10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: about 9 years ago

10.3389/fnut.2021.640100

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome
Cited by: 7
Author(s): Jason W. Arnold, Hunter D. Whittington, Sue F. Dagher, Jeffery Roach, M. Andrea Azcárate-Peril, José M. Bruno-Bárcena
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2018.00902

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Cited by: 74
Author(s): Gloria Torres-Cortés, Sophie Bonneau, Olivier Bouchez, Clémence Genthon, Martial Briand, Marie‐Agnès Jacques, Matthieu Barret
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pcbi.1009131

MiDAS—Meaningful Immunogenetic Data at Scale
Cited by: 9
Author(s): Maciej Migdał, Dan Fu Ruan, William F. Forrest, Amir Horowitz, Christian Hammer
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2016.00603

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Cited by: 22
Author(s): Beverly E. Flood, Palmer Fliss, Daniel S. Jones, Gregory J. Dick, Sunit Jain, Anne‐Kristin Kaster, Matthias Winkel, Marc Mußmann, Jake V. Bailey
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-016-2925-6

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi
Cited by: 74
Author(s): S. Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valè, M. L. Gullino, D. Spadaro
Software Mentions: 4
Published: almost 10 years ago

10.1002/ece3.5965

Draft genome of the famous ornamental plant <i>Paeonia suffruticosa</i>
Cited by: 31
Author(s): Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kun Yu, Xiliang Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jun Huang, Gengyun Zhang, Zhang Can-jun
Software Mentions: 4
Published: about 6 years ago

10.1080/19490976.2021.1875797

Early life environmental exposures have a minor impact on the gut ecosystem following a natural birth
Cited by: 6
Author(s): Nishat Tasnim, Candice Quin, S K Gill, Chunping Dai, Miranda M. Hart, Deanna L. Gibson
Software Mentions: 4
Published: over 5 years ago

10.1186/s13395-021-00269-2

Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers
Cited by: 5
Author(s): Rohan Verma, Suraj Kannan, Brian L. Lin, Katherine M. Fomchenko, Tim O. Nieuwenhuis, Arun H. Patil, Clarisse Lukban, Xiao‐Ping Yang, Karen Fox-Talbot, Matthew N. McCall, Chulan Kwon, David A. Kass, Avi Rosenberg, Marc K. Halushka
Software Mentions: 4
Published: about 5 years ago

10.3390/e23010117

Probabilistic Models with Deep Neural Networks
Cited by: 3
Author(s): Andrés R. Masegosa, Rafael Cabañas, Helge Langseth, Thomas D. Nielsen, Antonio Salmerón
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.3608

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands?
Cited by: 16
Author(s): Michael McTee, Ylva Lekberg, Dan Mummey, Alexii Rummel, Philip W. Ramsey
Software Mentions: 4
Published: over 8 years ago

10.1038/s42003-021-01661-w

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
Cited by: 16
Author(s): Christoph Niemöller, Julius Wehrle, Julian Riba, Rainer Claus, Nathalie Renz, Janika Rhein, Sabine Bleul, Juliane M. Stosch, Justus Duyster, Christoph Plass, Pavlo Lutsik, Daniel B. Lipka, Michael Lübbert, Heiko Becker
Software Mentions: 4
Published: over 5 years ago

10.3389/fpsyg.2019.01594

Acoustic Correlates of Auditory Object and Event Perception: Speakers, Musical Timbres, and Environmental Sounds
Cited by: 5
Author(s): Mattson Ogg, L. Robert Slevc
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-83514-4

Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
Cited by: 7
Author(s): Constanza Chialva, Thomas Blein, Martín Crespi, Diego Lijavetzky
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0247378

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling
Cited by: 11
Author(s): José Diógenes Jaimes, Andrea Slavíčková, Jakub Hurych, Ondřej Cinek, Ben Nichols, Lucie Vodolánová, K. Černý, Jaroslav Havlík
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400777

<i>rmtA</i>-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in<i>Aspergillus flavus</i>
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.20940

