10.1371/journal.pgen.1000832

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Cited by: 238
Author(s): Michael J. Clark, Nils Homer, Brian D. O’Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson
Software Mentions: 4
Published: over 16 years ago

10.1002/ece3.5066

Environmental and demographic drivers of male mating success vary across sequential reproductive episodes in a polygynous breeder
Cited by: 3
Author(s): Jeffrey A. Manning, Philip D. McLoughlin
Software Mentions: 4
Published: over 7 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: about 10 years ago

10.1002/cbic.202000509

Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein
Cited by: 3
Author(s): Simon Hoffmann, Tobias M. E. Terhorst, Rohit Singh, Daniel Kümmel, Shmuel Pietrokovski, Henning D. Mootz
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1009107

Mycolactone toxin induces an inflammatory response by targeting the IL-1β pathway: Mechanistic insight into Buruli ulcer pathophysiology
Cited by: 23
Author(s): Mélanie Foulon, Marie Robbe-Saule, Jérémy Manry, Lucille Esnault, Yan Boucaud, Alexandre Alcaïs, Marine Malloci, Martine Fanton d’Andon, Tiffany Beauvais, Nathalie Labarrière, Pascale Jeannin, Laurent Abel, Jean‐Paul Saint‐André, Anne Croué, Yves Delneste, Ivo Gomperts Boneca, Laurent Marsollier, Estelle Marion
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-70353-y

Single-cell RNA sequencing uncovers heterogenous transcriptional signatures in macrophages during efferocytosis
Cited by: 43
Author(s): Connor Lantz, Behram Radmanesh, Esther Liu, Edward B. Thorp, Jennie Lin
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.667566

Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis
Cited by: 6
Author(s): Yendi E. Navarro‐Noya, Nina Montoya‐Ciriaco, Ligia Catalina Muñoz-Arenas, Stephanie Hereira-Pacheco, Arturo Estrada–Torres, Luc Dendooven
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21020440

Anisotropic Platinum Nanoparticle-Induced Cytotoxicity, Apoptosis, Inflammatory Response, and Transcriptomic and Molecular Pathways in Human Acute Monocytic Leukemia Cells
Cited by: 24
Author(s): Sangiliyandi Gurunathan, M. Jeyaraj, Hyeonwoo La, Hyunjin Yoo, Youngsok Choi, Jeong Tae, Chankyu Park, Jin‐Hoi Kim, Kwonho Hong
Software Mentions: 4
Published: over 6 years ago

10.1186/s12967-020-02327-7

Identification of hub genes in papillary thyroid carcinoma: robust rank aggregation and weighted gene co-expression network analysis
Cited by: 15
Author(s): Yang Liu, Ting‐Yu Chen, Zhi-Yan Yang, Wei Bin Fang, Qian Wu, Zhang Chao
Software Mentions: 4
Published: over 6 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

10.1038/s41598-020-61394-4

Janzen-Connell effects shape gene flow patterns and realized fitness in the tropical dioecious tree Spondias purpurea (ANACARDIACEAE)
Cited by: 7
Author(s): E. Jacob Cristóbal‐Pérez, Eric J. Fuchs, Ulises Olivares-Pinto, Maurício Quesada
Software Mentions: 4
Published: over 6 years ago

10.3390/ani11051336

Use of the Milan Pet Quality of Life Instrument (MPQL) to Measure Pets’ Quality of Life during COVID-19
Cited by: 14
Author(s): Patrizia Piotti, Christos Karagiannis, Liam Satchell, M. Michelazzi, M. Albertini, Enrico Alleva, Federica Pirrone
Software Mentions: 4
Published: about 5 years ago

10.1186/s12909-015-0358-6

Developing a clinical teaching quality questionnaire for use in a university osteopathic pre-registration teaching program
Cited by: 12
Author(s): Brett Vaughan
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-017-4186-4

