10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.3390/genes11091027

A Highly Polymorphic Panel Consisting of Microhaplotypes and Compound Markers with the NGS and Its Forensic Efficiency Evaluations in Chinese Two Groups
Cited by: 8
Author(s): Xiaoye Jin, Xingru Zhang, Chunmei Shen, Yanfang Liu, Wei Cui, Chong Chen, Yuxin Guo, Bofeng Zhu
Software Mentions: 3
Published: almost 6 years ago

10.3390/biomedicines8020019

A Multi-Omics Analysis of Bone Morphogenetic Protein 5 (BMP5) mRNA Expression and Clinical Prognostic Outcomes in Different Cancers Using Bioinformatics Approaches
Cited by: 23
Author(s): Md. Adnan Karim, Abdus Samad, Utpal Adhikari, Md. Ashraful Kader, Md. Masnoon Kabir, Md. Aminul Islam, Md. Nazmul Hasan
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0012336

Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies
Cited by: 124
Author(s): M. Jeanmougin, Aurélien de Reyniès, Laëtitia Marisa, Caroline Paccard, Grégory Nuel, Mickaël Guedj
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2334-10-176

Tracking the transcriptional host response from the acute to the regenerative phase of experimental pneumococcal meningitis
Cited by: 16
Author(s): Matthias Wittwer, Denis Grandgirard, Janine Rohrbach, Stephen L. Leib
Software Mentions: 3
Published: about 16 years ago

10.3390/genes12020254

Paracellular and Transcellular Leukocytes Diapedesis Are Divergent but Interconnected Evolutionary Events
Cited by: 20
Author(s): Michel‐Edwar Mickael, Norwin Kubick, Pavel Klimovich, Patrick Henckell Flournoy, Irmina Bieńkowska, Mariusz Sacharczuk
Software Mentions: 3
Published: over 5 years ago

10.1186/1754-6834-4-4

Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi
Cited by: 195
Author(s): Brian Christopher King, K. D. Waxman, Nicholas V Nenni, Larry P. Walker, Gary C. Bergstrom, Donna M. Gibson
Software Mentions: 3
Published: over 15 years ago

10.1186/s10020-019-0113-2

Integrated transcriptomic analysis reveals hub genes involved in diagnosis and prognosis of pancreatic cancer
Cited by: 30
Author(s): Yangyang Zhou, Liping Chen, Yi Zhang, Sunkuan Hu, Zhaojun Dong, Ming Wu, Qiuxiang Chen, Zhizhi Zhuang, Xiaojing Du
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13068-014-0171-1

System-level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation
Cited by: 83
Author(s): Luís Valledor, Takeshi Furuhashi, Luis Recuenco-Muñoz, Stefanie Wienkoop, Wolfram Weckwerth
Software Mentions: 3
Published: over 11 years ago

10.1038/srep25107

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Cited by: 27
Author(s): Weike Duan, Zhinan Huang, Xiaoming Song, Tongkun Liu, Hailong Liu, Xilin Hou, Ying Liu
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0049918

Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines
Cited by: 17
Author(s): Santosh K. Patnaik, Jesper Dahlgaard, Wiktor Mazin, Eric Kannisto, Thomas E. Jensen, Steen Knudsen, Sai Yendamuri
Software Mentions: 3
Published: over 13 years ago

10.1186/s13068-020-01677-0

Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus
Cited by: 25
Author(s): Hans Kristian Mattila, Mari Mäkinen, Taina Lundell
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.52370

Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity
Cited by: 14
Author(s): Erin Clark, Michael Rutlin, Lucia Capano, Samuel Aviles, Jordan R Saadon, Praveen Taneja, Qiyu Zhang, James B. Bullis, Timothy Lauer, Emma Myers, Anton Schulmann, Douglas Forrest, Sacha B. Nelson
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: over 7 years ago

10.1038/srep39281

Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster
Cited by: 18
Author(s): Mark Phillips, Anthony D. Long, Zachary S. Greenspan, Lee F. Greer, Molly K. Burke, Bryant Villeponteau, Kennedy Matsagas, Cristina L. Rizza, Laurence D. Mueller, Michael R. Rose
Software Mentions: 3
Published: over 9 years ago

