bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-36376-2

Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii)
Cited by: 20
Author(s): Nan Jiang, Yuding Fan, Yong Zhou, Weiling Wang, Jie Ma, Lingbing Zeng
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37177-3

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome
Cited by: 15
Author(s): Heidi H. Pak, Nicole E. Cummings, Cara L Green, Jacqueline A. Brinkman, Deyang Yu, Jay L. Tomasiewicz, Shany E. Yang, Colin Boyle, Elizabeth N. Konon, Irene M. Ong, Dudley W. Lamming
Software Mentions: 1
Published: almost 8 years ago

10.1080/21505594.2020.1838741

Aprepitant, an antiemetic agent, interferes with metal ion homeostasis ofCandida aurisand displays potent synergistic interactions with azole drugs
Cited by: 18
Author(s): Hassan E. Eldesouky, Nadia A. Lanman, Tony R. Hazbun, Mohamed N. Seleem
Software Mentions: 1
Published: about 6 years ago

10.3390/molecules22081292

Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus
Cited by: 28
Author(s): Minqian Wang, Jenni Firrman, Liqing Zhang, Gustavo Arango-Argoty, Peggy M. Tomasula, LinShu Liu, Weidong Xiao, Kit L. Yam
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0239617

Comparative transcriptome analysis reveals candidate genes related to cadmium accumulation and tolerance in two almond mushroom (Agaricus brasiliensis) strains with contrasting cadmium tolerance
Cited by: 3
Author(s): Penghu Liu, Zaixing Huang, Xuhui Luo, Hua Cai, Weng Bo-qi, Yixiang Wang, Li‐Song Chen
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.ppat.1009030

A human secretome library screen reveals a role for Peptidoglycan Recognition Protein 1 in Lyme borreliosis
Cited by: 9
Author(s): Akash Gupta, Gunjan Arora, Connor Rosen, Zachary A. Kloos, Yongguo Cao, Jiří Černý, Andaleeb Sajid, Dieuwertje Hoornstra, Maryna Golovchenko, Nataliia Rudenko, Ulrike G. Munderloh, Joppe W. Hovius, Carmen J. Booth, Christine Jacobs‐Wagner, Noah W. Palm, Aaron M. Ring, Erol Fikrig
Software Mentions: 1
Published: almost 6 years ago

10.1080/21505594.2020.1726561

Distinct host-immune response toward species related intracellular mycobacterial killing: A transcriptomic study
Cited by: 9
Author(s): Abhilasha Madhvi, Hridesh Mishra, Novel N. Chegou, Gerard Tromp, Carel Jacobus Van Heerden, Ray-Dean Pietersen, Gina Leisching, Bienyameen Baker
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0137726

Social Regulation of Gene Expression in Threespine Sticklebacks
Cited by: 23
Author(s): Anna K. Greenwood, Catherine L. Peichel
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0130885

Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis
Cited by: 65
Author(s): Jie Ye, Tixu Hu, Congmei Yang, Hanxia Li, Mingze Yang, Raina Ijaz, Zhibiao Ye, Yuyang Zhang
Software Mentions: 1
Published: over 11 years ago

10.3390/vetsci8080156

Transcriptomic Profiling of Dromedary Camels Immunised with a MERS Vaccine Candidate
Cited by: 0
Author(s): Sharif Hala, Paolo Ribeca, Haya A. Aljami, Suliman A. Alsagaby, Ibrahim Qasim, Sarah C. Gilbert, Naif Khalaf Alharbi
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0198221

AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection
Cited by: 34
Author(s): Audrey C. Papp, Abul K. Azad, Maciej Pietrzak, Amanda Williams, Samuel K. Handelman, Robert P. Igo, Catherine M. Stein, Katherine E. Hartmann, Larry S. Schlesinger, Wolfgang Sadée
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-36726-0

Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues
Cited by: 17
Author(s): Songqian Huang, Yūki Ichikawa, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0219976

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes
Cited by: 8
Author(s): Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0154156

Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis
Cited by: 11
Author(s): Elaine C. Lee, Heejung Kim, Jennifer Ditano, Dacie Manion, Benjamin L. King, Kevin Strange
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-35891-6

De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms
Cited by: 34
Author(s): Muhammad Sarwar, Zarnab Ahmad, Bushra Rashid, Sahar Hassan, Per L. Gregersen, Maria De la O. Leyva, István Nagy, Torben Asp, Tayyab Husnain
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0116935

Transcriptional Regulation and Adaptation to a High-Fiber Environment in Bacillus subtilis HH2 Isolated from Feces of the Giant Panda
Cited by: 11
Author(s): Ziyao Zhou, Xiaoxiao Zhou, Li Jin, Zhijun Zhong, Wei Li, Xuehan Liu, Furui Liu, Huaiyi Su, Yongjiu Luo, Wuyang Gu, Chengdong Wang, Hemin Zhang, Desheng Li, Tiantian He, Hualin Fu, Suizhong Cao, Jinjiang Shi, Guangneng Peng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0084311

The MicroRNA Expression Signature of Bladder Cancer by Deep Sequencing: The Functional Significance of the miR-195/497 Cluster
Cited by: 130
Author(s): Toshihiko Iwamoto, Naohiko Seki, Hirofumi Yoshino, Takeshi Chiyomaru, Takahiro Yamasaki, Hideo Hidaka, Tomokazu Yonezawa, Nijiro Nohata, Takashi Kinoshita, Masayuki Nakagawa, Hideki Enokida
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0169595

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis
Cited by: 33
Author(s): Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protásio Pereira
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0159295

Transcriptome Profiling Reveals Disruption of Innate Immunity in Chronic Heavy Ethanol Consuming Female Rhesus Macaques
Cited by: 29
Author(s): Suhas Sureshchandra, Maham Rais, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0090895

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]
Cited by: 9
Author(s): Yan Ling, Yinghong Gu, Tao Xiang, Xianjun Lai, Yizheng Zhang, Xuemei Tan, Haiyan Wang
Software Mentions: 1
Published: over 12 years ago

10.3390/polym12040937

Performance of a Biodegradable Composite with Hydroxyapatite as a Scaffold in Pulp Tissue Repair
Cited by: 14
Author(s): Masakazu Okamoto, Shigeto Matsumoto, Ayato Sugiyama, Kei Kanie, Masakatsu Watanabe, Haozhang Huang, Muslim Ali, Yuki Ito, Jiro Miura, Yujiro Hirose, Koichiro Uto, Mitsuhiro Ebara, Ryuji Kato, Aika Yamawaki-Ogata, Yuji Narita, Shigetada Kawabata, Yusuke Takahashi, Mikako Hayashi
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-37422-9

Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa
Cited by: 51
Author(s): Won Ju Hwang, Sang Sun Yoon
Software Mentions: 1
Published: almost 8 years ago

10.1098/rspb.2014.2519

Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs
Cited by: 39
Author(s): Jan de Vries, Christian Woehle, Gregor Christa, Heike Wägele, Aloysius G.M. Tielens, Peter Jahns, Sven B. Gould
Software Mentions: 1
Published: over 11 years ago

10.1098/rspb.2017.0360

Unravelling the relationship between the tsetse fly and its obligate symbiont Wigglesworthia : transcriptomic and metabolomic landscapes reveal highly integrated physiological networks
Cited by: 50
Author(s): Xiao‐Li Bing, Geoffrey M. Attardo, Aurélien Vigneron, Emre Aksoy, Francesca Scolari, Anna R. Malacrida, Brian L. Weiss, Serap Aksoy
Software Mentions: 1
Published: over 9 years ago

10.1098/rspb.2017.1393

Rapid functional and evolutionary changes follow gene duplication in yeast
Cited by: 26
Author(s): Samina Naseeb, Ryan M. Ames, Daniela Delneri, Simon C. Lovell
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0208459