<i>PTEN</i> loss is associated with prostate cancer recurrence and alterations in tumor DNA methylation profiles
Cited by: 29
Author(s): Milan S. Geybels, Min Fang, Jonathan L. Wright, Xiaoyu Qu, Marina Bibikova, Brandy Klotzle, Jie Fan, Ziding Feng, Elaine A. Ostrander, Peter S. Nelson, Janet L. Stanford
Software Mentions: 4
Published: almost 9 years ago

10.3390/cancers12092474

Identification of Clinical and Socioeconomic Predictors of Adjuvant Therapy after Trans-Oral Robotic Surgery in Patients with Oropharyngeal Squamous Cell Carcinoma
Cited by: 5
Author(s): Sujith Baliga, Brett Klamer, Sachin R. Jhawar, M.E. Gamez, Darrion Mitchell, Adriana Blakaj, J.C. Grecula, Ulysses Gardner, Khaled Dibs, Matthew Old, Nolan B. Seim, Stephen Y. Kang, Ricardo L. Carrau, Amit Agrawal, Vidhya Karivedu, Priyanka Bhateja, Enver Özer, James W. Rocco, Marcelo Bonomi, Dukagjin Blakaj
Software Mentions: 4
Published: almost 6 years ago

10.3390/s17102321

Design of a Low-Cost Air Levitation System for Teaching Control Engineering
Cited by: 31
Author(s): Jesús Chacón, Jacobo Sáenz, Luís de la Torre, José Quintanal Díaz, Francisco Esquembre
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0234414

Is amblyopia associated with school readiness and cognitive performance during early schooling? Findings from the Millennium Cohort Study
Cited by: 6
Author(s): Lisanne A. Gitsels, Mario Cortina‐Borja, Jugnoo S Rahi
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2018.00321

DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information
Cited by: 7
Author(s): Weiwei Zhang, Hang Long, Binsheng He, Jialiang Yang
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1004261

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Cited by: 329
Author(s): Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R. Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W. L. Chow, Jean Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J. Gerik, Jonathan M. Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L. Hamlin, Yu-Ting Hsueh, Giuseppe Ianiri, Steven J.M. Jones, Chinnappa D. Kodira, Lukasz Kozubowski, Woei C. Lam, Marco A. Marra, Larry D. Mesner, Piotr A. Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E. Schein, Sheng Sun, Carolin Wollschlaeger, Ian Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S. Newlon, John R. Perfect, Jennifer K. Lodge, Alexander Idnurm, Jason E. Stajich, James W. Kronstad, Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
Software Mentions: 4
Published: over 12 years ago

10.1038/s42003-020-1028-8

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures
Cited by: 31
Author(s): Åsa Wallén-Mackenzie, Sylvie Dumas, Maria Papathanou, Mihaela M. Martis, Bianca Vlcek, Niclas König, Åsa K. Björklund
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2019.00149

The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax
Cited by: 8
Author(s): Alexey Moskalev, Zulfiya G. Guvatova, Mikhail Shaposhnikov, Ekaterina Lashmanova, Ekaterina Proshkina, Liubov Koval, Alex Zhavoronkov, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1006828

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
Cited by: 15
Author(s): Sungho Shin, Ophelia S. Venturelli, Ví­ctor M. Zavala
Software Mentions: 4
Published: over 7 years ago

10.1186/1756-8935-7-26

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2
Cited by: 23
Author(s): Heba Saadeh, Reiner Schulz
Software Mentions: 4
Published: almost 12 years ago

10.7717/peerj-cs.161

An integrated platform for intuitive mathematical programming modeling using LaTeX
Cited by: 4
Author(s): Charalampos Triantafyllidis, Lazaros G. Papageorgiou
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12859-016-0963-3

Leveraging protein quaternary structure to identify oncogenic driver mutations
Cited by: 8
Author(s): Gregory A. Ryslik, Yu‐Wei Cheng, Yorgo Modis, Hongyu Zhao
Software Mentions: 4
Published: over 10 years ago

10.1098/rspb.2021.0721

Characterizing the modern light environment and its influence on circadian rhythms
Cited by: 5
Author(s): Dennis Khodasevich, Susan Tsui, Darwin Keung, Debra J. Skene, Victoria L. Revell, Micaela E Martinez
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1008661