10.1038/srep40301

Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi
Cited by: 25
Author(s): Peng Wang, Hong Wang, Jiangtao Gai, Xiaoli Tian, Xiaoxiao Zhang, Yongzhi Lv, Yi Jiang
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: over 7 years ago

10.1001/jamanetworkopen.2018.1018

Development and Validation of an Electronic Health Record–Based Machine Learning Model to Estimate Delirium Risk in Newly Hospitalized Patients Without Known Cognitive Impairment
Cited by: 94
Author(s): Andrew Wong, A. E. Young, April S. Liang, Ralph Gonzales, Vanja C. Douglas, Dexter Hadley
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.20083

Reduced expression of BMP3 contributes to the development of pulmonary fibrosis and predicts the unfavorable prognosis in IIP patients
Cited by: 8
Author(s): Xiaoting Yu, Pan Gu, Ziling Huang, Fang Xia, Ying Jiang, Qun Luo, Xia Li, Xuyou Zhu, Mengna Zhan, Junbang Wang, Lu Fan, Rongchang Chen, Juehua Yu, Yingying Gu, Aibin Liang, Xianghua Yi
Software Mentions: 3
Published: about 9 years ago

10.1186/s12935-020-01309-5

Increased expression of YTHDF1 and HNRNPA2B1 as potent biomarkers for melanoma: a systematic analysis
Cited by: 28
Author(s): Tengda Li, Mingli Gu, Anmei Deng, Cheng Qing
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0082638

Evaluation of Current and New Biomarkers in Severe Preeclampsia: A Microarray Approach Reveals the VSIG4 Gene as a Potential Blood Biomarker
Cited by: 33
Author(s): Julien Textoris, Delphine Ivorra, Amira Ben Amara, Florence Sabatier, Jean-Pierre Ménard, H. Heckenroth, Florence Bretelle, Jean‐Louis Mège
Software Mentions: 3
Published: over 12 years ago

10.1186/s12918-016-0336-6

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Cited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: almost 10 years ago

10.1534/g3.118.200910

Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr <i>Salvelinus fontinalis</i>
Cited by: 18
Author(s): Ben J. G. Sutherland, Jenni M. Prokkola, Céline Audet, Louis Bernatchez
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2020.586050

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial
Cited by: 13
Author(s): Robin Raveau, Joël Fontaine, Mohamed Hijri, Anissa Lounès-Hadj Sahraoui
Software Mentions: 3
Published: over 5 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-017-1993-1

Improved high-dimensional prediction with Random Forests by the use of co-data
Cited by: 11
Author(s): Dennis E. te Beest, Steven W. Mes, Saskia M. Wilting, Ruud H. Brakenhoff, Mark A. van de Wiel
Software Mentions: 3
Published: over 8 years ago

10.1186/s13637-015-0034-5

Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer
Cited by: 2
Author(s): Hiroko Kato Solvang, Arnoldo Frigessi, Fatemeh Kaveh, Margit Riis, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen, Bettina Kulle Andreassen
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-18575-5

Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle
Cited by: 45
Author(s): Bernardo Villarreal‐Ramos, Stefan Berg, Adam O. Whelan, Sébastien Holbert, Florence Carreras, Francisco J. Salguero, Bhagwati Khatri, Kerri M. Malone, Kévin Rue-Albrecht, Ronan G. Shaughnessy, Alicia Smyth, Gobena Ameni, Abraham Aseffa, Pierre Sarradin, Nathalie Winter, Martin Vordermeier, Stephen V. Gordon
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-016-0775-7

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)
Cited by: 53
Author(s): Wei Huang, Yan Du, Xin Zhao, Weiwei Jin
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-84928-w

Gut microbiota markers associated with obesity and overweight in Italian adults
Cited by: 132
Author(s): Vanessa Palmas, Silvia Pisanu, Veronica Madau, Emanuela Casula, Andrea Deledda, Roberto Cusano, Paolo Uva, Sarah Vascellari, Andrea Loviselli, Aldo Manzin, Fernanda Velluzzi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-44157-8

Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status
Cited by: 27
Author(s): Seppo Virtanen, Tiina Rantsi, Anni Virtanen, Kaisa Kervinen, Pekka Nieminen, Ilkka Kalliala, Anne Salonen
Software Mentions: 3
Published: about 7 years ago