Gene landscape and correlation between B-cell infiltration and programmed death ligand 1 expression in lung adenocarcinoma patients from The Cancer Genome Atlas data set
Cited by: 18
Author(s): Kuo‐Hao Ho, Chih‐Ju Chang, Tsung-Hui Huang, Chwen‐Ming Shih, Ann‐Jeng Liu, Peng-Hsu Chen, Kur‐Ta Cheng, Ku‐Chung Chen
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0226338

Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development
Cited by: 10
Author(s): Safoora Amini, Khadijah Rosli, Mohd-Faizal Abu-Bakar, Hamidah Alias, Mohd-Noor Mat-Isa, Mohd-Afiq-Aizat Juhari, Jumaat Haji-Adam, Hoe-Han Goh, Kiew Lian Wan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0147527

Use of De Novo Transcriptome Libraries to Characterize a Novel Oleaginous Marine Chlorella Species during the Accumulation of Triacylglycerols
Cited by: 16
Author(s): Cresten Mansfeldt, Lubna V. Richter, Beth A. Ahner, William P. Cochlan, Ruth Richardson
Software Mentions: 1
Published: over 10 years ago

10.3390/vetsci6030059

Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis
Cited by: 15
Author(s): Marielle H. van den Esker, Ad P. Koets
Software Mentions: 1
Published: over 7 years ago

10.1186/s13567-020-00793-x

Systematic identification of chicken type I, II and III interferon-stimulated genes
Cited by: 12
Author(s): Manman Dai, Tingting Xie, Ming Liao, Xiquan Zhang, Mei Feng
Software Mentions: 1
Published: over 6 years ago

10.1186/s13567-015-0279-8

Transcriptomic analysis of the host response to an iridovirus infection in Chinese giant salamander, Andrias davidianus
Cited by: 30
Author(s): Yuding Fan, Ming Xian Chang, Jie Ma, Scott E. LaPatra, Yi Hu, Lili Huang, Pin Nie, Lingbing Zeng
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0175622

Correlation of EGFR or KRAS mutation status with 18F-FDG uptake on PET-CT scan in lung adenocarcinoma
Cited by: 19
Author(s): Kazuya Takamochi, Kaoru Mogushi, Hideya Kawaji, Kota Imashimizu, Manabu Fukui, Shiaki Oh, Masayoshi Itoh, Yoshihide Hayashizaki, Weijey Ko, Masao Akeboshi, Kenji Suzuki
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-37763-5

Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy
Cited by: 2
Author(s): Ryan Sprissler, Robert W. Bina, Willard S. Kasoff, Marlys H. Witte, Michael Bernas, C. Walter, David M. Labiner, Branden Lau, Michael F. Hammer, Martin E. Weinand
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0179881

Loss of prion protein induces a primed state of type I interferon-responsive genes
Cited by: 15
Author(s): Giulia Malachin, Malin Rokseth Reiten, Øyvind Salvesen, Håvard Aanes, Jorke H. Kamstra, Kerstin Skovgaard, Peter M. H. Heegaard, Cecilie Ersdal, Arild Espenes, Michael A. Tranulis, Maren Bakkebø
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0213149

Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission
Cited by: 7
Author(s): Md. Shamimuzzaman, Daniel K. Hasegawa, Wenbo Chen, Alvin M. Simmons, Zhangjun Fei, Kai-Shu Ling
Software Mentions: 1
Published: over 7 years ago

10.1080/15476286.2020.1727694

Transcriptional profiling of human macrophages during infection withBordetella pertussis
Cited by: 13
Author(s): Denisa Petráčková, Mariam R. Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Držmíšek, Ivo L. Hofacker, Marı́a Eugenia Rodrı́guez, Branislav Večerek
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0120388

A Genome-Wide Scan Reveals Important Roles of DNA Methylation in Human Longevity by Regulating Age-Related Disease Genes
Cited by: 37
Author(s): Fu-Hui Xiao, Yonghan He, Qi-Gang Li, Huan Wu, Longhai Luo, Qing‐Peng Kong
Software Mentions: 1
Published: over 11 years ago

10.1098/rsos.180413

Identification and characterization of circular RNAs in Qinchuan cattle testis
Cited by: 40
Author(s): Yuan Gao, Mingli Wu, Yanhui Fan, Shipeng Li, Zhenyu Lai, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Hong Chen, Ruihua Dang
Software Mentions: 1
Published: over 8 years ago