The gene SMART study: method, study design, and preliminary findings
Cited by: 45
Author(s): Xu Yan, Nir Eynon, Ioannis Papadimitriou, Jujiao Kuang, Fiona Munson, Oren Tirosh, Lannie O’Keefe, Lyn R. Griffiths, Kevin J. Ashton, Nuala M. Byrne, Yannis Pitsiladis, David Bishop
Software Mentions: 4
Published: over 8 years ago

10.3390/ijerph17082964

The Association of Work Satisfaction and Burnout Risk in Endoscopy Nursing Staff—A Cross-Sectional Study Using Canonical Correlation Analysis
Cited by: 12
Author(s): Charles Christian Adarkwah, Oliver Hirsch
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22020574

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: over 5 years ago

10.1186/s13568-019-0747-z

Dietary supplementation with fermented Mao-tai lees beneficially affects gut microbiota structure and function in pigs
Cited by: 18
Author(s): Huan Li, Huawei Li, Peifeng Xie, Zhihua Li, Yulong Yin, François Blachier, Xiangfeng Kong
Software Mentions: 4
Published: over 7 years ago

10.1099/mgen.0.000426

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings
Cited by: 4
Author(s): Benjamin J. Perry, John T. Sullivan, Elena Colombi, Riley Murphy, Joshua P. Ramsay, Clive W. Ronson
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21082966

Differential Expression and Function of Bicellular Tight Junctions in Skin and Oral Wound Healing
Cited by: 20
Author(s): Trevor R. Leonardo, Junhe Shi, Dandan Chen, Harsh M. Trivedi, Lin Chen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-66199-z

Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men
Cited by: 17
Author(s): Aidin Rawshani, Björn Eliasson, Araz Rawshani, Josefin Henninger, Adil Mardinoğlu, Åsa Carlsson, Maja Sohlin, Maria Ljungberg, Ann Hammarstedt, Annika Rosengren, Ulf Smith
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-020-06789-3

Distinctions between sex and time in patterns of DNA methylation across puberty
Cited by: 11
Author(s): Sarah R. Moore, Kathryn L. Humphreys, Natalie L. Colich, Elena Goetz Davis, David Lin, Julia L. MacIsaac, Michæl S. Kobor, Ian H. Gotlib
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2021.609048

kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets
Cited by: 8
Author(s): Elies Ramon, Lluís A. Belanche-Muñoz, F. Molist, Raquel Quintanilla, Miguel Pérez‐Enciso, Yuliaxis Ramayo-Caldas
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-1716-9

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system
Cited by: 66
Author(s): Rodrigo Pulgar, Christian Hödar, Dante Travisany, Alejandro Zúñiga, Cristina Ruesca Domínguez, Alejandro Maass, Maurício González, Verónica Cambiazo
Software Mentions: 4
Published: about 11 years ago

10.3389/fmicb.2019.02558

Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments
Cited by: 14
Author(s): Claus Pelikan, Marion Jaussi, Kenneth Wasmund, Marit‐Solveig Seidenkrantz, Christof Pearce, Zou Zou A. Kuzyk, Craig W. Herbold, Hans Røy, Kasper Urup Kjeldsen, Alexander Loy
Software Mentions: 4
Published: over 6 years ago

10.1128/AEM.02658-18

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
Cited by: 5
Author(s): Urse Scheel Krüger, Arnaud Dechesne, Friedhelm Bak, Nora Badawi, Ole Nybroe, Jens Aamand
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2019.01057

Prognostic Value of Texture Analysis Based on Pretreatment DWI-Weighted MRI for Esophageal Squamous Cell Carcinoma Patients Treated With Concurrent Chemo-Radiotherapy
Cited by: 8
Author(s): Zhenjiang Li, Chun Han, Lan Wang, Jian Zhu, Yong Yin, Baosheng Li
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0062439

Novel Algorithm for Non-Invasive Assessment of Fibrosis in NAFLD
Cited by: 50
Author(s): Jan-Peter Sowa, Dominik Heider, Lars P. Bechmann, Guido Gerken, Daniel Hoffmann, Ali Canbay
Software Mentions: 4
Published: about 13 years ago

