10.1016/j.immuni.2021.08.011

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses
Cited by: 58
Author(s): Qingli Tang, Rachel E. Rigby, George R. Young, Astrid Korning Hvidt, Tanja Davis, Tiong Kit Tan, Anne Bridgeman, Alain Townsend, George Kassiotis, Jan Rehwinkel
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2014.00358

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Cited by: 239
Author(s): Ryan J. Williams, Adina Howe, Kirsten Hofmockel
Software Mentions: 6
Published: almost 12 years ago

10.1093/bioinformatics/btaa591

Epiviz File Server: Query, transform and interactively explore data from indexed genomic files
Cited by: 4
Author(s): Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Héctor Corrada Bravo
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pcbi.1007162

Cross-species functional modules link proteostasis to human normal aging
Cited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: almost 7 years ago

10.3390/e22090937

belg: A Tool for Calculating Boltzmann Entropy of Landscape Gradients
Cited by: 7
Author(s): Jakub Nowosad, Peichao Gao
Software Mentions: 6
Published: almost 6 years ago

10.1186/s40168-020-00917-7

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation
Cited by: 56
Author(s): Na Li, Bo Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao, Junjun Wang
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0204970

Network of small no-take marine reserves reveals greater abundance and body size of fisheries target species
Cited by: 28
Author(s): Fernanda A. Rolim, Tim Langlois, Pedro Furtado Costa Rodrigues, Todd Bond, Fábio S. Motta, Leonardo Mitrano Neves, Otto Bismarck Fazzano Gadig
Software Mentions: 6
Published: over 7 years ago

10.1016/j.celrep.2019.03.102

The Spectrum of Asynchronous Dynamics in Spiking Networks as a Model for the Diversity of Non-rhythmic Waking States in the Neocortex
Cited by: 14
Author(s): Yann Zerlaut, Stefano Zucca, Stefano Panzeri, Tommaso Fellin
Software Mentions: 6
Published: over 7 years ago

10.1186/s12920-021-01036-4

Multi-factor regulatory network and different clusters in hypertrophic obstructive cardiomyopathy
Cited by: 3
Author(s): Xianyu Qin, Lei Huang, Sicheng Chen, Shaoxian Chen, Pengju Wen, Yueheng Wu, Jian Zhuang
Software Mentions: 6
Published: almost 5 years ago

10.1186/1471-2105-14-164

Learning smoothing models of copy number profiles using breakpoint annotations
Cited by: 44
Author(s): Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix‐Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis Bach, Jean-Philippe Vert
Software Mentions: 6
Published: about 13 years ago

10.1371/journal.pbio.3000675

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Cited by: 35
Author(s): Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1007633

Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion
Cited by: 45
Author(s): Yasmine J. Liu, Georges E. Janssens, Rebecca L. McIntyre, Marte Molenaars, Rashmi Kamble, Arwen W. Gao, Aldo Jongejan, Michel van Weeghel, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pbio.3000559

Human sperm displays rapid responses to diet
Cited by: 102
Author(s): Daniel Nätt, Unn Kugelberg, Eduard Casas, Elizabeth Nedstrand, Stefan Zalavary, Pontus Henriksson, Carola Nijm, Julia Jäderquist, Johanna Sandborg, Eva Flinke, Rashmi Ramesh, Lovisa Örkenby, Filip Appelkvist, Thomas Lingg, Nicola Guzzi, Cristian Bellodi, Marie Löf, Tanya Vavouri, Anita Öst
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.6726

Repeatedly adopting power postures does not affect hormonal correlates of dominance and affiliative behavior
Cited by: 4
Author(s): Hannah Metzler, Julie Grèzes
Software Mentions: 6
Published: about 7 years ago

10.1186/s40462-020-00236-4

Winter fidelity, movements, and energy expenditure of Midcontinent Greater White-fronted Geese
Cited by: 10
Author(s): Jay A. VonBank, Mitch D. Weegman, Paul Link, Stephanie A. Cunningham, Kevin J. Kraai, Daniel P. Collins, Bart M. Ballard
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-021-01108-8

Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model
Cited by: 13
Author(s): Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Hao Zhang, Ruifu Yang, Colin Hill, Yu‐Jun Cui, Qixiao Zhai
Software Mentions: 6
Published: almost 5 years ago

10.3390/ph14020115

Simulation-Based Assessment of the Impact of Non-Adherence on Endoxifen Target Attainment in Different Tamoxifen Dosing Strategies
Cited by: 4
Author(s): Anna Mueller‐Schoell, Lena Klopp‐Schulze, Robin Michelet, Madelé van Dyk, Thomas E. Mürdter, Matthias Schwab, Markus Joerger, Wilhelm Huisinga, Gerd Mikus, Charlotte Kloft
Software Mentions: 6
Published: over 5 years ago

10.1007/s00572-021-01042-5

Ancient lineages of arbuscular mycorrhizal fungi provide little plant benefit
Cited by: 21
Author(s): Verena Säle, Javier Palenzuela, Concepción Azcón–Aguilar, Iván Sánchez-Castro, Gladstone Alves da Silva, Benjamin Seitz, Ewald Sieverding, Marcel G. A. van der Heijden, Fritz Oehl
Software Mentions: 6
Published: almost 5 years ago

10.1002/ece3.5690

Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed fly <i>Coelopa frigida</i>
Cited by: 9
Author(s): Emma L. Berdan, Swantje Enge, Göran M. Nylund, Maren Wellenreuther, Gerrit A. Martens, Henrik Pavia
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0096376

Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
Cited by: 38
Author(s): Daniel Nätt, Beatrix Agnvall, Per Jensen
Software Mentions: 6
Published: about 12 years ago

10.3389/fgene.2019.00025

LncRNAs GIHCG and SPINT1-AS1 Are Crucial Factors for Pan-Cancer Cells Sensitivity to Lapatinib
Cited by: 20
Author(s): Zhen Xiang, Shuzheng Song, Zhenggang Zhu, Wenhong Sun, Jaron E. Gifts, Sam Q. Sun, Qiushi Shauna Li, Yingyan Yu, Keqin Kathy Li
Software Mentions: 6
Published: over 7 years ago

10.15252/msb.20209833

Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection
Cited by: 17
Author(s): Sergio Triana, Megan L. Stanifer, Camila Metz-Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordoñez-Rueda, Malte Paulsen, Vladimı́r Beneš, Steeve Boulant, Theodore Alexandrov
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2019.01120

Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets
Cited by: 12
Author(s): Pablo Ivan Pereira Ramos, Luis Willian Pacheco Arge, Nicholas Costa Barroso Lima, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: over 6 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N ₂ Fixation in the Unicellular Cyanobacterium “ <i>Candidatus</i> Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0153355

Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates
Cited by: 20
Author(s): Julie M. Yabu, Janet Siebert, Holden T. Maecker
Software Mentions: 6
Published: about 10 years ago

10.1098/rstb.2020.0366

Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification
Cited by: 16
Author(s): Kenneth De Baets, John Warren Huntley, Daniele Scarponi, Adiël A. Klompmaker, Aleksandra Skawina
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-018-21219-x

Interactions between predation and disturbances shape prey communities
Cited by: 22
Author(s): Canan Karakoç, Viktoriia Radchuk, Hauke Harms, Antonis Chatzinotas
Software Mentions: 6
Published: over 8 years ago

10.3390/biom9090396

Jumping on the Edge—First Evidence for a 2 × 6-meric Hemocyanin in Springtails
Cited by: 0
Author(s): Juliane Schmidt, Heinz Decker, Michael Thomas Marx
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0015581

Therapeutic Implications of GIPC1 Silencing in Cancer
Cited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: over 15 years ago

10.1371/journal.pone.0187091

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network
Cited by: 43
Author(s): Divya Mistry, Roger P. Wise, Julie A. Dickerson
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1004994

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
Cited by: 147
Author(s): Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts
Software Mentions: 6
Published: over 11 years ago

