10.1186/1471-2164-14-653

HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploids
Cited by: 9
Author(s): Aziz Mithani, Eric J. Belfield, C. Titus Brown, Caifu Jiang, Lindsey Leach, Nicholas P. Harberd
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0065324

To Clone or Not to Clone? Induced Pluripotent Stem Cells Can Be Generated in Bulk Culture
Cited by: 34
Author(s): Charlotte A. Willmann, Hatim Hemeda, Lisa A. Pieper, Michael Lenz, Jie Qin, Sylvia Joussen, Stephanie Sontag, Paul Wanek, Bernd Denecke, H Schüler, Martin Zenke, Wolfgang Wagner
Software Mentions: 2
Published: about 13 years ago

10.3389/fmicb.2018.02827

BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes
Cited by: 12
Author(s): Irina Garanina, Gleb Y. Fisunov, Vadim M. Govorun
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-5-203

Cited by: 94
Author(s): Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi‐Castagnoli
Software Mentions: 2
Published: over 22 years ago

10.3390/v9080226

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing
Cited by: 9
Author(s): Alison M. Morse, Kaitlyn R. Calabro, Justin M. Fear, David C. Bloom, Lauren McIntyre
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2017.01672

Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698
Cited by: 0
Author(s): Elena Ferrari, Mathias C. Walter, Christopher Huptas, Siegfried Scherer, Stefanie Müller-Herbst
Software Mentions: 2
Published: almost 9 years ago

10.1155/2008/892927

Bayesian Mixture Model Analysis for Detecting Differentially Expressed Genes
Cited by: 4
Author(s): Zhenyu Jia, Shizhong Xu
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-10-295

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus
Cited by: 20
Author(s): Christian Obermeier, Bashir Hosseini, W. Friedt, Rod J. Snowdon
Software Mentions: 2
Published: over 17 years ago

10.3389/fmicb.2020.591778

Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins
Cited by: 5
Author(s): Rishikesh Lotke, Ulrike Schneeweiß, Marcel Pietrek, Thomas Guenther, Adam Grundhoff, Magdalena Weidner-Glunde, Thomas F. Schulz
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2018.00882

Transcriptome Changes of Escherichia coli, Enterococcus faecalis, and Escherichia coli O157:H7 Laboratory Strains in Response to Photo-Degraded DOM
Cited by: 6
Author(s): Adelumola Oladeinde, Erin K. Lipp, Chiaying Chen, Richard W. Muirhead, Travis C. Glenn, Kyle DeMeo Cook, Marirosa Molina
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-11-388

Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients
Cited by: 8
Author(s): Tineke C. T. M. van der Pouw Kraan, Stephan H. Schirmer, Joost O. Fledderus, Perry D. Moerland, Josefien M. Baggen, Thomas A. Leyen, A.M. van der Laan, Jan J. Piek, Niels van Royen, Anton J.G. Horrevoets
Software Mentions: 2
Published: over 16 years ago

10.3389/fmolb.2021.724947

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction
Cited by: 16
Author(s): Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara
Software Mentions: 2
Published: almost 5 years ago

10.1155/2012/831460

SNP Discovery through Next-Generation Sequencing and Its Applications
Cited by: 211
Author(s): Santosh Kumar, Travis Banks, Sylvie Cloutier
Software Mentions: 2
Published: over 13 years ago

10.3389/fnmol.2021.651355

Single-Nucleus Chromatin Accessibility Landscape Reveals Diversity in Regulatory Regions Across Distinct Adult Rat Cortex
Cited by: 7
Author(s): Yeya Yu, Xiaoyü Wei, Qiuting Deng, Qing Lan, Yiping Guo, Lei Han, Yue Yuan, Peng Fan, Peng Wu, Shuncheng Shangguan, Yang Liu, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Chuanyu Liu, Yong Hou, Longqi Liu
Software Mentions: 2
Published: about 5 years ago

10.3389/fnmol.2018.00290

Salivary MicroRNAs: Diagnostic Markers of Mild Traumatic Brain Injury in Contact-Sport
Cited by: 68
Author(s): Valentina Di Pietro, Edoardo Porto, Marco Ragusa, Cristina Barbagallo, David Davies, Mario Forcione, Ann Logan, Cinzia Di Pietro, Michele Purrello, Michael J. Grey, Douglas Hammond, Vijay Sawlani, Aron K. Barbey, Antonio Belli
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2021.640054