10.3390/jcm9113405

Executive Functions Are Associated with Fall Risk but not Balance in Chronic Cerebrovascular Disease
Cited by: 7
Author(s): Cosimo Tuena, Valentina Mancuso, Ilaria Maria Antonietta Benzi, Pietro Cipresso, Alice Chirico, Karine Goulene, Giuseppe Riva, Marco Stramba-Badiale, Elisa Pedroli
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2407-14-739

MicroRNA expression as risk biomarker of breast cancer metastasis: a pilot retrospective case-cohort study
Cited by: 42
Author(s): Augusto L F Marino, Adriane Feijó Evangelista, René Aloísio da Costa Vieira, Taciane Macedo, Lígia Maria Kerr, Lucas Faria Abrahão-Machado, Adhemar Longatto‐Filho, Henrique C. S. Silveira, Márcia Maria Chiquitelli Marques
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0244495

Assessment of fishery resources using environmental DNA: Small yellow croaker (Larimichthys polyactis) in East China Sea
Cited by: 10
Author(s): Xiaoyan Wang, Guoqing Lu, Linlin Zhao, Qiao Yang, Tianxiang Gao
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-213X-13-13

miRNA regulated pathways in late stage murine lung development
Cited by: 47
Author(s): Sana Mujahid, Tanya Logvinenko, MaryAnn V. Volpe, Heber C. Nielsen
Software Mentions: 4
Published: about 13 years ago

10.1186/s12986-020-00538-9

Combined Lycium barbarum polysaccharides and C-phycocyanin increase gastric Bifidobacterium relative abundance and protect against gastric ulcer caused by aspirin in rats
Cited by: 14
Author(s): Shu-Yu Hsieh, Yu Lian, I‐Hsuan Lin, Yuxing Yang, Alexey A. Tinkov, Anatoly V. Skalny, Jane C.-J. Chao
Software Mentions: 4
Published: over 5 years ago

10.1038/srep38046

THD-Module Extractor: An Application for CEN Module Extraction and Interesting Gene Identification for Alzheimer’s Disease
Cited by: 10
Author(s): Tulika Kakati, Hirak J. Kashyap, Dhruba K. Bhattacharyya
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-28550-3

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas
Cited by: 92
Author(s): Bhabatosh Das, Tarini Shankar Ghosh, Saurabh Kedia, Ritika Rampal, Shruti Saxena, Satyabrata Bag, Ridhima Mitra, Mayanka Dayal, Ojasvi Mehta, Adarsh Surendranath, Simon Travis, Prabhanshu Tripathi, G. Balakrish Nair, Vineet Ahuja
Software Mentions: 4
Published: about 8 years ago

10.3389/fphys.2021.668645

A Holistic Assessment of Polyethylene Fiber Ingestion in Larval and Juvenile Japanese Medaka Fish
Cited by: 4
Author(s): Elizabeth DiBona, Lee J. Pinnell, Annika Heising-Huang, Simon Joscha Geist, John Turner, Frauke Seemann
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2105-12-390

Classification of microarrays; synergistic effects between normalization, gene selection and machine learning
Cited by: 28
Author(s): Jenny Önskog, Eva Freyhult, Mattias Landfors, Patrik Rydén, Torgeir R. Hvidsten
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-11-23

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development
Cited by: 37
Author(s): Wen Huang, Brian S. Yandell, Hasan Khatib
Software Mentions: 4
Published: over 16 years ago

10.3390/cancers12061431

Characterization of a Myeloid Activation Signature That Correlates with Survival in Melanoma Patients
Cited by: 1
Author(s): Mirela Kremenovic, Nives Rombini, Alfred A. Chan, Thomas Gruber, Lukas Bäriswyl, Delphine J. Lee, Mirjam Schenk
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-15-1179

