive Niches
Cited by: 9
Author(s): Jean Marc Tsagmo Ngoune, Flobert Njiokou, Béatrice Loriod, Ginette Irma Kame‐Ngasse, Nicolas Fernandez-Nunez, Claire Rioualen, Jacques van Helden, Anne Geiger
Software Mentions: 2
Published: about 9 years ago

10.1099/mgen.0.000148

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

10.1099/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

10.1080/19490976.2016.1186334

The mucin-degradation strategy of<i>Ruminococcus gnavus</i>: The importance of intramolecular<i>trans</i>-sialidases
Cited by: 101
Author(s): Emmanuelle H. Crost, Louise E. Tailford, Marie Monestier, David Swarbreck, Bernard Henrissat, Lisa Crossman, Nathalie Juge
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0209496

Inflammation and transcriptional responses of peripheral blood mononuclear cells in classic ataxia telangiectasia
Cited by: 17
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Joseph M. Collaco, Cynthia Rothblum-Oviatt, Jonathan H. Wright, Michael A. O’Reilly, Benjamin D. Singer, Howard M. Lederman
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1000843

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Cited by: 55
Author(s): Augix Guohua Xu, Lin He, Zhongshan Li, Ying Xu, Mingfeng Li, Xing Fu, Yanyan Zheng, Yuan Yuan, Corinna Menzel, Na Li, Mehmet Somel, Hao Hu, Wei Chen, Svante Pääbo, Philipp Khaitovich
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pcbi.1005562

ROTS: An R package for reproducibility-optimized statistical testing
Cited by: 98
Author(s): Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo
Software Mentions: 2
Published: over 9 years ago

10.12688/f1000research.6402.2

The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
Cited by: 11
Author(s): Jóhannes Guðbrandsson, Ehsan Pashay Ahi, Sigríður Rut Franzdóttir, Kalina H. Kapralova, Bjarni K. Kristjánsson, S. Sophie Steinhaeuser, Valerie H. Maier, Isak M. Johannesson, Sigurður S. Snorrason, Zophonı́as O. Jónsson, Arnar Pálsson
Software Mentions: 2
Published: over 10 years ago

10.3389/fimmu.2021.650977

T Cell-Intrinsic CDK6 Is Dispensable for Anti-Viral and Anti-Tumor Responses In Vivo
Cited by: 3
Author(s): Klara R. Klein, Agnieszka Witalisz‐Siepracka, Dagmar Gotthardt, Benedikt Agerer, Felix Locker, Reinhard Grausenburger, Vanessa M. Knab, Andréas Bergthaler, Veronika Sexl
Software Mentions: 2
Published: about 5 years ago

10.1099/mgen.0.000194

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

10.3389/fimmu.2020.01073

Prediabetes Induced by a Single Autoimmune B Cell Clone
Cited by: 1
Author(s): Nathaniel Phillips, Eugene Ke, Amy Nham, Maximilian Seidl, Brent Freeman, Justin R. Abadejos, Changchun Xiao, David Nemazee, Manching Ku, Oktay Kirak
Software Mentions: 2
Published: about 6 years ago

10.1099/mgen.0.000246

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

10.1038/s41438-021-00542-x

Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Cited by: 65
Author(s): Pengjie Wang, Jiaxin Yu, Shan Jin, Shuai Chen, Chuan Yue, Wenling Wang, Shuilian Gao, Hongli Cao, Yuanrun Zheng, Mengya Gu, Xuejin Chen, Yun Sun, Yuqiong Guo, Jing Yang, Xingtan Zhang, Naixing Ye
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1008857

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
Cited by: 14
Author(s): Josh L. Espinoza, Chris L. Dupont, Aubrie O’Rourke, Sinem Beyhan, Pavel Morales, Amy L. Spoering, Kirsten J. Meyer, Agnes P. Chan, Yongwook Choi, William C. Nierman, Kim Lewis, Karen E. Nelson
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-020-00421-x

Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox
Cited by: 22
Author(s): Zhineng Li, Ning Liu, Wei Zhang, C. F. Wu, Yunbin Jiang, Jing Ma, Mingyang Li, Shunzhao Sui
Software Mentions: 2
Published: over 5 years ago