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data
Cited by: 4
Author(s): Katerina Jureckova, Hana Raschmanová, Jan Kolek, Maryna Vasylkivska, Barbora Branská, Petra Patáková, Ivo Provazník, Karel Sedlář
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2017.00248

Translational Identification of Transcriptional Signatures of Major Depression and Antidepressant Response
Cited by: 26
Author(s): Mylène Hervé, Aurélie Bergon, Anne-Marie Le Guisquet, Samuel Leman, Julia-Lou Consoloni, Nicolas Fernandez-Nunez, Marie-Noëlle Lefebvre, Wissam El‐Hage, Raoul Belzeaux, Catherine Belzung, El Chérif Ibrahim
Software Mentions: 2
Published: almost 9 years ago

10.3389/fninf.2019.00066

Exploring EEG Effective Connectivity Network in Estimating Influence of Color on Emotion and Memory
Cited by: 25
Author(s): Meei Tyng Chai, Hafeez Ullah Amin, Lila Iznita Izhar, Mohamad Naufal Mohamad Saad, Mohammad Abdul Rahman, Aamir Saeed Malik, Tong Boon Tang
Software Mentions: 2
Published: almost 7 years ago

10.3390/v11040323

Interpreting Viral Deep Sequencing Data with GLUE
Cited by: 16
Author(s): Joshua B. Singer, Emma C. Thomson, Joseph Hughes, Elihu Aranday-Cortes, John McLauchlan, Ana da Silva Filipe, L. Tong, Carmen F. Manso, Robert J. Gifford, David L. Robertson, Eleanor Barnes, Azim Ansari, Jean L. Mbisa, David F. Bibby, Daniel Bradshaw, David A. Smith
Software Mentions: 2
Published: over 7 years ago

10.3390/v12040472

RSV Reprograms the CDK9•BRD4 Chromatin Remodeling Complex to Couple Innate Inflammation to Airway Remodeling
Cited by: 17
Author(s): Allan R. Brasier
Software Mentions: 2
Published: over 6 years ago

10.1186/s12862-015-0378-1

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)8 isomerase evolutionary intermediates from a diverse metagenome
Cited by: 16
Author(s): Lianet Noda‐Garcia, Ana Lilia Juárez-Vázquez, María C. Ávila-Arcos, E.A. Verduzco-Castro, Gabriela M. Montero-Morán, Paul Gaytán, Mauricio Carrillo‐Tripp, Francisco Barona‐Gómez
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0045506

Microarray Meta-Analysis Identifies Acute Lung Injury Biomarkers in Donor Lungs That Predict Development of Primary Graft Failure in Recipients
Cited by: 18
Author(s): Pingzhao Hu, Xinchen Wang, Jack J. Haitsma, Suleiman Furmli, Hussain Masoom, Mingyao Liu, Yumiko Imai, Arthur S. Slutsky, Joseph Beyene, Celia M.T. Greenwood, Claudia C. dos Santos
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-13-68

Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis
Cited by: 38
Author(s): Yang Wang, Chong Liu, Yīng Fāng, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen, Qigai He
Software Mentions: 2
Published: over 14 years ago

10.1186/2041-2223-5-9

Validation of high throughput sequencing and microbial forensics applications
Cited by: 56
Author(s): Bruce Budowle, Nancy Connell, Anna Bielecka-Oder, Rita R. Colwell, Cindi R. Corbett, Jacqueline Fletcher, Mats Forsman, Dana R Kadavy, Alemka Markotić, Stephen Morse, Randall S. Murch, Antti Sajantila, Sarah E. Schmedes, Krista Ternus, Stephen D. Turner, Samuel S. Minot
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-9-478

Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma
Cited by: 19
Author(s): Mary H. Estler, Goran Bošković, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0095481

Global Gene Expression Analysis of Canine Cutaneous Mast Cell Tumor: Could Molecular Profiling Be Useful for Subtype Classification and Prognostication?
Cited by: 21
Author(s): Mery Giantin, Anna Granato, Chiara Baratto, Laura Marconato, Marta Vascellari, Emanuela Morello, Alessandro Vercelli, Franco Mutinelli, Mauro Dacasto
Software Mentions: 2
Published: over 12 years ago

10.3389/fnins.2016.00601

Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies
Cited by: 62
Author(s): Ashley Ansel, Joshua P. Rosenzweig, Philip D. Zisman, Michal L. Melamed, Benjamin Gesundheit
Software Mentions: 2
Published: over 9 years ago