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Cited by: 34
Author(s): Kate J. Howell, Lucy A. Weinert, Roy R. Chaudhuri, Shi-Lu Luan, Sarah Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragón, Albert Bensaid, Susanna Williamson, Julian Parkhill, Paul R. Langford, Andrew N. Rycroft, Brendan W. Wren, Matthew T. G. Holden, Alexander W. Tucker, Duncan J. Maskell
Software Mentions: 4
Published: over 12 years ago

10.3390/ijms22063079

A Novel Position-Specific Encoding Algorithm (SeqPose) of Nucleotide Sequences and Its Application for Detecting Enhancers
Cited by: 7
Author(s): Xuechen Mu, Yueying Wang, Meiyu Duan, Shuai Liu, Fēi Li, Xiuli Wang, Kai Zhang, Lan Huang, Fengfeng Zhou
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.652601

Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
Cited by: 8
Author(s): Xiong Guo, Xiaolong Liang, Yujun Wang, Anqi Cheng, Chuan Qin, Han Zhang, Ziwei Wang
Software Mentions: 4
Published: about 5 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

10.3389/fmicb.2017.02550

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces
Cited by: 20
Author(s): Marion Pohlner, Julius Degenhardt, Avril Jean Elisabeth von Hoyningen-Huene, Bernd Wemheuer, Nora Erlmann, Bernhard Schnetger, Thomas H. Badewien, Bert Engelen
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2020.01305

Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions
Cited by: 21
Author(s): Stefanos Banos, Deisy Morselli Gysi, Tim Richter-Heitmann, Frank Oliver Glöckner, Maarten Boersma, Karen Helen Wiltshire, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 4
Published: about 6 years ago

10.1093/conphys/coaa040

A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders
Cited by: 3
Author(s): Erin K. Kenison, Obed Hernández‐Gómez, Rod N. Williams
Software Mentions: 4
Published: over 6 years ago

10.3390/s21051794

Multi-U-Net: Residual Module under Multisensory Field and Attention Mechanism Based Optimized U-Net for VHR Image Semantic Segmentation
Cited by: 6
Author(s): Si Ran, Jianli Ding, Bohua Liu, Xiangyu Ge, Guolin Ma
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.8168

Resident microbes of lactation rooms and daycares
Cited by: 1
Author(s): Diana H. Taft, Samir Akre, Nicolas Madrid, A. Knoesen, David A. Mills, Zachery T. Lewis
Software Mentions: 4
Published: over 6 years ago

10.3390/s21030761

Detection-Based Object Tracking Applied to Remote Ship Inspection
Cited by: 12
Author(s): Jing Xie, Erik Stensrud, Torbjørn Skramstad
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-021-02438-4

CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Cited by: 6
Author(s): Yongjin Park, M Kellis
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-017-0337-8

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis
Cited by: 22
Author(s): Antonios Michas, Gisle Vestergaard, Kathleen Trautwein, Pavlos Avramidis, Dimitris G. Hatzinikolaou, Constantinos E. Vorgias, Heinz Wilkes, Ralf Rabus, Michael Schloter, Anne Schöler
Software Mentions: 4
Published: almost 9 years ago

10.3390/s20164481

A Deep-Learning Approach for Foot-Type Classification Using Heterogeneous Pressure Data
Cited by: 10
Author(s): Jonghyeok Chae, Young-Jin Kang, Yoojeong Noh
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-018-2512-8

A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data
Cited by: 9
Author(s): A. M. C. Chan, Amy L. Williams, Jean‐Luc Jannink
Software Mentions: 4
Published: over 7 years ago

10.1128/mBio.02500-18

Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides
Cited by: 8
Author(s): Andrew Hesketh, Marta Vergnano, Stephen G. Oliver
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-60981-9

NBIA: a network-based integrative analysis framework – applied to pathway analysis
Cited by: 7
Author(s): Tin Nguyen, Adib Shafi, Tuan-Minh Nguyen, A. Grant Schissler, Sorin Drăghici
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02878