An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem
Cited by: 15
Author(s): Hasthi Ram, Sudeep Sahadevan, Nittaya Gale, Monica Pia Caggiano, Xiulian Yu, Carolyn Ohno, Marcus G. Heisler
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.6001

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics
Cited by: 27
Author(s): Nicholas M. Sard, Seth Smith, Jared J. Homola, Jeannette Kanefsky, Gale A. Bravener, Jean V. Adams, Christopher M. Holbrook, Peter J. Hrodey, Kevin Tallon, Kim T. Scribner
Software Mentions: 4
Published: over 6 years ago

10.1155/2017/6896390

Gene Expression Profiling of the Optic Nerve Head of Patients with Primary Open-Angle Glaucoma
Cited by: 4
Author(s): Xinrong Wang, KeWei Gong, Haiyan Li, Cong Yi Wang, Chaoyi Qu, Hui Li
Software Mentions: 4
Published: over 9 years ago

10.1186/s12874-021-01318-6

High performance implementation of the hierarchical likelihood for generalized linear mixed models: an application to estimate the potassium reference range in massive electronic health records datasets
Cited by: 1
Author(s): Cristian Bologa, V. Shane Pankratz, Mark Unruh, Maria Roumelioti, Vallabh O. Shah, Kamran Shaffi, Soraya Arzhan, John P. Cook, Christos Argyropoulos
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-72861-3

Dietary fatty acid intake and gut microbiota determine circulating endocannabinoidome signaling beyond the effect of body fat
Cited by: 48
Author(s): Sophie Castonguay-Paradis, Sébastien Lacroix, Gabrielle Rochefort, Lydiane Parent, Julie Perron, Cyril Martin, Benoît Lamarche, Frédéric Raymond, Nicolas Flamand, Vincenzo Di Marzo, Alain Veilleux
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpsyg.2019.00480

BEEP—Bodily and Emotional Perception of Pain. A Questionnaire to Measure Reaction to Pain in Chronic Pain Disorders
Cited by: 3
Author(s): Antonio Preti, Serena Stocchino, Francesca Pinna, Manuela Deidda, Mario Musu, Federica Sancassiani, Ferdinando Romano, Sérgio Machado, Gabriele Finco, Mauro Giovanni Carta
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0249792

Face masks reduce emotion-recognition accuracy and perceived closeness
Cited by: 130
Author(s): Felix Grundmann, Kai Epstude, Susanne Scheibe
Software Mentions: 4
Published: over 5 years ago

10.3389/fpsyt.2019.00896

Population Survey Data Informing the Therapeutic Potential of Classic and Novel Phenethylamine, Tryptamine, and Lysergamide Psychedelics
Cited by: 28
Author(s): James D Sexton, Charles D. Nichols, Peter S. Hendricks
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2021.697688

Multi-Locus Genome-Wide Association Study and Genomic Selection of Kernel Moisture Content at the Harvest Stage in Maize
Cited by: 5
Author(s): Guangfei Zhou, Qiuli Zhu, Yuxiang Mao, Guoqing Chen, Li Xue, Hailiang Lu, Mei Shi, Zhenliang Zhang, Xiaokai Song, Huimin Zhang, Dejun Hao
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2017.01861

Belowground Plant–Herbivore Interactions Vary among Climate-Driven Range-Expanding Plant Species with Different Degrees of Novel Chemistry
Cited by: 21
Author(s): Rutger A. Wilschut, Júlio Carlos Pereira da Silva, Paolina Garbeva, Wim H. van der Putten
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2020.00091

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer
Cited by: 14
Author(s): Peng Song, Lei Wu, Wenxian Guan
Software Mentions: 4
Published: over 6 years ago

10.1098/rsos.160557

Invasive mutualisms between a plant pathogen and insect vectors in the Middle East and Brazil
Cited by: 30
Author(s): Renan Batista Queiróz, Philip Donkersley, Fábio Nascimento Silva, Issa Hashil Al-Mahmmoli, Abdullah M. Al-Sadi, Claudine M. Carvalho, Simon L. Elliot
Software Mentions: 4
Published: over 9 years ago