10.1186/2040-2392-5-38

Integrative proteomic analysis of the NMDA NR1 knockdown mouse model reveals effects on central and peripheral pathways associated with schizophrenia and autism spectrum disorders
Cited by: 31
Author(s): Hendrik Wesseling, Paul C. Guest, Chi-Ming Lee, Erik H. F. Wong, Hassan Rahmoune, Sabine Bahn
Software Mentions: 3
Published: about 12 years ago

10.1073/pnas.1811797116

Rivers across the Siberian Arctic unearth the patterns of carbon release from thawing permafrost
Cited by: 104
Author(s): Birgit Wild, August Andersson, Lisa Bröder, Jorien E. Vonk, Gustaf Hugelius, J. W. McClelland, Wenjun Song, Peter A. Raymond, Örjan Gustafsson
Software Mentions: 3
Published: over 7 years ago

10.1155/2014/857245

Intestinal Parasites Coinfection Does Not Alter Plasma Cytokines Profile Elicited in Acute Malaria in Subjects from Endemic Area of Brazil
Cited by: 13
Author(s): Juan Camilo Sánchez‐Arcila, Daiana de Souza Perce-da-Silva, Mariana Pinheiro Alves Vasconcelos, Rodrigo Nunes Rodrigues-da-Silva, Virgínia Araújo Pereira, Cesarino Junior Lima Aprígio, Cleoni Alves Mendes de Lima, Bruna de Paula Fonseca e Fonseca, Dalma Maria Banic, Josué da Costa Lima-Junior, Joseli Oliveira-Ferreira
Software Mentions: 3
Published: over 12 years ago

10.1155/2021/8836243

Altered Genes and Biological Functions in Response to Severe Burns
Cited by: 2
Author(s): Xinheng Liu, Yong-Xian Rong, Deng-Shing Huang, Zheng Liang, Xiao-Lin Yi, Fengyao Wu, Dandan Zhu, Steven Mo, Wenhai Nong, Hong-Mian Li
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.97018

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site
Cited by: 16
Author(s): Hao Cheng, Sebastian K. Grimm, M.S.A. Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, G. Donofrio, Gunilla B. Karlsson Hedestam, Mattia Bonsignori, Barton F. Haynes, Timothy Lahey, Isaac Maro, C. Fordham von Reyn, Miroslaw K. Gorny, Susan Zolla‐Pazner, Bruce D. Walker, Galit Alter, Dennis R. Burton, Merlin L. Robb, Shelly J. Krebs, Michael S. Seaman, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-94396-x

Niche partitioning among dead wood-dependent beetles
Cited by: 1
Author(s): Jakub Horák
Software Mentions: 3
Published: about 5 years ago

10.1186/s13195-020-00657-8

Association of glial and neuronal degeneration markers with Alzheimer’s disease cerebrospinal fluid profile and cognitive functions
Cited by: 17
Author(s): Unnur D. Teitsdottir, Marıá K. Jónsdóttir, Sigrún H. Lund, Taher Darreh‐Shori, Jón Snædal, Petur H. Petersen
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers13163978

Drug Repurposing to Identify a Synergistic High-Order Drug Combination to Treat Sunitinib-Resistant Renal Cell Carcinoma
Cited by: 12
Author(s): Magdalena Rausch, Adriano Rutz, Pierre‐Marie Allard, Céline Delucinge-Vivier, Mylène Docquier, Olivier Dormond, Paul J. Dyson, Jean‐Luc Wolfender, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: about 5 years ago

10.3390/genes12020185

Graph Algorithms for Mixture Interpretation
Cited by: 4
Author(s): Benjamin Crysup, August E. Woerner, Jonathan L. King, Bruce Budowle
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-021-03009-2

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)
Cited by: 8
Author(s): Guozhong Zhu, Shuang Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen, Wangzhen Guo
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-37792-0

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: over 7 years ago

10.1186/s12983-017-0245-6

Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics
Cited by: 17
Author(s): Yalin Cheng, Bin Gao, Haitao Wang, Ning Han, Shimiao Shao, Shaoyuan Wu, Gang Song, Yong E. Zhang, Zhu Xihua, Xin Lü, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: over 8 years ago