10.1186/s12934-021-01626-y

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

10.3389/fimmu.2020.568565

Dynamic Transcriptome Reveals the Mechanism of Liver Injury Caused by DHAV-3 Infection in Pekin Duck
Cited by: 4
Author(s): Junting Cao, Yunsheng Zhang, Ying Chen, Shuang Liang, Dapeng Liu, Wenlei Fan, Yaxi Xu, Hehe Liu, Zhengkui Zhou, Xiaolin Liu, Shuisheng Hou
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-021-00619-7

DNA methylation affects photoperiodic tuberization in potato (Solanum tuberosum L.) by mediating the expression of genes related to the photoperiod and GA pathways
Cited by: 13
Author(s): Yanjun Ai, Shenglin Jing, Zhengnan Cheng, Botao Song, Conghua Xie, Jun Liu, Jun Zhou
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms20236083

Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host–Pathogen Interactions
Cited by: 22
Author(s): Micael F. M. Gonçalves, R. Nunes, Laurentijn Tilleman, Yves Van de Peer, Dieter Deforce, Filip Van Nieuwerburgh, Ana Cristina Esteves, Artur Alves
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-021-00532-z

Underpinning the molecular programming attributing heat stress associated thermotolerance in tea (Camellia sinensis (L.) O. Kuntze)
Cited by: 16
Author(s): Romit Seth, Tony Kipkoech Maritim, Rajni Parmar, Ram Kumar Sharma
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-021-00481-7

Genome sequence and evolution of <i>Betula platyphylla</i>
Cited by: 46
Author(s): Su Chen, Yucheng Wang, Lili Yu, Tao Zheng, Sui Wang, Zhen Yue, Jing Jiang, Sapna Kumari, Chunfang Zheng, Haibao Tang, Jun Li, Yuqi Li, Jiongjiong Chen, Wenbo Zhang, Hanhui Kuang, Jon S. Robertson, Patrick Xuechun Zhao, Huiyu Li, Shengqiang Shu, Yordan S. Yordanov, Hongyan Huang, David Goodstein, Ying Gai, Qi Qi, Min Jiang, Chunyan Xu, SongBo Wang, Guanzheng Qu, Andrew H. Paterson, David Sankoff, Hairong Wei, Guifeng Liu, Chuanping Yang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms19010002

Exploring the Mechanisms of Electroacupuncture-Induced Analgesia through RNA Sequencing of the Periaqueductal Gray
Cited by: 19
Author(s): Manli Hu, Hongmei Zhu, Qiulin Zhang, Jingjing Liu, Yi Ding, Juming Zhong, Vitaly Vodyanoy, Mingxing Ding
Software Mentions: 2
Published: over 8 years ago

10.1038/s41438-019-0134-6

Identification of genes preferentially expressed in wild strawberry receptacle fruit and demonstration of their promoter activities
Cited by: 5
Author(s): Rachel Shahan, Dongdong Li, Zhongchi Liu
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.01733

Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread
Cited by: 22
Author(s): Marcello Abbondio, Antonio Palomba, Alessandro Tanca, Cristina Fraumene, Daniela Pagnozzi, Mauro Serra, Fabio Marongiu, Ezio Laconi, Sergio Uzzau
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.01443

Impact of Pb on Chlamydomonas reinhardtii at Physiological and Transcriptional Levels
Cited by: 22
Author(s): Canqi Zheng, Muhammad Aslam, Xiaojuan Liu, Hong Du, Xihui Xie, Haojie Jia, Nan Huang, Kaiming Tang, Yingquan Yang, Ping Li
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2020.01055

Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cited by: 19
Author(s): Marina Cavaiuolo, Carine Chagneau, Soumaya Laalami, Harald Putzer
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-019-0131-9

Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat (Eriobotrya japonica) fruit
Cited by: 28
Author(s): Wenli Liu, Jing Zhang, Chen Jiao, Yin X, Zhangjun Fei, Qingbiao Wu, Kunsong Chen
Software Mentions: 2
Published: over 7 years ago

10.1186/s13104-018-3154-7

Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout
Cited by: 3
Author(s): Hao Ma, Guangtu Gao, Gregory M. Weber
Software Mentions: 2
Published: over 8 years ago