10.1007/s10162-019-00718-2

Evaluating Psychophysical Polarity Sensitivity as an Indirect Estimate of Neural Status in Cochlear Implant Listeners
Cited by: 30
Author(s): Kelly N. Jahn, Julie G. Arenberg
Software Mentions: 4
Published: over 7 years ago

10.1016/j.dib.2016.06.001

Microarray dataset of Jurkat cells following miR-93 over-expression
Cited by: 0
Author(s): Silvia Gioiosa, Lorena Verduci, Gianluca Azzalin, Claudia Carissimi, Valerio Fulci, Giuseppe Macino
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0236982

Is short-term-variation of fetal-heart-rate a better predictor of fetal acidaemia in labour? A feasibility study
Cited by: 5
Author(s): Habiba Kapaya, Richard Jacques, Thomas Almond, Miss Hilary Rosser, Dilly Anumba
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1006777

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes
Cited by: 138
Author(s): Romain Blanc-Mathieu, Laetitia Perfus‐Barbeoch, Jean‐Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martín-Jimenez, Marc Bailly‐Bechet, Philippe Castagnone‐Sereno, Jean‐François Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yujin Kim, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G. J. Danchin
Software Mentions: 4
Published: about 9 years ago

10.3389/fgene.2015.00331

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
Cited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-021-02289-z

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
Cited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.1066

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
Cited by: 33
Author(s): Nagesh A. Kuravadi, Vijay A. Yenagi, Kannan Rangiah, H. B. Mahesh, Anantharamanan Rajamani, Meghana Deepak Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, S Shilpa, Aishwarya Ramamurthy, B. N. Sathyanarayana, Malali Gowda
Software Mentions: 4
Published: about 11 years ago

10.1038/s41422-020-00445-x

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Cited by: 88
Author(s): Luca Mazzurana, Paulo Czarnewski, Viktor Jönsson, Leif Wigge, Markus Ringnér, Teresa C. Williams, Avinash Ravindran, Åsa K. Björklund, Jesper Säfholm, Gunnar Nilsson, Sven Erik Dahlén, Ann Charlotte Orre, Mamdoh Al‐Ameri, Charlotte Höög, Charlotte Hedin, Sylwester Szczegielniak, Sven Almér, Jenny Mjösberg
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.560229

A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related Genes
Cited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0123346

Community-Wide Spatial and Temporal Discordances of Seed-Seedling Shadows in a Tropical Rainforest
Cited by: 9
Author(s): Débora Cristina Rother, Marco A. Pizo, Tadeu Siqueira, Ricardo Ribeiro Rodrigues, Pedro Jordano
Software Mentions: 4
Published: over 11 years ago

10.1186/s13073-021-00922-x

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Cited by: 52
Author(s): Siel Olbrecht, Pieter Busschaert, Jun Qian, Adriaan Vanderstichele, Liselore Loverix, Toon Van Gorp, Els Van Nieuwenhuysen, Sileny Han, Annick Van den Broeck, An Coosemans, Anne‐Sophie Van Rompuy, Diether Lambrechts, Ignace Vergote
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1006899

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)
Cited by: 11
Author(s): Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein
Software Mentions: 4
Published: over 7 years ago

10.1038/s41396-021-00953-7

Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations
Cited by: 30
Author(s): Glen D’Souza, Vanessa R. Povolo, Johannes M. Keegstra, Roman Stocker, Martin Ackermann
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-019-0645-2

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month
Cited by: 99
Author(s): Nina Iszatt, Stefan Janssen, Virissa Lenters, Cecilie Dahl, Hein Stigum, Rob Knight, Siddhartha Mandal, Shyamal Peddada, Antonio González, Tore Midtvedt, Merete Eggesbø
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-18205-0

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex
Cited by: 26
Author(s): Susanta K. Behura, P. C. Tizioto, JaeWoo Kim, Natália Vinhal Grupioni, Christopher M. Seabury, Robert D. Schnabel, Laurel J. Gershwin, Alison L. Van Eenennaam, Rachel L. Toaff-Rosenstein, Holly L. Neibergs, Luciana Correia de Almeida Regitano, Jeremy F. Taylor
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.119.400716