10.1186/s12943-021-01392-w

Using single-cell sequencing technology to detect circulating tumor cells in solid tumors
Cited by: 32
Author(s): Jiasheng Xu, Kaili Liao, Yang Xi, Chengfeng Wu, Wei Wu, Shuwen Han
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.8456

Key genes and co-expression modules involved in asthma pathogenesis
Cited by: 12
Author(s): Yuyi Huang, Hui Liu, Li Zuo, Ailin Tao
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.02699

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study
Cited by: 78
Author(s): Edda Russo, Giovanni Bacci, Carolina Chiellini, Camilla Fagorzi, Elena Niccolai, Antonio Taddei, Francesca Ricci, Maria Novella Ringressi, Rossella Borrelli, Filippo Melli, Manouela Miloeva, Paolo Bechi, Alessio Mengoni, Renato Fani, Amedeo Amedei
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-340

Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions
Cited by: 98
Author(s): Liangliang Gao, Zheng Jin Tu, Benjamin P. Millett, James M. Bradeen
Software Mentions: 3
Published: about 13 years ago

10.3390/ijms14048000

Proteins Involved in Distinct Phases of Cold Hardening Process in Frost Resistant Winter Barley (Hordeum vulgare L.) cv Luxor
Cited by: 41
Author(s): Iva Hlaváčková, Pavel Vítámvás, Jiří Šantrůček, Klára Kosová, Sylva Zelenková, Ilja Tom Prášil, Jaroslava Ovesná, Radovan Hynek, Milan Kodı́ček
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-019-48200-6

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
Cited by: 27
Author(s): Carlos Eduardo Posada-Perlaza, Adán Andrés Ramírez Rojas, Paola Porras, Boahemaa Adu-Oppong, Ana María Botero-Coy, Félix Hernández, Juan Manuel Anzola, Lorena Díaz, Gautam Dantas, Alejandro Reyes, María Mercedes Zambrano
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-27705-6

Need for focus on microbial species following ice melt and changing freshwater regimes in a Janus Arctic Gateway
Cited by: 17
Author(s): Nathalie Joli, Michel Gosselin, Mathieu Ardyna, Marcel Babin, Deo Florence L. Onda, Jean‐Éric Tremblay, Connie Lovejoy
Software Mentions: 3
Published: about 8 years ago

10.1186/s12934-019-1185-y

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Cited by: 12
Author(s): Sarada Raghavan, Sharon Chee, Juntao Li, Jérémie Poschmann, Niranjan Nagarajan, Siau Jia Wei, Chandra Verma, Farid J. Ghadessy
Software Mentions: 3
Published: almost 7 years ago

10.3390/genes12040522

Kinetics and Topology of DNA Associated with Circulating Extracellular Vesicles Released during Exercise
Cited by: 21
Author(s): Elmo Neuberger, Barlo Hillen, Katharina Mayr, Perikles Simon, Eva-Maria Krämer-Albers, Alexandra Brahmer
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.6090

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the<i>Firmicutes</i>phylum
Cited by: 34
Author(s): Craig Anderson, Michelle E. Peterson, Rebekah A. Frampton, Simon Bulman, Sandi Keenan, D. Curtin
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.23664

Clinical outcomes and differential effects of PI3K pathway mutation in obese versus non-obese patients with cervical cancer
Cited by: 14
Author(s): Perry W. Grigsby, Adnan Elhammali, Fiona Ruiz, Stephanie Markovina, Michael D. McLellan, Christopher A. Miller, Anupama Chundury, Ngoc Anh L. Ta, Ramachandran Rashmi, John D. Pfeifer, Robert S. Fulton, T.A. DeWees
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.13181

OTX015 (MK-8628), a novel BET inhibitor, exhibits antitumor activity in non-small cell and small cell lung cancer models harboring different oncogenic mutations
Cited by: 38
Author(s): María E. Riveiro, Lucile Astorgues‐Xerri, Ramiro Vàzquez, Roberta Frapolli, Ivo Kwee, Andrea Rinaldi, Elodie Odore, Keyvan Rezai, Mohamed Békradda, Giorgio Inghirami, Maurizio D’Incalci, Kay Noel, Esteban Cvitkovic, Éric Raymond, Francesco Bertoni
Software Mentions: 3
Published: almost 10 years ago