10.3835/plantgenome2017.03.0015

Prospects for Genomic Selection in Cassava Breeding
Cited by: 95
Author(s): Marnin D. Wolfe, Dunia Pino Del Carpio, Olumide Alabi, Lydia Ezenwaka, Ugochukwu N. Ikeogu, Siraj Ismail Kayondo, Roberto Lozano, Uche Godfrey Okeke, Alfred Ozimati, Williams Esuma, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 6
Published: over 8 years ago

10.1093/g3journal/jkab040

<i>EnvRtype</i>: a software to interplay enviromics and quantitative genomics in agriculture
Cited by: 44
Author(s): Germano Costa‐Neto, Giovanni Galli, Humberto Fanelli Carvalho, J. Crossa, Roberto Fritsche‐Neto
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-14788-w

Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship
Cited by: 50
Author(s): Francesco Marabita, Malin Almgren, Louise K. Sjöholm, Lara Kular, Yun Liu, Tojo James, Nimrod Kiss, Andrew P. Feinberg, Tomas Olsson, Ingrid Kockum, Lars Alfredsson, Tomas J. Ekström, Maja Jagodic
Software Mentions: 6
Published: over 8 years ago

10.1099/mgen.0.000320

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Cited by: 0
Author(s): Amol C. Shetty, John Mattick, Matthew Chung, Carrie McCracken, Anup Mahurkar, Scott G. Filler, Claire M. Fraser, David A. Rasko, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 6
Published: over 6 years ago

10.1128/mBio.00971-19

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages
Cited by: 48
Author(s): Travis N. Mavrich, Graham F. Hatfull
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0250725

Parrotfish corallivory on stress-tolerant corals in the Anthropocene
Cited by: 7
Author(s): Víctor Huertas, Renato A. Morais, Roberta M. Bonaldo, David R. Bellwood
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmolb.2021.644620

Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers
Cited by: 24
Author(s): Rui Li, Yunhong Yin, Xiu-Li Ji, Xiao Liu, Jianping Li, Yi-Qing Qu
Software Mentions: 6
Published: about 5 years ago

10.3390/insects11080488

Arthropod Communities in Urban Agricultural Production Systems under Different Irrigation Sources in the Northern Region of Ghana
Cited by: 3
Author(s): Louis Amprako, Kathrin Stenchly, Martin Wiehle, G. Nyarko, Andreas Buerkert
Software Mentions: 6
Published: almost 6 years ago

10.7717/peerj.3349

Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae)
Cited by: 24
Author(s): Valentina Amore, Malva Isabel Medina Hernández, Luis M. Carrascal, Jorge M. Lobo
Software Mentions: 6
Published: about 9 years ago

10.1186/s40168-020-00809-w

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases
Cited by: 15
Author(s): Eden Zhang, L Thibaut, Aleks Terauds, Mark Raven, Mark M. Tanaka, Josie van Dorst, Sin Yin Wong, Sally Crane, Belinda C. Ferrari
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-015-1840-6

Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin
Cited by: 38
Author(s): Jamie Lee, Stephenie D. Prokopec, John D. Watson, Ren Sun, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 6
Published: almost 11 years ago

10.1128/mSystems.00232-18

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems
Cited by: 31
Author(s): Sara F. Paver, Daniel Muratore, Ryan J. Newton, Maureen L. Coleman
Software Mentions: 6
Published: over 7 years ago

10.1186/s12859-018-2344-6

Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data
Cited by: 32
Author(s): Simon Klau, Vindi Jurinović, Roman Hornung, Tobias Herold, Anne‐Laure Boulesteix
Software Mentions: 6
Published: almost 8 years ago

10.1186/s40168-019-0781-8

Metagenomic analysis reveals the microbiome and resistome in migratory birds
Cited by: 96
Author(s): Jintao Cao, Yongfei Hu, Fei Liu, Yanan Wang, Yuhai Bi, Na Lv, Jing Li, Baoli Zhu, George F. Gao
Software Mentions: 6
Published: over 6 years ago

10.3389/fnins.2018.00368

From ERPs to MVPA Using the Amsterdam Decoding and Modeling Toolbox (ADAM)
Cited by: 94
Author(s): Johannes J. Fahrenfort, Joram van Driel, Simon van Gaal, Christian N. L. Olivers
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13071-015-1038-4