Whole Genome Sequencing and Comparative Genomics of Two Nematicidal <i>Bacillus</i> Strains Reveals a Wide Range of Possible Virulence Factors
Cited by: 9
Author(s): Nik Susič, Sandra Janežič, Maja Rupnik, Barbara Gerič Stare
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2019.00811

Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
Cited by: 25
Author(s): Dezhou Hu, Guizhen Kan, Wei Hu, Yali Li, Dejun Hao, Li Xiao, Hui Yang, Zhongyi Yang, Xiaohong He, Fang Huang, Deyue Yu
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2018.00874

Differential Effects of Climate Warming on the Nectar Secretion of Early- and Late-Flowering Mediterranean Plants
Cited by: 47
Author(s): Krista Takkis, Thomas Tscheulin, Theodora Petanidou
Software Mentions: 4
Published: about 8 years ago

10.1002/1878-0261.12811

High‐grade serous peritoneal cancer follows a high stromal response signature and shows worse outcome than ovarian cancer
Cited by: 1
Author(s): Francis Jacob, Rosa Lina Marchetti, André B. Kind, Kenneth J. Russell, Andreas Schoetzau, Viola Heinzelmann‐Schwarz
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0150568

Within-Host Models of High and Low Pathogenic Influenza Virus Infections: The Role of Macrophages
Cited by: 32
Author(s): Kasia A. Pawelek, Daniel Dor, Cristian Salmeron, Andreas Handel
Software Mentions: 4
Published: over 10 years ago

10.3390/nu9040407

Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats
Cited by: 24
Author(s): Bijaya Upadhyaya, Tricia D. Larsen, Shivon Barwari, Eli J. Louwagie, Michelle Baack, Moul Dey
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1006498

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
Cited by: 5
Author(s): Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.34864

Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Cited by: 51
Author(s): Maria A. Sacta, Bowranigan Tharmalingam, Maddalena Coppo, David A. Rollins, Dinesh K Deochand, Bradley Benjamin, Li Yu, Bin Zhang, Xiaoyu Hu, Rong Li, Yurii Chinenov, Inez Rogatsky
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.00288

Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations
Cited by: 24
Author(s): Bhusan K. Kuntal, Chetan Gadgil, Sharmila S. Mande
Software Mentions: 4
Published: over 7 years ago

10.3390/microorganisms8071061

Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold–Dry Limits of Life on Earth
Cited by: 2
Author(s): Lara Vimercati, Clifton P. Bueno de Mesquita, Steven K. Schmidt
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1008154

Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model
Cited by: 10
Author(s): Lorenz M. Loyola, Vasudevan Achuthan, Kathryn Gilroy, Gillian Borland, Anna Kilbey, Nancy MacKay, Margaret Bell, Jodie Hay, Sriram Aiyer, Dylan Fingerman, Rodrigo A. Villanueva, Ewan R. Cameron, Christine A. Kozak, Alan Engelman, James C. Neil, Monica J. Roth
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0009357

Mark-release-recapture of male Aedes aegypti (Diptera: Culicidae): Use of rhodamine B to estimate movement, mating and population parameters in preparation for an incompatible male program
Cited by: 10
Author(s): Brendan J Trewin, Dan Pagendam, Brian J. Johnson, Chris Paton, Nigel Snoad, Scott A. Ritchie, Kyran M. Staunton, Bradley J. White, Sara N. Mitchell, Nigel W. Beebe
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.595550

An Enhancer-Based Analysis Revealed a New Function of Androgen Receptor in Tumor Cell Immune Evasion
Cited by: 3
Author(s): Yuan Wang, Jiajia Li, Jingjing Li, Peipei Li, Li Wang, Lijun Di
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0257882

Angler and environmental influences on walleye Sander vitreus and muskellunge Esox masquinongy angler catch in Escanaba Lake, Wisconsin 2003–2015
Cited by: 5
Author(s): Stephanie L. Shaw, Kathryn M. Renik, Greg G. Sass
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0228668