10.1099/mgen.0.000154

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: over 8 years ago

10.1186/s12873-021-00459-7

Internal validation and comparison of the prognostic performance of models based on six emergency scoring systems to predict in-hospital mortality in the emergency department
Cited by: 10
Author(s): Zahra Rahmatinejad, Fariba Tohidinezhad, Fatemeh Rahmatinejad, Saeid Eslami, Ali Pourmand, Ameen Abu‐Hanna, Hamidreza Reihani
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: about 5 years ago

10.1002/mbo3.312

Evaluation of <scp>DNA</scp> extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
Cited by: 52
Author(s): Katharina Burbach, Jana Seifert, Dietmar H. Pieper, Amélia Camarinha‐Silva
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.30496

The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1 lymphocytes
Cited by: 53
Author(s): Yasmina Serroukh, Chunyan Gu-Trantien, Baharak Hooshiar Kashani, Matthieu Defrance, Thien‐Phong Vu Manh, Abdulkader Azouz, Aurélie Detavernier, Alice Hoyois, Jishnu Das, Martin Bizet, Émeline Pollet, Tressy Tabbuso, Emilie Calonne, Klaas P. J. M. van Gisbergen, Marc Dalod, François Fuks, Stanislas Goriely, Arnaud Marchant
Software Mentions: 3
Published: over 8 years ago

10.1111/j.1365-2958.2007.05827.x

A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis
Cited by: 186
Author(s): Sharon L. Kendall, Mike Withers, Catherine N. Soffair, Nicole J. Moreland, Sudagar S. Gurcha, Ben S. Sidders, Rosangela Frita, Annemieke Ten Bokum, Gurdyal S. Besra, J.S. Lott, Neil G. Stoker
Software Mentions: 3
Published: about 19 years ago

10.1371/journal.ppat.1009843

Hantavirus infection-induced B cell activation elevates free light chains levels in circulation
Cited by: 5
Author(s): Jussi Hepojoki, Luz E. Cabrera, Satu Hepojoki, Carla Bellomo, Lauri Kareinen, Leif C. Andersson, Antti Vaheri, Satu Mäkelä, Jukka Mustonen, Olli Vapalahti, Valeria P. Martínez, Tomas Strandin
Software Mentions: 3
Published: about 5 years ago

10.1002/jia2.25327

Oral abstracts of the 10th IAS Conference on HIV Science, 21‐24 July 2019, Mexico City, Mexico
Cited by: 12
Author(s):
Software Mentions: 3
Published: about 7 years ago

10.1099/mic.0.000550

Whole genome transcriptomics reveals global effects including up-regulation of Francisella pathogenicity island gene expression during active stringent response in the highly virulent Francisella tularensis subsp. tularensis SCHU S4
Cited by: 11
Author(s): Amber L. Murch, Paul Skipp, Peter L. Roach, Petra C. F. Oyston
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13287-021-02310-z

Hypoxic preconditioning induces epigenetic changes and modifies swine mesenchymal stem cell angiogenesis and senescence in experimental atherosclerotic renal artery stenosis
Cited by: 20
Author(s): Busra Isik, Roman Thaler, Busra B. Goksu, Sabena M. Conley, Hayder Al-Khafaji, Arjunmohan Mohan, Mohsen Afarideh, Abdelrhman Abumoawad, Xiang Yang Zhu, James D. Krier, Ishran M. Saadiq, Hui Tang, Alfonso Eirin, La Tonya J. Hickson, André J. van Wijnen, Stephen C. Textor, Lilach O. Lerman, Sandra M. Herrmann
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-11-574

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets
Cited by: 74
Author(s): Daniel M. Gatti, William T. Barry, Andrew B. Nobel, Ivan Rusyn, Fred A. Wright
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0013984

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Cited by: 1,757
Author(s): Daniele Merico, Ruth Isserlin, Oliver Stueker, Andrew Emili, Gary D. Bader
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pmed.1003393