Malaria vectors in South America: current and future scenarios
Cited by: 53
Author(s): Gabriel Zorello Laporta, Yvonne‐Marie Linton, Richard C. Wilkerson, Eduardo Sterlino Bergo, Sandra Sayuri Nagaki, Denise Cristina Sant'Ana, Maria Anice Mureb Sallum
Software Mentions: 6
Published: almost 11 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: over 14 years ago

10.3389/fmolb.2020.00148

Friend or Foe: Prognostic and Immunotherapy Roles of BTLA in Colorectal Cancer
Cited by: 23
Author(s): Jingjing Song, Lihui Wu
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2017.02222

Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients
Cited by: 126
Author(s): Jing Wang, Yang Wang, Xu Zhang, Jiaqi Liu, Qianpeng Zhang, Yu Zhao, Jinghua Peng, Qin Feng, Jianye Dai, Shujun Sun, Yuwu Zhao, Liping Zhao, Yongyu Zhang, Yiyang Hu, Menghui Zhang
Software Mentions: 6
Published: over 8 years ago

10.7717/peerj.11972

The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation
Cited by: 6
Author(s): Samuel E. Georgian, Lance E. Morgan, Daniel Wagner
Software Mentions: 6
Published: almost 5 years ago

10.1007/s10616-020-00384-w

Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR
Cited by: 1
Author(s): Aziza A. A. Adam, Aldo Jongejan, Perry D. Moerland, Vincent A. van der Mark, Ronald P.J. Oude Elferink, R. A. F. M. Chamuleau, Ruurdtje Hoekstra
Software Mentions: 6
Published: over 6 years ago

10.1111/mec.14123

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (<i>Dactylorhiza</i>) with distinct ecological optima
Cited by: 22
Author(s): Francisco Balao, Emiliano Trucchi, Thomas M. Wolfe, Bao Hai Hao, María Teresa Cáceres Lorenzo, Juliane Baar, Laura Sedman, Carolin Kosiol, Fabian Amman, Mark W. Chase, Mikael Hedrén, Ovidiu Paun
Software Mentions: 6
Published: about 9 years ago

10.1002/ece3.7129

A new approach to assessing the space use behavior of macroinvertebrates by automated video tracking
Cited by: 9
Author(s): Milad Shokri, Francesco Cozzoli, Mario Ciotti, Vojsava Gjoni, Vanessa Marrocco, Fabio Vignes, Alberto Basset
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: over 7 years ago

10.3390/jpm11060448

Stromal Heterogeneity in the Human Proliferative Endometrium—A Single-Cell RNA Sequencing Study
Cited by: 22
Author(s): Suzanna Queckbörner, Carolina von Grothusen, Nageswara Rao Boggavarapu, Roy Mathew Francis, Lindsay C. Davies, Kristina Gemzell‐Danielsson
Software Mentions: 6
Published: about 5 years ago

10.1186/s13024-017-0219-3

Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease
Cited by: 92
Author(s): Andrew McKenzie, Sarah Moyon, Minghui Wang, Igor Katsyv, Won Min Song, Xianxiao Zhou, Eric B. Dammer, Duc M. Duong, Joshua D. Aaker, Yang Zhao, Noam D. Beckmann, Pei Wang, Jun Zhu, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Brian Popko, Patrizia Casaccia, Bin Zhang
Software Mentions: 6
Published: over 8 years ago

10.1186/s12864-020-6684-z

Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines
Cited by: 7
Author(s): Ethel J. S. Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur, James Adjaye
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: almost 9 years ago

10.3389/fonc.2019.00692

Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia
Cited by: 16
Author(s): Subha Saha, Krushna Chandra Murmu, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta, Punit Prasad
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-016-3020-8

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Cited by: 27
Author(s): Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle R. Campbell, Frances M. Van Dolah
Software Mentions: 6
Published: almost 10 years ago

10.3390/cancers13102496

Differential Prognosis and Response of Denovo vs. Secondary Muscle-Invasive Bladder Cancer: An Updated Systematic Review and Meta-Analysis
Cited by: 8
Author(s): Matthias Pones, David D’Andrea, Keiichiro Mori, Mohammad Abufraj, Marco Moschini, Éva Compérat, Shahrokh F. Shariat
Software Mentions: 6
Published: about 5 years ago