Comparing acoustic and radar deterrence methods as mitigation measures to reduce human-bat impacts and conservation conflicts
Cited by: 10
Author(s): Lia R. V. Gilmour, Marc W. Holderied, S. P. C. Pickering, Gareth Jones
Software Mentions: 4
Published: over 6 years ago

10.3389/fmed.2021.646710

Dietary and Pharmacologic Manipulations of Host Lipids and Their Interaction With the Gut Microbiome in Non-human Primates
Cited by: 3
Author(s): Jennifer M. Lang, Leslie R. Sedgeman, Lei Cai, Joseph D. Layne, Zhen Wang, Calvin Pan, Richard Lee, Ryan E. Temel, Aldons J. Lusis
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers12020470

Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma
Cited by: 10
Author(s): Pedro Nicolau-Neto, Paulo Thiago de Souza-Santos, Mariana Severo Ramundo, Priscila Valverde, Ivanir Martins, Izabella Costa Santos, Fernando Luiz Dias, Tatiana de Almeida Simão, Luís Felipe Ribeiro Pinto
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1002415

A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Cited by: 30
Author(s): Chia Huey Ooi, Hue Kian Oh, H Wang, Angie Lay Keng Tan, Jeanie Wu, Ming‐Hui Lee, Sun Young Rha, Hyun Cheol Chung, David M. Virshup, Patrick Tan
Software Mentions: 4
Published: over 14 years ago

10.1093/bib/bbz170

Deep learning-based clustering approaches for bioinformatics
Cited by: 104
Author(s): Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz‐Schuhmann, Michael Cochez, Stefan Decker
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0224466

Monitoring hunted species of cultural significance: Estimates of trends, population sizes and harvesting rates of flying-fox (Pteropus sp.) in New Caledonia
Cited by: 5
Author(s): Malik Oedin, Fabrice Brescia, Mélanie Boissenin, Éric Vidal, Jean‐Jérôme Cassan, Jean-Claude Hurlin, Alexandre Millon
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.68714

Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes
Cited by: 17
Author(s): Francis Grafton, Jaclyn J. Ho, Sara Ranjbarvaziri, Farshad Farshidfar, Anastasiia Budan, Stephanie Steltzer, Mahnaz Maddah, Kevin E. Loewke, Kristina Green, Snahel Patel, Tim Hoey, Mohammad A. Mandegar
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0065598

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Cited by: 292
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
Software Mentions: 4
Published: about 13 years ago

10.1098/rsos.201622

Assessing the strength of case growth trends in the coronavirus pandemic
Cited by: 7
Author(s): Levente Kriston
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.60546

Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period
Cited by: 13
Author(s): Qiang Qiu, Yunming Wu, Limei Ma, Wenjing Xu, Max Hills, Vivekanandan Ramalingam, Chong Yu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-019-5501-z

Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach
Cited by: 7
Author(s): Qi Wei, Stephen A. Ramsey, Maureen K. Larson, Noah Berlow, Donasian O. Ochola, Christopher Shiprack, Amita Kashyap, Bernard Séguin, Charles Keller, Christiane V. Löhr
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0239367

Mining a human transcriptome database for chemical modulators of NRF2
Cited by: 18
Author(s): John P. Rooney, Brian N. Chorley, Steven Hiemstra, Steven Wink, Xuting Wang, Douglas A. Bell, Bob van de Water, J. Christopher Corton
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0214559

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus cattle rumen tissue
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Zan Liu, Jiuzhou Song
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1004982

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines
Cited by: 378
Author(s): Jennifer Spindel, Hamida Begum, Deniz Akdemir, P. S. Virk, B. C. Y. Collard, Edilberto D. Redoña, G. N. Atlin, Jean‐Luc Jannink, Susan R. McCouch
Software Mentions: 4
Published: over 11 years ago

10.1186/s12889-021-11648-1

Global, regional, and national prevalence, disability adjusted life years, and time trends for refraction disorders, 1990–2019: findings from the global burden of disease study 2019
Cited by: 8
Author(s): Heyan Li, Yueming Liu, Li Dong, Ruiheng Zhang, Wen-Da Zhou, Haotian Wu, Yifan Li, Yaxing Wang, Wenbin Wei
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1004595