The risk of Plasmodium vivax parasitaemia after P. falciparum malaria: An individual patient data meta-analysis from the WorldWide Antimalarial Resistance Network
Cited by: 29
Author(s): Mohammad Sharif Hossain, Robert J. Commons, Nicholas M. Douglas, Kamala Thriemer, Bereket Alemayehu, Chanaki Amaratunga, Anupkumar R. Anvikar, Elizabeth A. Ashley, Puji Budi Setia Asih, Verena I. Carrara, Chanthap Lon, Umberto D’Alessandro, Timothy Davis, Arjen M. Dondorp, Michael D. Edstein, Rick M. Fairhurst, Marcelo U. Ferreira, Jimee Hwang, Bart Janssens, Harin Karunajeewa, J. R. Kiechel, Simone Ladeia‐Andrade, Moses Laman, Mayfong Mayxay, Rose McGready, Brioni R. Moore, Ivo Müeller, Paul N. Newton, Nguyen Thanh Thuy-Nhien, Harald Noedl, François Nosten, Aung Phae Phyo, Jeanne Rini Poespoprodjo, David Saunders, Frank Smithuis, Michele Spring, Kasia Stepniewska, Seila Suon, Yupin Suputtamongkol, Din Syafruddin, Hien T. Tran, Neena Valecha, Michel Van Herp, Michèle van Vugt, Nicholas J. White, Philippe J. Guérin, Julie A. Simpson, Ric N. Price
Software Mentions: 3
Published: over 5 years ago

10.1007/s12035-018-1377-1

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
Cited by: 17
Author(s): Patrick Bovio, Henriette Franz, Stefanie Heidrich, Tudor Rauleac, Fabian Kilpert, Thomas Manke, Tanja Vogel
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.ebiom.2019.05.043

Childhood growth and neurocognition are associated with distinct sets of metabolites
Cited by: 24
Author(s): G. Brett Moreau, Girija Ramakrishnan, Heather Cook, Todd E. Fox, Uma Nayak, Z. Jennie, E. Ross Colgate, Beth D. Kirkpatrick, Rashidul Haque, William A. Petri
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.5743

Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
Cited by: 6
Author(s): Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-021-83935-1

No time to rest: seasonal dynamics of non-structural carbohydrates in twigs of three Mediterranean tree species suggest year-round activity
Cited by: 16
Author(s): Anna Davidson, Sylvia T Le, Katelyn B. Cooper, Eden Lange, Maciej A. Zwieniecki
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/5512325

Classification of Lung Adenocarcinoma Based on Immune Checkpoint and Screening of Related Genes
Cited by: 6
Author(s): Ting Zhou, Ping Yang, Sanyuan Tang, Zhongshan Zhu, Xiaobing Li, Yang Zhou, Ruoxi Wu, Xuefei Tian, Liang Li
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.147929

Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Cited by: 2
Author(s): Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, Nina Wietek, Matteo Morotti, Kay Y. Chong, Mohammad KaramiNejadRanjbar, Christos E. Zois, Sunanda Dhar, Salma El-Sahhar, Leticia Campo, Sarah P. Blagden, Stephen Damato, Pubudu Pathiraja, Shibani Nicum, Fergus Gleeson, A Laios, Abdulkhaliq Alsaadi, Laura Santana González, Takeshi Motohara, Ashwag Albukhari, Zhen Lü, Robert C. Bast, Adrian L. Harris, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka‐Spengler, Ashfaq Ahmed
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0155378

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Cited by: 7
Author(s): Laurie A. Steiner, Vincent P. Schulz, Yelena Makismova, Kimberly Lezon-Geyda, Patrick G. Gallagher
Software Mentions: 3
Published: about 10 years ago

10.1155/2019/5952836

<i>TP53</i>Mutations Promote Immunogenic Activity in Breast Cancer
Cited by: 45
Author(s): Zhixian Liu, Zhongshan Jiang, Yingsheng Gao, Lirui Wang, Chen Cai, Qianqian Wang
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0121507

Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR
Cited by: 22
Author(s): Christian Hinske, Pedro A. F. Galante, Elisabeth Limbeck, Patrick Möhnle, Raphael B. Parmigiani, Lucila Ohno-Machado, Anamaria A. Camargo, Simone Kreth
Software Mentions: 3
Published: over 11 years ago

10.7554/eLife.51406

Proteome profile of peripheral myelin in healthy mice and in a neuropathy model
Cited by: 52
Author(s): Sophie B Siems, Olaf Jahn, Maria A Eichel, Nirmal Kannaiyan, Lai Man Natalie Wu, Diane L. Sherman, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Robert Fledrich, Michael W. Sereda, Moritz J. Rossner, Peter Brophy, Hauke Werner
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2019.01470