10.3390/genes12050665

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
Cited by: 6
Author(s): Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0179092

Inter-rater reliability of categorical versus continuous scoring of fish vitality: Does it affect the utility of the reflex action mortality predictor (RAMP) approach?
Cited by: 12
Author(s): Pieter Meeremans, Noëlle Yochum, Marc Kochzius, Bart Ampe, Frank Tuyttens, Sven Sebastian Uhlmann
Software Mentions: 6
Published: almost 9 years ago

10.1186/1471-2105-14-7

GSVA: gene set variation analysis for microarray and RNA-Seq data
Cited by: 6,480
Author(s): Sonja Hänzelmann, Robert Castelo, Justin Guinney
Software Mentions: 6
Published: over 13 years ago

10.3389/fpls.2019.01184

Ramf: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi
Cited by: 2
Author(s): Marco Chiapello, Debatosh Das, Caroline Gutjahr
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41420-021-00567-0

Single-cell RNA-seq reveals cellular heterogeneity of mouse carotid artery under disturbed flow
Cited by: 22
Author(s): Fengchan Li, Kunmin Yan, Lili Wu, Zhong Zheng, Yinan Du, Ziting Liu, Luyao Zhao, Wei Li, Yulan Sheng, Luping Ren, Chaojun Tang, Li Zhu
Software Mentions: 6
Published: almost 5 years ago

10.18632/oncotarget.10962

Epigenetic reprogramming and aberrant expression of PRAME are associated with increased metastatic risk in Class 1 and Class 2 uveal melanomas
Cited by: 85
Author(s): Matthew G. Field, Michael A. Durante, Christina L. Decatur, Berçin Tarlan, Kristen M. Oelschlager, John F. Stone, Jeffim N. Kuznetsov, Anne M. Bowcock, Stefan Kurtenbach, J. William Harbour
Software Mentions: 6
Published: almost 10 years ago

10.3389/fninf.2013.00044

An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook
Cited by: 19
Author(s): Jean-Luc Stevens, Marco Elver, James A. Bednar
Software Mentions: 6
Published: over 13 years ago

10.1051/parasite/2019028

Studies of Laboulbeniales on<i>Myrmica</i>ants (IV): host-related diversity and thallus distribution patterns of<i>Rickia wasmannii</i>
Cited by: 8
Author(s): Danny Haelewaters, P. J. den. Boer, Ferenc Báthori, Zoltán Rádai, Ana Sofía P.S. Reboleira, András Tartally, Walter P. Pfliegler, André De Kesel, Oldřich Nedvěd
Software Mentions: 6
Published: over 7 years ago

10.1107/S160057752100521X

Tools for supporting solution scattering during the COVID-19 pandemic
Cited by: 8
Author(s): Lin Yang, Edwin Lazo, James R. Byrnes, Shirish Chodankar, Stephen Antonelli, Maksim Rakitin
Software Mentions: 6
Published: about 5 years ago

10.1186/1471-2105-13-102

Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: about 14 years ago

10.1002/ece3.3142

Plant diversity has contrasting effects on herbivore and parasitoid abundance in <i>Centaurea jacea</i> flower heads
Cited by: 10
Author(s): Norma Nitschke, Eric Allan, H. Zwölfer, Lysett Wagner, Sylvia Creutzburg, Hannes Baur, Stefan Schmidt, Wolfgang W. Weisser
Software Mentions: 6
Published: over 8 years ago

10.3390/insects11080517

The Gut–Brain–Microbiome Axis in Bumble Bees
Cited by: 8
Author(s): Laura Leger, Quinn S. McFrederick
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12882-019-1442-7

Ambulatory monitoring unmasks hypertension among kidney transplant patients: single center experience and review of the literature
Cited by: 6
Author(s): Eitan Gluskin, Keren Tzukert, Irit Mor‐Yosef Levi, Olga Gotsman, Itamar Sagiv, Roy Abel, Aharon Bloch, Dvorah Rubinger, Michal Aharon, Michal Dranitzki Elhalel, Iddo Z. Ben‐Dov
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13100-019-0156-5