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
Cited by: 26
Author(s): Aamna K Kaul, Eugene F. Schuster, Barbara Jennings
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12887-021-02540-3

Time series analysis of the relationship between diarrhea in children and Rota 2 vaccine in the Fanteakwa District of the eastern region of Ghana
Cited by: 2
Author(s): James Atampiiga Avoka, Elvis J. Dun-Dery, Issah Seidu, Armel N. E. Abou, Paul Twene, Isaac Obeng Tandoh, Frederick Dun-Dery
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.7504

Bats partition activity in space and time in a large, heterogeneous landscape
Cited by: 12
Author(s): Elizabeth A. Beilke, Rachel V. Blakey, Joy M. O’Keefe
Software Mentions: 4
Published: over 5 years ago

10.3389/fvets.2020.00251

Rumen Microbiota Distribution Analyzed by High-Throughput Sequencing After Oral Doxycycline Administration in Beef Cattle
Cited by: 5
Author(s): Fengmei Chen, Guangcun Cheng, Yan Xu, Yunzhou Wang, Qingxiang Xia, Shiqiang Hu
Software Mentions: 4
Published: about 6 years ago

10.3390/plants9111589

Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana
Cited by: 11
Author(s): Dragana D Antonić, Angelina Subotić, Milan Dragićević, Danijel Pantelić, Snežana Milošević, Ana Simonović, Ivana Momčilović
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-021-08173-0

Comprehensive analyses of competing endogenous RNA networks reveal potential biomarkers for predicting hepatocellular carcinoma recurrence
Cited by: 3
Author(s): Ping Yan, Zuotian Huang, Tong Mou, Yunhai Luo, Yanyao Liu, Baoyong Zhou, Zhen-Rui Cao, Zhongjun Wu
Software Mentions: 4
Published: over 5 years ago

10.1007/s00430-020-00691-1

Bacterial aggregate size determines phagocytosis efficiency of polymorphonuclear leukocytes
Cited by: 31
Author(s): Morten Alhede, Marcel Lorenz, Blaine Gabriel Fritz, Peter Østrup Jensen, Hans Christian Ring, Lene Bay, Thomas Bjarnsholt
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2017.01284

Assessment of the Combined Effect of Epstein–Barr Virus and Plasmodium falciparum Infections on Endemic Burkitt Lymphoma Using a Multiplex Serological Approach
Cited by: 13
Author(s): Ruth Aguilar, Delphine Casabonne, Cristina O’Callaghan-Gordo, Marta Vidal, Joseph J. Campo, Nora Mutalima, Evelina Angov, Sandeep Dutta, Deepak Gaur, Chetan E. Chitnis, Virander S. Chauhan, Angelika Michel, Sílvia de Sanjosé, Tim Waterboer, Manolis Kogevinas, Rob Newton, Carlota Dobaño
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12989-017-0239-8

Maternal engineered nanomaterial inhalation during gestation alters the fetal transcriptome
Cited by: 36
Author(s): Phoebe A. Stapleton, Quincy A. Hathaway, C.E. Nichols, Alaeddin B. Abukabda, Mark V. Pinti, Danielle L. Shepherd, Carroll R. McBride, Jinghai Yi, Vincent Castranova, John M. Hollander, Timothy R. Nurkiewicz
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1008326

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Cited by: 31
Author(s): Paja Sijacic, Dylan H Holder, Marko Bajic, Roger B. Deal
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-015-1706-y

Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells
Cited by: 3
Author(s): Anyou Wang, Qianchuan He, Yan Zhong
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pcbi.1003361

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
Cited by: 33
Author(s): Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano
Software Mentions: 4
Published: over 12 years ago

10.3389/fpls.2021.678959

Variation in Methyl Jasmonate-Induced Defense Among Norway Spruce Clones and Trade-Offs in Resistance Against a Fungal and an Insect Pest
Cited by: 10
Author(s): Adriana Puentes, Tao Zhao, Lina Lundborg, Niklas Björklund, Anna‐Karin Borg‐Karlson
Software Mentions: 4
Published: about 5 years ago