Biological Determinants of Chemo-Radiotherapy Response in HPV-Negative Head and Neck Cancer: A Multicentric External Validation
Cited by: 16
Author(s): Martijn van der Heijden, Paul Essers, Monique C. de Jong, Reinout H. de Roest, Sebastian Sanduleanu, Caroline V.M. Verhagen, Olga Hamming‐Vrieze, Frank Hoebers, Philippe Lambin, Harry Bartelink, C. René Leemans, Marcel Verheij, Ruud H. Brakenhoff, Michiel W. M. van den Brekel, Conchita Vens
Software Mentions: 3
Published: over 6 years ago

10.3389/fbioe.2020.00930

Immune Cytolytic Activity as an Indicator of Immune Checkpoint Inhibitors Treatment for Prostate Cancer
Cited by: 18
Author(s): Zhe Gao, Yiran Tao, Yue‐Yun Lai, Qiong Wang, Zean Li, Shirong Peng, Junxiu Chen, Wenli Cai, Kaiwen Li, Hai Huang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-5900-1

Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data
Cited by: 5
Author(s): Fernando Carazo, Marian Gimeno, Juan A Ferrer-Bonsoms, Ángel Rubio
Software Mentions: 3
Published: about 7 years ago

10.7150/jca.57231

A clinical prediction model identifies a subgroup with inferior survival within intermediate risk acute myeloid leukemia
Cited by: 8
Author(s): Xiaoxia Hu, Bianhong Wang, Qi Chen, Aijie Huang, Weijia Fu, Lixia Liu, Ying Zhang, Gusheng Tang, Hui Cheng, Xiong Ni, Lei Gao, Jie Chen, Li Chen, Weiping Zhang, Jianmin Yang, Shanbo Cao, Li Yu, Jianmin Wang
Software Mentions: 3
Published: over 5 years ago

10.15252/emmm.201708274

Identification of potential therapeutic targets in prostate cancer through a cross‐species approach
Cited by: 30
Author(s): Sarah Jurmeister, Antonio Ramos-Montoya, Carmen Sandi, Nelma Pértega‐Gomes, Karan Wadhwa, Alastair Lamb, Mark J. Dunning, Jan Attig, Jason S. Carroll, Lee G.D. Fryer, Sérgio Luís Felisbino, David E. Neal
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-11-344

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays
Cited by: 18
Author(s): Cyril Dégletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier, Claude Duchamp
Software Mentions: 3
Published: about 16 years ago

10.1186/s12864-015-2237-2

Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions
Cited by: 76
Author(s): Laura A. L. Dillon, Rahul Suresh, Kwame Okrah, Héctor Corrada Bravo, David M. Mosser, Najib M. El-Sayed
Software Mentions: 3
Published: over 10 years ago

10.1002/ece3.3542

Precopulatory but not postcopulatory male reproductive traits diverge in response to mating system manipulation in<i>Drosophila melanogaster</i>
Cited by: 15
Author(s): Kristina U. Wensing, Mareike Koppik, Claudia Fricke
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0240250

Multicenter analysis of sputum microbiota in tuberculosis patients
Cited by: 7
Author(s): Claudia Sala, Andrej Benjak, Delia Goletti, Sayera Banu, Jesica Mazza-Stadler, Katia Jaton, Philippe Busso, Sille Remm, Marion Leleu, Jacques Rougemont, Fabrizio Palmieri, Gilda Cuzzi, Ornella Butera, Valentina Vanini, Shahjahan Kabir, S. M. Mazidur Rahman, Laurent Nicod, Stewart T. Cole
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms20184498

Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)
Cited by: 14
Author(s): Jiaojiao Wu, Jing Gao, Weishuai Bi, Jianjun Zhao, Xiaoyan Yu, Zaifeng Li, Daqun Liu, Bo Liu, Xiaodong Wang
Software Mentions: 3
Published: almost 7 years ago

10.3389/fbioe.2015.00038

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses
Cited by: 33
Author(s): Takeshi Ara, Mitsuo Enomoto, Masanori Arita, Chiaki Ikeda, Kota Kera, Manabu Yamada, Takaaki Nishi­oka, Tasuku Ikeda, Yoshito Nihei, Daisuke Shibata, Shigehiko Kanaya, Nozomu Sakurai
Software Mentions: 3
Published: over 11 years ago