10.1098/rsos.181869

Collembola interact with mycorrhizal fungi in modifying oak morphology, C and N incorporation and transcriptomics
Cited by: 12
Author(s): Marcel Graf, Markus Bönn, Lasse Feldhahn, Florence Kurth, Thorsten E. E. Grams, Sylvie Herrmann, Mika Tarkka, François Buscot, Stefan Scheu
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37609-0

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone
Cited by: 20
Author(s): Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Jennifer Tickner, Nathan J. Pavlos, Frank Dudbridge, Jiake Xu, John P. Walsh, Scott G. Wilson
Software Mentions: 1
Published: over 7 years ago

10.1098/rsos.192243

Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq
Cited by: 9
Author(s): Zhenhua Guo, Lijun Cai, Chuanxue Liu, Chao Huang, Zhiqiang Chen, Guoqing Pan, Tao Guo
Software Mentions: 1
Published: over 6 years ago

10.1098/rsos.200637

Growth, physiological and transcriptomic analysis of the perennial ryegrassLolium perennein response to saline stress
Cited by: 6
Author(s): Haishun Xu, Shaodong Guo, Lin Zhu, Jin-Cheng Xing
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0175315

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus
Cited by: 26
Author(s): Jianjian Lv, Longtao Zhang, Ping Liu, Jian Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0228078

Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation
Cited by: 8
Author(s): Sang Hoon Kim, Se Won Kim, Gah‐Hyun Lim, Jae Il Lyu, Hong‐Il Choi, Yeong Deuk Jo, Si-Yong Kang, Byoung-Cheorl Kang, Jin-Baek Kim
Software Mentions: 1
Published: almost 7 years ago

10.18699/VJ21.054

Parent-of-origin effects on nuclear chromatin organization and behavior in a Drosophila model for Williams–Beuren Syndrome
Cited by: 1
Author(s): А. В. Медведева, Elena V. Tokmatcheva, A. N. Kaminskaya, S. A. Vasileva, Е. А. Никитина, Aleksandr V. Zhuravlev, Г. А. Захаров, Olga G. Zatsepina, Е. В. Савватеева-Попова
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0113091

Comparative Transcriptomic Analysis of the Response to Cold Acclimation in Eucalyptus dunnii
Cited by: 18
Author(s): Yiqing Liu, Yi Jiang, Jianbin Lan, Yong Zou, Junping Gao
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12931-015-0228-0

The LIM-domain only protein 4 contributes to lung epithelial cell proliferation but is not essential for tumor progression
Cited by: 6
Author(s): Aliaksei Z. Holik, Caitlin E. Filby, Julie Pasquet, Kati Viitaniemi, John Ciciulla, Kate D. Sutherland, Marie Liesse Asselin-Labat
Software Mentions: 1
Published: over 11 years ago

10.3390/vaccines9020067

Human Transcriptomic Response to the VSV-Vectored Ebola Vaccine
Cited by: 8
Author(s): Francesco Santoro, Alessia Donato, Simone Lucchesi, Sara Sorgi, Alice Gerlini, Mariëlle C. Haks, Tom H. M. Ottenhoff, Patrícia Gonzalez-Dias, VSV-EBOVAC Consortium, VSV-EBOPLUS Consortium, Hidehiko Nakaya, Angela Huttner, Claire‐Anne Siegrist, Donata Medaglini, Gianni Pozzi
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0116437

Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
Cited by: 19
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: over 11 years ago

10.1186/s12931-020-01552-4

Bacteria and sputum inflammatory cell counts; a COPD cohort analysis
Cited by: 33
Author(s): Augusta Beech, Simon Lea, Umme Kolsum, Zhang Wang, Bruce E. Miller, Gavin C. Donaldson, Jadwiga A. Wedzicha, Christopher E. Brightling, Dave Singh
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pntd.0004929

The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach
Cited by: 21
Author(s): Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew R. Moorhead, Steven A. Williams, Timothy G. Geary
Software Mentions: 1
Published: about 10 years ago