10.1016/j.immuni.2020.07.004

Flexible Usage and Interconnectivity of Diverse Cell Death Pathways Protect against Intracellular Infection
Cited by: 83
Author(s): Marcel Doerflinger, Yexuan Deng, Paul G. Whitney, Ranja Salvamoser, Sven Engel, Andrew J. Kueh, Lin Tai, Annabell Bachem, Elise Gressier, Niall Geoghegan, Stephen Wilcox, Kelly L. Rogers, Alexandra L. Garnham, Michael A. Dengler, Stefanie Bader, Gregor Ebert, Jaclyn S. Pearson, Dominic De Nardo, Nancy Wang, Chenying Yang, Milton Pereira, Clare E. Bryant, Richard A. Strugnell, James E. Vince, Marc Pellegrini, Andreas Strasser, Sammy Bedoui, Marco J. Herold
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.immuni.2020.10.020

Antagonistic Inflammatory Phenotypes Dictate Tumor Fate and Response to Immune Checkpoint Blockade
Cited by: 113
Author(s): Eduardo Bonavita, Christian P. Bromley, Gustav Jonsson, Victoria S. Pelly, Sudhakar Sahoo, Katherine Walwyn-Brown, Sofia Mensurado, Agrin Moeini, Eimear Flanagan, Charlotte R. Bell, Shih‐Chieh Chiang, C.P. Chikkanna-Gowda, Neil C. Rogers, Bruno Silva‐Santos, Sébastien Jaillon, Alberto Mantovani, Caetano Reis e Sousa, Nadia Guerra, Daniel M. Davis, Santiago Zelenay
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.01247

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum
Cited by: 15
Author(s): Wonyong Kim, Brad Cavinder, Robert H. Proctor, Kerry O’Donnell, Jeffrey P. Townsend, Frances Trail
Software Mentions: 2
Published: about 7 years ago

10.1111/jeb.12895

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy
Cited by: 21
Author(s): Luke T. Dunning, Helen Hipperson, William J. Baker, Roger K. Butlin, Céline Devaux, I. Hutton, Javier Igea, Alexander S. T. Papadopulos, Xiangqian Quan, Carole Smadja, Colin Turnbull, Vincent Savolainen
Software Mentions: 2
Published: about 10 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

10.1242/jeb.226233

High temperature induces transcriptomic changes in <i>Crassostrea gigas</i> that hinders progress of Ostreid herpesvirus (OsHV-1) and promotes survival
Cited by: 18
Author(s): Lizenn Delisle, Marianna Pauletto, Jérémie Vidal-Dupiol, Bruno Petton, Luca Bargelloni, Caroline Montagnani, Fabrice Pernet, Charlotte Corporeau, Elodie Fleury
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.02397

Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli FORC_035 Reveals the Essential Role of Iron Acquisition for Survival in Canola Sprouts and Water Dropwort
Cited by: 0
Author(s): Hongjun Na, Yeonkyung Kim, Dajeong Kim, Hyunjin Yoon, Sangryeol Ryu
Software Mentions: 2
Published: almost 8 years ago

10.1093/jxb/erw346

Analysis of high iron rice lines reveals new miRNAs that target iron transporters in roots
Cited by: 25
Author(s): Soumitra Paul, Dipak Gayen, Swapan K. Datta, Karabi Datta
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erw347

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development
Cited by: 56
Author(s): Jelle Van Leene, Jonas Blomme, Shubhada Rajabhau Kulkarni, Bernard Cannoot, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Leen Vercruysse, Robin Vanden Bossche, Ken S. Heyndrickx, Steffen Vanneste, Alain Goossens, Kris Gevaert, Klaas Vandepoele, Nathalie González, Dirk Inzé, Geert De Jaeger
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erw361

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways
Cited by: 94
Author(s): Qili Fei, Yang Li, Wanqi Liang, Dabing Zhang, Blake C. Meyers
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pbio.3000415

MDT-15/MED15 permits longevity at low temperature via enhancing lipidostasis and proteostasis
Cited by: 50
Author(s): Dong-Yeop Lee, Seon Woo A. An, Yoonji Jung, Yasuyo Yamaoka, Youngjae Ryu, Grace Ying Shyen Goh, Arshia Beigi, Jun Yang, Gyoo Yeol Jung, K. Dengke, Chang Man Ha, Stefan Taubert, Youngsook Lee, Seung-Jae Lee
Software Mentions: 2
Published: about 7 years ago