10.1186/s12967-021-02972-6

The germline/somatic DNA damage repair gene mutations modulate the therapeutic response in Chinese patients with advanced pancreatic ductal adenocarcinoma
Cited by: 9
Author(s): Lin Shui, Xiaofen Li, Yang Peng, Jiangfang Tian, Shuangshuang Li, Du He, Ang Li, Bole Tian, Mao Li, Heli Gao, Ning An, Cheng Yi, Dan Cao
Software Mentions: 3
Published: about 5 years ago

10.3390/genes12091374

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods
Cited by: 5
Author(s): Yibing Liu, Ying Yu, Ai Hong, Fengxia Zhang, Xitong Zhao, Huatao Liu, Yong Shi, Kai Xing, Chuduan Wang
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2019.00070

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase
Cited by: 6
Author(s): Seon‐Kap Hwang, S. S. Singh, Jitendra Maharana, S. N. Kalita, Aytuğ Tuncel, Tanmayee Rath, Debashis Panda, Mahendra Kumar Modi, Thomas W. Okita
Software Mentions: 3
Published: over 7 years ago

10.7150/ijms.47356

Potential mechanism of RRM2 for promoting Cervical Cancer based on weighted gene co-expression network analysis
Cited by: 11
Author(s): Jingtao Wang, Yuexiong Yi, Yurou Chen, Ye Xiong, Wei Zhang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-07862-w

E-Liquid Autofluorescence can be used as a Marker of Vaping Deposition and Third-Hand Vape Exposure
Cited by: 15
Author(s): Eric S. Davis, Maria F. Sassano, Henry P. Goodell, Robert Tarran
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.11469

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability
Cited by: 55
Author(s): Judith Schütte, Huange Wang, Stella Antoniou, Andrew Jarratt, Nicola K. Wilson, Joey Riepsaame, Fernando J. Calero-Nieto, Victoria Moignard, Silvia Basilico, Sarah Kinston, Rebecca Hannah, Mun Chiang Chan, Sylvia Nürnberg, Willem H. Ouwehand, Nicola Bonzanni, Marella Ftr de Bruijn, Berthold Göttgens
Software Mentions: 3
Published: over 10 years ago

10.1186/s12916-016-0762-8

Unraveling the associations of age and menopause with cardiovascular risk factors in a large population-based study
Cited by: 92
Author(s): Annelien C de Kat, Veerle Dam, N. Charlotte Onland‐Moret, Marinus J.C. Eijkemans, Frank J. Broekmans, Yvonne T. van der Schouw
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0006735

Identification of Genes Responsive to Solar Simulated UV Radiation in Human Monocyte-Derived Dendritic Cells
Cited by: 18
Author(s): Hortensia de la Fuente, Amalia Lamana, Marı́a Mittelbrunn, S. Pérez‐Gala, Salvador González, Amaro García‐Díez, Miguel A. Vega, Francisco Sánchez-Madrid
Software Mentions: 3
Published: almost 17 years ago

10.1186/s12974-020-01900-7

A1 reactive astrocytes and a loss of TREM2 are associated with an early stage of pathology in a mouse model of cerebral amyloid angiopathy
Cited by: 30
Author(s): Xavier Taylor, Pablo Cisternas, Yanwen You, Yingjian You, Shunian Xiang, Yamil Marambio, Jie Zhang, Rubén Vidal, Cristian A. Lasagna‐Reeves
Software Mentions: 3
Published: about 6 years ago

10.7717/peerj.7488

Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study
Cited by: 17
Author(s): Harris Onywera, Anna‐Lise Williamson, Zizipho Z. A. Mbulawa, David Coetzee, Tracy L. Meiring
Software Mentions: 3
Published: about 7 years ago

10.3390/cancers13102499

Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma
Cited by: 3
Author(s): Lisanne Noordam, Zhouhong Ge, Hadiye Özturk, Michail Doukas, Shanta Mancham, Patrick P.C. Boor, Lucia Campos Carrascosa, Guoying Zhou, Thierry van den Bosch, Qiuwei Pan, Jan N.M. IJzermans, Marco J. Bruno, Dave Sprengers, Jaap Kwekkeboom
Software Mentions: 3
Published: about 5 years ago