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea
Cited by: 51
Author(s): Kosuke Yamamoto, Yuh Shiwa, Taichiro Ishige, Hikaru Sakamoto, Keisuke Tanaka, Makoto Uchino, Naoto Tanaka, Suguru Oguri, Hiromasa Saitoh, Seiya Tsushima
Software Mentions: 4
Published: over 7 years ago

10.1534/genetics.119.302089

<i>beditor</i>: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing
Cited by: 32
Author(s): Rohan Dandage, Philippe Després, Nozomu Yachie, Christian R. Landry
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2019.00599

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs
Cited by: 11
Author(s): Benjamin Zwirzitz, Beate Pinior, Barbara U. Metzler‐Zebeli, Monika Handler, Kristina Gense, Christian Knecht, Andrea Ladinig, Monika Dzieciol, Stefanie U. Wetzels, Martin Wagner, Stephan Schmitz‐Esser, Evelyne Mann
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.ppat.1008401

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
Cited by: 35
Author(s): Jérémie Bazin, Kadarkaraisamy Mariappan, Yunhe Jiang, Thomas Blein, Ronny Völz, Martín Crespi, Heribert Hirt
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-36293-4

Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR
Cited by: 71
Author(s): P Heinrich, Christian Köhler, Lisa Ellmann, Paul Kuerner, Rainer Spang, Peter J. Oefner, Katja Dettmer
Software Mentions: 4
Published: over 7 years ago

10.1186/s12879-020-05464-y

Risk factors associated with infection of blood-borne virus among people who used methamphetamine
Cited by: 17
Author(s): Yilin Cai, Zheng Dai, Sijin Wen, Ruchi Bhandari
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-020-02392-6

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
Cited by: 37
Author(s): Colin Kruse, Alexander Meyers, Proma Basu, Sarahann Hutchinson, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-020-03632-0

Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data
Cited by: 9
Author(s): Avi Kumar, Jack Mitchener, Zachary A. King, Christian M. Metallo
Software Mentions: 4
Published: about 6 years ago

10.1007/s00248-021-01700-3

Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity
Cited by: 9
Author(s): Florian Caillon, Katharina Besemer, Peter Peduzzi, Jakob Schelker
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2018.00588

Applying a Global Sensitivity Analysis Workflow to Improve the Computational Efficiencies in Physiologically-Based Pharmacokinetic Modeling
Cited by: 51
Author(s): Nan‐Hung Hsieh, Brad Reisfeld, Frédéric Bois, Weihsueh A. Chiu
Software Mentions: 4
Published: about 8 years ago

10.1186/1752-0509-7-S5-S1

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Cited by: 68
Author(s): Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
Software Mentions: 4
Published: over 12 years ago

10.1016/j.ejps.2011.10.026

Model-based global sensitivity analysis as applied to identification of anti-cancer drug targets and biomarkers of drug resistance in the ErbB2/3 network
Cited by: 33
Author(s): Galina Lebedeva, Anatoly Sorokin, Dana Faratian, Peter Mullen, Alexey Goltsov, Simon P. Langdon, David J. Harrison, Igor Goryanin
Software Mentions: 4
Published: about 14 years ago

10.3390/ijms21207648

Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein–Inhibitor Complexes in Relevance to Developing Parkinson’s Therapeutics
Cited by: 8
Author(s): Natarajan Arul Murugan, Charuvaka Muvva, Chitra Jeyarajpandian, Jeyaraman Jeyakanthan, V. Subramanian
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.1487

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Cited by: 224
Author(s): Sarah L. Westcott, Patrick D. Schloss
Software Mentions: 4
Published: over 10 years ago

10.3897/BDJ.7.e31817

A benchmark dataset of herbarium specimen images with label data
Cited by: 23
Author(s): Mathias Dillen, Quentin Groom, Simon Chagnoux, Anton Güntsch, Alex Hardisty, Elspeth Haston, Laurence Livermore, Veljo Runnel, Leif Schulman, Luc Willemse, Zhipeng Wu, Sarah Phillips
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