10.1093/jxb/erx164

Increased temperature and CO2 alleviate photoinhibition in Desmarestia anceps: from transcriptomics to carbon utilization
Cited by: 28
Author(s): Concepción Iñíguez, S. Heinrich, Lars Harms, Francisco J. L. Gordillo
Software Mentions: 2
Published: about 9 years ago

10.1111/pbi.12777

Production of red‐flowered oilseed rape via the ectopic expression of <i><scp>O</scp>rychophragmus violaceus <scp>O</scp>v<scp>PAP</scp>2</i>
Cited by: 32
Author(s): Wenqin Fu, Daozong Chen, Qi Pan, Fengfeng Li, Zhigang Zhao, Xianhong Ge, Zaiyun Li
Software Mentions: 2
Published: about 9 years ago

10.1093/jxb/erx336

A disulfide bond A-like oxidoreductase is a strong candidate gene for self-incompatibility in apricot (Prunus armeniaca) pollen
Cited by: 20
Author(s): Juan Vicente Muñoz-Sanz, Elena Zuriaga, M. L. Badenes, Carlos Romero
Software Mentions: 2
Published: almost 9 years ago

10.1093/jxb/erx254

Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Cited by: 43
Author(s): Pavel Cherenkov, Daria D. Novikova, N. A. Omelyanchuk, Victor G. Levitsky, Ivo Große, Dolf Weijers, В. В. Миронова
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.01130

Essential Role of σ Factor RpoF in Flagellar Biosynthesis and Flagella-Mediated Motility of Acidithiobacillus caldus
Cited by: 12
Author(s): Chunhua Yang, Xianke Chen, Rui Wang, Jianqiang Lin, Xiangmei Liu, Xin Pang, Cheng‐Jia Zhang, Lin-Xu Chen
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.2004880

METTL3-mediated m6A modification is required for cerebellar development
Cited by: 195
Author(s): Chenxin Wang, Guanshen Cui, Xiu Ying Liu, Kai Xu, Meng Wang, Xinxin Zhang, Liyuan Jiang, Ang Li, Ying Yang, Weiyi Lai, Bao‐Fa Sun, Guibin Jiang, Hailin Wang, Wei‐Min Tong, Wei Li, Xiu‐Jie Wang, Yun‐Gui Yang, Qi Zhou
Software Mentions: 2
Published: about 8 years ago

10.1093/jxb/ery020

The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides
Cited by: 57
Author(s): Xiaoming Sun, José Tomás Matus, Darren Chern Jan Wong, Zemin Wang, Fengmei Chai, Langlang Zhang, Ting Fang, Li Zhao, Yi Wang, Yuepeng Han, Qingfeng Wang, Shaohua Li, Zhenchang Liang, H. P. Xin
Software Mentions: 2
Published: over 8 years ago

10.1093/jxb/ery132

miR156-SPL modules regulate induction of somatic embryogenesis in citrus callus
Cited by: 72
Author(s): Long Jiang, Chaoyang Liu, Meng-Qi Feng, Yun Liu, Xiaomeng Wu, Wen‐Wu Guo
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.01457

Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?
Cited by: 16
Author(s): Caroline Poyntner, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 2
Published: about 8 years ago

10.1523/ENEURO.0397-19.2019

Identification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult Mice
Cited by: 18
Author(s): Casey J. A. Smith-Anttila, Elizabeth A. Mason, Christine Wells, Bruce J. Aronow, Peregrine B. Osborne, Janet R. Keast
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erz523

The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing
Cited by: 15
Author(s): Bangshing Wang, Haoxi Chai, Yaohua Zhong, Yun Shen, Wei Yang, Junping Chen, Zhanguo Xin, Huazhong Shi
Software Mentions: 2
Published: almost 7 years ago

10.1111/1751-7915.12713

Transcriptional response of<i>Escherichia coli</i>to 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

10.3389/fmicb.2021.634325

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi
Cited by: 9
Author(s): Luigi Orrù, Loredana Canfora, Alessandra Trinchera, Melania Migliore, Bruno Pennelli, A. Marcucci, Roberta Farina, Flavia Pinzari
Software Mentions: 2
Published: about 5 years ago