Subtype classification and functional annotation of L1Md retrotransposon promoters
Cited by: 15
Author(s): Meng Zhou, Andrew D. Smith
Software Mentions: 6
Published: about 7 years ago

10.1186/s12859-020-03544-z

Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform
Cited by: 3
Author(s): Yijia Zhao, Yifan Zhou, Yuan Liu, Yinyi Hao, Menglong Li, Xuemei Pu, Chuan Li, Zhining Wen
Software Mentions: 6
Published: about 6 years ago

10.3390/genes11121500

Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis
Cited by: 7
Author(s): Panqiao Wang, Xiaqing Yu, Zhanguo Zhu, Yufei Zhai, Qinzheng Zhao, Meng Yang, Ji Li, Qunfeng Lou, Jinfeng Chen
Software Mentions: 6
Published: over 5 years ago

10.1186/s40168-021-01070-5

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission
Cited by: 4
Author(s): Giovanni Bacci, Alessio Mengoni, Giovanni Emiliani, Carolina Chiellini, Edoardo Giovanni Cipriani, Giovanna Bianconi, Francesco Canganella, Renato Fani
Software Mentions: 6
Published: about 5 years ago

10.1111/hex.13227

Shortening and validation of the Patient Engagement In Research Scale (PEIRS) for measuring meaningful patient and family caregiver engagement
Cited by: 16
Author(s): Clayon B. Hamilton, Alison M. Hoens, Annette McKinnon, Shanon McQuitty, Kelly English, Lisa D. Hawke, Linda Li
Software Mentions: 6
Published: over 5 years ago

10.1155/2020/8182358

Two Gene Set Variation Index as Biomarker of Bacterial and Fungal Sepsis
Cited by: 4
Author(s): Xiaowen Zheng, Yifeng Luo, Qian Li, Jihua Feng, Chunling Zhao, Junyu Lu, Jiefeng Luo, Jianfeng Zhang
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: over 8 years ago

10.1186/s13058-020-01350-2

Prognostic value of 18F-FDG PET and PET/CT for assessment of treatment response to neoadjuvant chemotherapy in breast cancer: a systematic review and meta-analysis
Cited by: 19
Author(s): Sangwon Han, Ju Young Choi
Software Mentions: 6
Published: over 5 years ago

10.3390/biomedicines9091192

Self-Organization Provides Cell Fate Commitment in MSC Sheet Condensed Areas via ROCK-Dependent Mechanism
Cited by: 3
Author(s): Peter Nimiritsky, Ekaterina Novoseletskaya, Roman Eremichev, Natalya Alexandrushkina, Maxim Karagyaur, O. V. Vetrovoy, Nataliya Basalova, А. М. Хрусталева, Alexander Tyakht, Anastasia Efimenko, В. А. Ткачук
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13073-016-0302-3

An adaptive association test for microbiome data
Cited by: 63
Author(s): Chong Wu, Jun Chen, Junghi Kim, Wei Pan
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pone.0219986

Year-round distribution, activity patterns and habitat use of a poorly studied pelagic seabird, the fluttering shearwater Puffinus gavia
Cited by: 5
Author(s): Martin Berg, Jannie Fries Linnebjerg, Graeme A. Taylor, Stefanie M. H. Ismar-Rebitz, Mike Bell, Chris P. Gaskin, Susanne Åkesson, Matt J. Rayner
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-017-3568-y

Conserved expression of transposon-derived non-coding transcripts in primate stem cells
Cited by: 41
Author(s): LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage, Guillaume Bourque
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-020-79246-6

Dominance style only partially predicts differences in neophobia and social tolerance over food in four macaque species
Cited by: 14
Author(s): Federica Amici, Anja Widdig, Andrew J. J. MacIntosh, Víctor Beltrán Francés, Alba Castellano-Navarro, Álvaro López Caicoya, Karimullah Karimullah, Risma Illa Maulany, Putu Oka Ngakan, Andi Siady Hamzah, Bonaventura Majolo
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008372

Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game
Cited by: 13
Author(s): Joseph M Barnby, Vaughan Bell, Mitul A. Mehta, Michael Moutoussis
Software Mentions: 6
Published: over 5 years ago

10.3390/ani11072144

Personality and Cognitive Profiles of Animal-Assisted Intervention Dogs and Pet Dogs in an Unsolvable Task
Cited by: 1
Author(s): Patrizia Piotti, M. Albertini, Lidia Pia Trabucco, Lucia Ripari, Christos Karagiannis, Claudio Bandi, Federica Pirrone
Software Mentions: 6
Published: almost 5 years ago

10.1098/rspb.2016.2872

Stable producer–scrounger dynamics in wild birds: sociability and learning speed covary with scrounging behaviour
Cited by: 28
Author(s): Lucy M. Aplin, Julie Morand‐Ferron
Software Mentions: 6
Published: about 9 years ago

10.1111/cns.13701

Establishment of a nomogram with EMP3 for predicting clinical outcomes in patients with glioma: A bi‐center study
Cited by: 5
Author(s): Anke Zhang, Houshi Xu, Zeyu Zhang, Yibo Liu, Xiaying Han, Ling Yuan, Yunjia Ni, Shiqi Gao, Yuanzhi Xu, Sheng Chen, Junkun Jiang, Yike Chen, Xiaotao Zhang, Meiqing Lou, Jianmin Zhang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2019.02887

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient
Cited by: 13
Author(s): Emily C. Farrer, Dorota L. Porazinska, Marko J. Spasojevic, Andrew J. King, Clifton P. Bueno de Mesquita, Samuel A. Sartwell, J. A. Smith, C. T. White, Steven K. Schmidt, Katharine N. Suding
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-021-84995-z

Genetic co-expression networks contribute to creating predictive model and exploring novel biomarkers for the prognosis of breast cancer
Cited by: 1
Author(s): Yuan-Kuei Li, Huan-Ming Hsu, Meng-Chiung Lin, Chi‐Wen Chang, Chi‐Ming Chu, Yu‐Jia Chang, Jyh‐Cherng Yu, Chien-Ting Chen, Chen-En Jian, Chien‐An Sun, Kanghua Chen, Ming-Hao Kuo, Chia-Shiang Cheng, Ya-Ting Chang, Yi-Syuan Wu, Hao-Yi Wu, Yating Yang, Chen Lin, Hung‐Che Lin, Je-Ming Hu, Yu-Tien Chang
Software Mentions: 6
Published: over 5 years ago

10.3389/fbioe.2021.612893

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering
Cited by: 4
Author(s): Somtirtha Roy, Tijana Radivojević, Mark Forrer, Jose Manuel Martí, Vamshi Jonnalagadda, Tyler W. H. Backman, William Morrell, Hector Plahar, Joonhoon Kim, Nathan J. Hillson, Héctor García Martín
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-87143-9

Stock delineation of striped snakehead, Channa striata using multivariate generalised linear models with otolith shape and chemistry data
Cited by: 3
Author(s): Sanaullah Khan, Hayden T. Schilling, Mohammad Afzal Khan, Devendra Kumar Patel, Ben Maslen, Kaish Miyan
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.12135

Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics
Cited by: 9
Author(s): Ashley K. Coons, Kathrin Busch, Mark Lenz, Ute Hentschel, Erik Borchert
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13072-021-00411-w

Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
Cited by: 4
Author(s): Arkadiy K. Golov, Anastasia V. Golova, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 6
Published: almost 5 years ago

10.3390/molecules25061442

Discrimination of Gentiana and Its Related Species Using IR Spectroscopy Combined with Feature Selection and Stacked Generalization
Cited by: 26
Author(s): Tao Shen, Hong Yu, Yuanzhong Wang
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-019-44370-5

Rensch’s rule in avian lice: contradictory allometric trends for sexual size dimorphism
Cited by: 6
Author(s): Imre Sándor Piross, Andrea Harnos, Lajos Rózsa
Software Mentions: 6
Published: about 7 years ago