10.1093/bib/bbw008

A benchmark of gene expression tissue-specificity metrics
Cited by: 231
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 4
Published: over 10 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/s12936-021-03918-5

Transcriptome-based analysis of blood samples reveals elevation of DNA damage response, neutrophil degranulation, cancer and neurodegenerative pathways in Plasmodium falciparum patients
Cited by: 1
Author(s): Akua A. Karikari, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-015-0133-2

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles
Cited by: 64
Author(s): Yasir Tarabichi, K. Li, Shishan Hu, Cam Nguyen, X. Wang, David Elashoff, Kazima Saira, Bryan Frank, Monika Bihan, Elodie Ghedin, Barbara A. Methé, Jane C. Deng
Software Mentions: 4
Published: over 10 years ago

10.3390/microorganisms8060940

Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum
Cited by: 3
Author(s): Jennifer Yuzon, Renaud Travadon, Mathu Malar C, Sucheta Tripathy, Nathan E. Rank, Heather K. Mehl, David M. Rizzo, Richard C. Cobb, Corinn Small, Tiffany Tang, Haley E. McCown, Matteo Garbelotto, Takao Kasuga
Software Mentions: 4
Published: about 6 years ago

10.3390/metabo9100210

Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy
Cited by: 41
Author(s): Hemalatha Babu, Maike Sperk, Anoop T. Ambikan, Gladys Rachel, Vinod Kumar Viswanathan, Srikanth Tripathy, Piotr Nowak, Luke Elizabeth Hanna, Ujjwal Neogi
Software Mentions: 4
Published: almost 7 years ago

10.3390/s21093239

Proposal of an Economy of Things Architecture and an Approach Comparing Cryptocurrencies
Cited by: 0
Author(s): Bruno Machado Agostinho, Mário A. R. Dantas, Alex Sandro Roschildt Pinto
Software Mentions: 4
Published: about 5 years ago

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: about 9 years ago

10.1155/2020/2123787

Identification of lncRNA and mRNA Biomarkers in Osteoarthritic Degenerative Meniscus by Weighted Gene Coexpression Network and Competing Endogenous RNA Network Analysis
Cited by: 4
Author(s): Jun Zhao, Yu Su, Jianfei Jiao, Zhengchun Wang, Xiangchun Fang, Xuefeng He, Xiaofeng Zhang, Zhao Liu, Xilin Xu
Software Mentions: 4
Published: about 6 years ago

10.3390/s19214724

The Advent of the Internet of Things in Airfield Lightning Systems: Paving the Way from a Legacy Environment to an Open World
Cited by: 2
Author(s): Enrico Buzzoni, Fabio Forlani, Carlo Giannelli, Matteo Mazzotti, Stefano Parisotto, Alessandro Pomponio, Cesare Stefanelli
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0001274

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Cited by: 88
Author(s): Sophia J. Parker-Manuel, Alasdair Ivens, G. Dillon, R. A. Wilson
Software Mentions: 4
Published: almost 15 years ago

10.1038/s41598-017-07975-2

Signs of innate immune activation and premature immunosenescence in psoriasis patients
Cited by: 30
Author(s): Liisi Šahmatova, Elena Sügis, Marina Šunina, Helen Hermann, Ele Prans, Maire Pihlap, Kristi Abram, Ana Rebane, Hedi Peterson, Pärt Peterson, Külli Kingo, Kai Kisand
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12859-019-2659-y

IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis
Cited by: 2
Author(s): Mohieddin Jafari, Payman Nickchi, Soheil Jahangiri, Abdollah Safari, Mehdi Mirzaie, Mohieddin Jafari
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-020-03729-6

Theoretical characterisation of strand cross-correlation in ChIP-seq
Cited by: 2
Author(s): Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0029021

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Cited by: 72
Author(s): Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antònia Navarro, Diana Monsivais, John S. Coon, Julie Kim, Yang Dai, Serdar E. Bulun
Software Mentions: 4
Published: over 14 years ago