10.1186/s12986-019-0339-6

Dietary iron interacts with genetic background to influence glucose homeostasis
Cited by: 7
Author(s): Mario A. Miranda, Celine L. St. Pierre, Juan F Macias-Velasco, Harrison P. Nguyen, Heather Schmidt, Lucian T. Agnello, Jessica P Wayhart, Heather A. Lawson
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.25730

Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment
Cited by: 72
Author(s): Cemre Celen, Jen‐Chieh Chuang, Xin Luo, Nadine Nijem, Angela K. Walker, Fei Chen, Shuyuan Zhang, Angie Y. Chung, Liem H. Nguyen, Ibrahim Nassour, Albert Budhipramono, Xuxu Sun, Levinus A. Bok, Meriel McEntagart, Evelien Gevers, Shari G. Birnbaum, Amelia J. Eisch, Craig M. Powell, Woo-Ping Ge, Gijs W.E. Santen, Maria H. Chahrour, Min Zhu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1003896

RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation
Cited by: 60
Author(s): Meleri Jones, Inga Dry, Dan Frampton, Manuraj Singh, Ravinder K. Kanda, Michael B. Yee, Paul Kellam, Michael Hollinshead, Paul R. Kinchington, Edel A. O’Toole, Judith Breuer
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1003962

Reversible Silencing of Cytomegalovirus Genomes by Type I Interferon Governs Virus Latency
Cited by: 55
Author(s): Franziska Dağ, Lars Dölken, Julia Holzki, Anja Drabig, Adrien Weingärtner, Johannes Schwerk, Stefan Lienenklaus, Ianina Conte, Robert Geffers, Colin Davenport, Ulfert Rand, Mario Köster, Siegfried Weiß, Barbara Adler, Dagmar Wirth, Martin Messerle, Hansjörg Hauser, Luka Čičin‐Šain
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1004250

Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset
Cited by: 185
Author(s): Darryl Falzarano, Emmie de Wit, Friederike Feldmann, Angela L. Rasmussen, Atsushi Okumura, Xinxia Peng, Matthew Thomas, Neeltje van Doremalen, Elaine Haddock, Lee Nagy, Rachel LaCasse, Tingting Liu, Jiang Zhu, Jason S. McLellan, Dana Scott, Michael G. Katze, Heinz Feldmann, Vincent J. Munster
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.ppat.1004765

Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response
Cited by: 35
Author(s): Punita Juneja, Cristina V. Ariani, Yung Shwen Ho, Jewelna Akorli, William J. Palmer, Arnab Pain, Francis M. Jiggins
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1005218

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
Cited by: 48
Author(s): Michael Tscherner, Florian Zwolanek, Sabrina Jenull, Fritz J. Sedlazeck, Andriy Petryshyn, Ingrid E. Frohner, John Mavrianos, Neeraj Chauhan, Arndt von Haeseler, Karl Kuchler
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1005536

Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
Cited by: 75
Author(s): Stephanie M. Rainey, Julien Martinez, Melanie McFarlane, Punita Juneja, Peter Sarkies, Aleksei Lulla, Esther Schnettler, Margus Varjak, Andres Merits, Eric A. Miska, Francis M. Jiggins, Alain Kohl
Software Mentions: 2
Published: over 10 years ago

10.1111/pbi.12991

Transcriptome and metabolome reveal distinct carbon allocation patterns during internode sugar accumulation in different sorghum genotypes
Cited by: 42
Author(s): Yin Li, Wen-Qin Wang, Yaping Feng, Min Tu, P. Wittich, Nicholas J. Bate, Joachim Messing
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1006046

Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection
Cited by: 25
Author(s): Mary F. Fontana, Gabrielly Lunkes de Melo, Chioma Anidi, Rebecca Hamburger, Charles C. Kim, So Youn Lee, Jennifer Pham
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1006143

RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature
Cited by: 27
Author(s): Coralie Viollet, David A. Davis, Shewit S. Tekeste, Martin Reczko, Joseph M. Ziegelbauer, Francesco Pezzella, Jiannis Ragoussis, Robert Yarchoan
Software Mentions: 2
Published: over 9 years ago