10.1016/j.omtm.2021.03.026

Discovery of key genes as novel biomarkers specifically associated with HPV-negative cervical cancer
Cited by: 13
Author(s): Yi Liu, Yichi Xu, Wenxiao Jiang, Huihui Ji, Zhiwei Wang, Xueqiong Zhu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12284-018-0229-y

Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq
Cited by: 36
Author(s): Liang Chen, Jianmin Bian, Shilai Shi, Jianfeng Yu, Hira Khanzada, Ziming Wu, Zhu C, Xin Luo, Shan Tong, Xiaorong Yang, Xiaosong Peng, Shuang Yong, Qi Yu, Xu He, Junru Fu, Xiaorong Chen, Lifang Hu, Liang Ouyang, Haohua He
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-37755-5

Reference assembly and gene expression analysis of Apostichopus japonicus larval development
Cited by: 9
Author(s): Alexey V. Boyko, Alexander S. Girich, М. Г. Елисейкина, С. И. Масленников, Igor Yu. Dolmatov
Software Mentions: 1
Published: over 7 years ago

10.1186/s12284-019-0265-2

Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1
Cited by: 8
Author(s): Jun Wang, Qiang Zhang, Yi Wang, Jing Huang, Nengjie Luo, Shengbo Wei, Jiaxin Jin
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-38368-8

Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Cited by: 31
Author(s): Ki Wook Kim, Jessica L. Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A. Bull, Fabio Luciani, Marc R. Wilkins, Jacki Catteau, W. Ian Lipkin, William D. Rawlinson, Thomas Briese, Maria E. Craig
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-42010-6

A Network-guided Association Mapping Approach from DNA Methylation to Disease
Cited by: 16
Author(s): Yandan Lin, De-Shuang Huang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-38628-1

Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Cited by: 38
Author(s): Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
Software Mentions: 1
Published: over 7 years ago

10.1126/sciadv.aaw0070

The genetic mechanism of selfishness and altruism in parent-offspring coadaptation
Cited by: 7
Author(s): Min Wu, Jean‐Claude Walser, Lei Sun, Mathias Kölliker
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0005691

Effect of praziquantel on the differential expression of mouse hepatic genes and parasite ATP binding cassette transporter gene family members during Schistosoma mansoni infection
Cited by: 17
Author(s): Melissa C. Sanchez, Katina V. Krasnec, Amalia S. Parra, Christian von Cabanlong, Geoffrey N. Gobert, Boris Umylny, Pauline M. Cupit, Charles Cunningham
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0005527

A third generation vaccine for human visceral leishmaniasis and post kala azar dermal leishmaniasis: First-in-human trial of ChAd63-KH
Cited by: 101
Author(s): Mohamed Osman, Anoop Mistry, Ada Keding, Rhian Gabe, Liz Cook, Sarah Forrester, Rebecca Wiggins, Stefania Di Marco, Stefano Colloca, Loredana Siani, Riccardo Cortese, Deborah F. Smith, Toni Aebischer, Paul M. Kaye, Charles Lacey
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1003834

The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone
Cited by: 134
Author(s): Minh-Duy Phan, Kate M. Peters, Sohinee Sarkar, Samuel W. Lukowski, Luke P. Allsopp, Danilo Gomes Moriel, Maud E. S. Achard, Makrina Totsika, Vikki M. Marshall, Mathew Upton, Scott A. Beatson, Mark A. Schembri
Software Mentions: 1
Published: about 13 years ago

10.1186/s12943-019-1056-5

A novel tumor suppressor protein encoded by circular AKT3 RNA inhibits glioblastoma tumorigenicity by competing with active phosphoinositide-dependent Kinase-1
Cited by: 193
Author(s): Xin Xia, Xixi Li, Fanying Li, Xujia Wu, Maolei Zhang, Huangkai Zhou, Nunu Huang, Xuesong Yang, Feizhe Xiao, Dawei Liu, Lixuan Yang, Nu Zhang
Software Mentions: 1
Published: about 7 years ago