10.3390/microorganisms8060842

Transcriptome Profiling of Toxoplasma gondii-Infected Human Cerebromicrovascular Endothelial Cell Response to Treatment with Monensin
Cited by: 5
Author(s): Mohammad Syamsul Reza Harun, Mica Taylor, Xing‐Quan Zhu, Hany M. Elsheikha
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0032394

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data
Cited by: 24
Author(s): Morten Hansen, Thomas Alexander Gerds, Ole Haagen Nielsen, Jakob Benedict Seidelin, Jesper T. Troelsen, Jørgen Olsen
Software Mentions: 4
Published: over 14 years ago

10.1093/bioinformatics/btaa919

ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data
Cited by: 3
Author(s): Johannes Smolander, Sini Junttila, Mikko S Venäläinen, Laura L. Elo
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms9071378

Effects of Wine and Its Microbial-Derived Metabolites on Intestinal Permeability Using Simulated Gastrointestinal Digestion/Colonic Fermentation and Caco-2 Intestinal Cell Models
Cited by: 11
Author(s): Irene Zorraquín‐Peña, Diego Taladrid, Alba Tamargo, Mariana Silva, Natalia Molinero, Dolores González de Llano, Begoňa Bartolomé, M. Victoria Moreno‐Arribas
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms22147266

Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Cited by: 12
Author(s): Weitao Li, Li Huang, Nian Liu, Manish K. Pandey, Yuning Chen, Cheng Ling, Jianbin Guo, Bin Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.578345

Integration of Online Omics-Data Resources for Cancer Research
Cited by: 43
Author(s): Tonmoy Das, Geoffroy Andrieux, Musaddeque Ahmed, Sajib Chakraborty
Software Mentions: 4
Published: over 5 years ago

10.1007/s00125-018-4612-4

Patterns of differential gene expression in a cellular model of human islet development, and relationship to type 2 diabetes predisposition
Cited by: 12
Author(s): Marta Perez-Alcantara, Christian Honoré, Agata Wesolowska-Andersen, Anna L. Gloyn, Mark I. McCarthy, Mattias Hansson, Nicola L. Beer, Martijn van de Bunt
Software Mentions: 4
Published: over 8 years ago

10.1093/bib/bbz121

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping
Cited by: 43
Author(s): Anita Sathyanarayanan, Rohit Gupta, Erik W. Thompson, Dale R. Nyholt, Denis C. Bauer, Shivashankar H. Nagaraj
Software Mentions: 4
Published: over 6 years ago

10.12688/wellcomeopenres.16164.2

The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study
Cited by: 28
Author(s): Trystan Leng, Connor White, Joe Hilton, Adam J. Kucharski, Lorenzo Pellis, Helena B. Stage, Nicholas Davies, Matthew James Keeling, Stefan Flasche
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0248635

Heterospecific pollination by an invasive congener threatens the native American bittersweet, Celastrus scandens
Cited by: 4
Author(s): David N. Zaya, Stacey A. Leicht‐Young, Noel B. Pavlovic, Mary V. Ashley
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.01084

Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1
Cited by: 27
Author(s): Jialian Xie, Shaojun Li, Chenmi Mo, Xiangyu Xiao, Deliang Peng, Gaofeng Wang, Yanan Xiao
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2105-16-S17-S10

SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data
Cited by: 3
Author(s): Chong Chu, Li X, Yufeng Wu
Software Mentions: 4
Published: over 10 years ago

10.1016/j.omto.2020.04.001

A Cross-Reactive Small Protein Binding Domain Provides a Model to Study Off-Tumor CAR-T Cell Toxicity
Cited by: 6
Author(s): Joanne A. Hammill, Jacek M. Kwiecień, Anna Dvorkin‐Gheva, Vivian Wing Chong Lau, Christopher L. Baker, Ying Wu, Ksenia Bezverbnaya, Craig Aarts, Christopher W. Heslen, Galina Denisova, Heather Derocher, Katy Milne, Brad H. Nelson, Jonathan L. Bramson
Software Mentions: 4
Published: about 6 years ago