10.3390/molecules23123276

Effect of Aspergillus flavus Fungal Elicitor on the Production of Terpenoid Indole Alkaloids in Catharanthus roseus Cambial Meristematic Cells
Cited by: 18
Author(s): Chuxin Liang, Chang Chen, Pengfei Zhou, Lv Xu, Jianhua Zhu, Jincai Liang, Jiachen Zi, Rongmin Yu
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.omtm.2020.08.007

Generation of Nonhuman Primate Model of Cone Dysfunction through In Situ AAV-Mediated CNGB3 Ablation
Cited by: 14
Author(s): Qiang Lin, Ji‐Neng Lv, Kun Wu, Chang-Jun Zhang, Qin Liu, Zi‐Bing Jin
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1007511

Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism
Cited by: 23
Author(s): Karl G. Thieme, Jennifer Gerke, Christoph Sasse, Oliver Valerius, Razieh Karimi, Antje K. Heinrich, Florian Finkernagel, Kristina M. Smith, Helge B. Bode, Michael Freitag, Arthur F. J. Ram, Gerhard H. Braus
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24509-6

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages
Cited by: 69
Author(s): Sugata Roy, Sebastian Schmeier, Bogumił Kaczkowski, Peter Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Reto Guler, Vladimir B. Bajic, Frank Brombacher, Harukazu Suzuki
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2021.651744

Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Cited by: 11
Author(s): Carlo R. Carere, Kiel Hards, Kathryn Wigley, Luke Carman, Karen M. Houghton, Gregory M. Cook, Matthew B. Stott
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.02452

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities
Cited by: 10
Author(s): Qin Ma, Heike Bücking, Jose L. Gonzalez-Hernandez, Senthil Subramanian
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2017.01266

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere
Cited by: 54
Author(s): Ubiana C. Silva, Julliane Dutra Medeiros, Laura Hora Rios Leite, Daniel Morais, Sara Cuadros-Orellana, Carlos A. S. Oliveira, U. G. de P. Lana, E. A. Gomes, Vera Lúcia dos Santos
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007327

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases
Cited by: 31
Author(s): Ruth Barshir, Idan Hekselman, Netta Shemesh, Moran Sharon, Lena Novack, Esti Yeger-Lotem
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2016.00880

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms
Cited by: 41
Author(s): Rachel E. Diner, Sarah M. Schwenck, John P. McCrow, Hong Zheng, Andrew E. Allen
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2018.00299

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse
Cited by: 22
Author(s): Diego Javier Jiménez, Maryam Chaib De Mares, Joana Falcão Salles
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.00848

Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth
Cited by: 11
Author(s): Alvaro Fuertes, Sergio Pérez-Burillo, Iñigo Apaolaza, Yvonne Vallès, M. Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25611-5

Ca2+ imaging and gene expression profiling of Lonicera Confusa in response to calcium-rich environment
Cited by: 10
Author(s): Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.00150

Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Cited by: 35
Author(s): Murugesan Sivaranjani, Katarzyna Leskinen, Chairmandurai Aravindraja, Päivi Saavalainen, Shunmugiah Karutha Pandian, Mikael Skurnik, Arumugam Veera Ravi
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39273-4

A RNA sequencing-based six-gene signature for survival prediction in patients with glioblastoma
Cited by: 41
Author(s): Shuguang Zuo, Xinhong Zhang, Liping Wang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-25103-6

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis
Cited by: 35
Author(s): Lingbin Liu, Qihai Xiao, Elizabeth R. Gilbert, Zhifu Cui, Xiaoling Zhao, Yan Wang, Huadong Yin, Diyan Li, Haihan Zhang, Qing Zhu
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2016.01279

Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51
Cited by: 55
Author(s): Wesley J. Mair, Wei‐Wei Deng, Jonathan Mullins, Samuel West, Penghao Wang, Naghmeh Besharat, Simon R. Ellwood, Richard P. Oliver, Francisco J. López-Ruiz
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-25516-3

Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Cited by: 18
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.02569

Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems
Cited by: 39
Author(s): Mina Bižić-Ionescu, Danny Ionescu, Hans‐Peter Grossart
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2015.00631

Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation
Cited by: 36
Author(s): Zhenfeng Liu, Amy E. Koid, Ramón Terrado, Victoria Campbell, David A. Caron, Karla B. Heidelberg
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-018-24999-4

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant
Cited by: 18
Author(s): Qianqian Shi, Zhenchuan Mao, Xi Zhang, Xiaoping Zhang, Yunsheng Wang, Jian Ling, Runmao Lin, Denghui Li, Xincong Kang, Wenxian Sun, Bingyan Xie
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005666

A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen
Cited by: 31
Author(s): Michael C. Chao, Shijia Zhu, Satoshi Kimura, Brigid M. Davis, Eric E. Schadt, Gang Fang, Matthew K. Waldor
Software Mentions: 1
Published: almost 11 years ago

10.15252/msb.20145470

An organ boundary‐enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
Cited by: 92
Author(s): Caihuan Tian, Xiaoni Zhang, Jun He, Haopeng Yu, Ying Wang, Bihai Shi, Yingying Han, Guoxun Wang, Xiaoming Feng, Cui Zhang, Jin Wang, Jiyan Qi, Rong Yu, Yuling Jiao
Software Mentions: 1
Published: about 12 years ago

10.3389/fmicb.2018.01643

Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils
Cited by: 54
Author(s): Liu Jin, Barbara J. Cade-Menun, Jianjun Yang, Yongfeng Hu, Corey W. Liu, Julien Tremblay, Kerry LaForge, Michael P. Schellenberg, Chantal Hamel, Luke D. Bainard
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.00189

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium
Cited by: 10
Author(s): Nathan G. Walworth, Michael D. Lee, Christopher Suffridge, Pingping Qu, Fei-Xue Fu, Mak A. Saito, Eric A. Webb, Sergio A. Sañudo‐Wilhelmy, David A. Hutchins
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.539702

Calcineurin Regulates Conidiation, Chlamydospore Formation and Virulence in Fusarium oxysporum f. sp. lycopersici
Cited by: 10
Author(s): Yi-Hsuan Hou, Li-Hang Hsu, Hsuan-Fu Wang, Yu-Hsin Lai, Ying-Lien Chen
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2019.01622

Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease
Cited by: 13
Author(s): Ammar Aziz, Derek S. Sarovich, Elizabeth Nosworthy, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan, Erin P. Price, Tegan M. Harris
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.00859

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8
Cited by: 62
Author(s): Helen L. Hayden, Keith W. Savin, Jenny Wadeson, Vadakattu V. S. R. Gupta, Pauline M. Mele
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.00752

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae
Cited by: 30
Author(s): Mohammad Moniruzzaman, Eric R. Gann, Steven W. Wilhelm
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.01765

Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose
Cited by: 18
Author(s): Sabrina Giaretta, Laura Treu, Veronica Vendramin, Vinícius da Silva Duarte, Armin Tarrah, Stefano Campanaro, Viviana Corich
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2016.01465

Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole
Cited by: 7
Author(s): Michele Cristine Ribeiro de Freitas, Juliana Alves Resende, Alessandra Barbosa Ferreira-Machado, Guadalupe del Rosario Quispe Saji, Ana Tereza Ribeiro de Vasconcelos, Vânia Lúcia da Silva, Marisa Fabiana Nicolás, Cláudio Galuppo Diniz
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.02308

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells
Cited by: 7
Author(s): Gaofeng Ni, Sebastian Canizales, Elias Broman, Domenico Simone, Viraja R. Palwai, Daniel Lundin, Margarita López-Fernández, Tom Sleutels, Mark Dopson
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2014.00430

Wolbachia is not all about sex: male-feminizing Wolbachia alters the leafhopper Zyginidia pullula transcriptome in a mainly sex-independent manner
Cited by: 12
Author(s): Hosseinali Asgharian, Peter L. Chang, Peter John Mazzoglio, Ilaria Negri
Software Mentions: 1
Published: about 12 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568