10.1186/1743-422X-10-279

Differential cellular gene expression in duck trachea infected with a highly or low pathogenic H5N1 avian influenza virus
Cited by: 5
Author(s): Pascale Massin, Claire Deléage, Aurélie Oger, François-Xavier Briand, Hélène Quenault, Yannick Blanchard
Software Mentions: 2
Published: almost 13 years ago

10.12688/wellcomeopenres.15603.1

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe
Cited by: 88
Author(s): Martin Hunt, Phelim Bradley, Simon Lapierre, S Heys, Mark Thomsit, Michael B. Hall, Kerri M. Malone, Penelope Wintringer, Timothy M Walker, Daniela María Cirillo, Iñaki Comas, Maha Farhat, Philip W. Fowler, Jennifer L. Gardy, Nazir Ismail, Thomas A. Kohl, Vanessa Mathys, Matthias Merker, Stefan Niemann, Shaheed V. Omar, Vitali Sintchenko, Grace Smith, Dick van Soolingen, Philip Supply, Sabira Tahseen, Mark H. Wilcox, Irena Arandjelović, Tim Peto, Derrick W. Crook, Zamin Iqbal
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2017.02394

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici
Cited by: 25
Author(s): Chongjing Xia, Meinan Wang, Omar E. Cornejo, Derick Jiwan, Deven R. See, Xianming Chen
Software Mentions: 2
Published: over 8 years ago

10.3389/fnins.2020.616802

A Sextuple Knockout Cell Line System to Study the Differential Roles of CRY, PER, and NR1D in the Transcription-Translation Feedback Loop of the Circadian Clock
Cited by: 4
Author(s): Yi Ying Chiou, Tzu-Ying Li, Yanyan Yang, Aziz Sancar
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0065571

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia
Cited by: 36
Author(s): Qiaojun Wen, Linda Y. Liu, Ting Yang, Cantas Alev, Shao-Yi Wu, David K. Stevenson, Guojun Sheng, Atul J. Butte, Xuefeng B. Ling
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0105920

A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans
Cited by: 22
Author(s): Jacobo Pardo‐Seco, Alberto Gómez‐Carballa, Jorge Amigo, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0041001

Transcriptome Profiling of the Cancer, Adjacent Non-Tumor and Distant Normal Tissues from a Colorectal Cancer Patient by Deep Sequencing
Cited by: 65
Author(s): Yanan Wu, Xuetao Wang, WU Fang-bo, Ruolei Huang, Fangqin Xue, Guantao Liang, Min Tao, Peng Cai, Yi Huang
Software Mentions: 2
Published: almost 14 years ago

10.1186/1743-422X-5-150

Evolutionary and structural analyses of alpha-papillomavirus capsid proteins yields novel insights into L2 structure and interaction with L1
Cited by: 32
Author(s): John J. Lowe, Debasis Panda, Suzanne Rose, Ty Jensen, Willie A. Hughes, For Yue Tso, Peter C. Angeletti
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2105-9-214

M-BISON: Microarray-based integration of data sources using networks
Cited by: 9
Author(s): Bernie J. Daigle, Russ B. Altman
Software Mentions: 2
Published: over 18 years ago

10.3389/fnins.2020.580970

Expected Valence Predicts Choice in a Recurrent Decision Task
Cited by: 1
Author(s): Daniel Thomas Jäger, Melanie Boltzmann, Jens D. Rollnik, Jascha Rüsseler
Software Mentions: 2
Published: over 5 years ago

10.1186/1743-422X-5-92

Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
Cited by: 56
Author(s): Ana Patrícia, Pablo Carbonell, Francisca de la Iglesia, Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Miguel A. Pérez‐Amador, Santiago F. Elena
Software Mentions: 2
Published: almost 18 years ago

10.3897/zookeys.700.11784

Revision of the ant genus Melophorus (Hymenoptera, Formicidae)
Cited by: 8
Author(s): Brian E. Heterick, Mark A. Castalanelli, Steven O. Shattuck
Software Mentions: 2
Published: almost 9 years ago

10.1179/2046904714Z.000000000218

Severe acute malnutrition and infection
Cited by: 99
Author(s): Kelsey Jones, James A. Berkley
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0111581

MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models
Cited by: 9
Author(s): Sébastien Floor, Aline Hébrant, Jaime Miguel Gomes Pita, Manuel Saiselet, Christophe Trésallet, Frédérick Libert, Guy Andry, Jacques Emile Dumont, Wilma Van Staveren, Carine Maenhaut
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-11-121

Mayday - integrative analytics for expression data
Cited by: 107
Author(s): Florian Battke, Stephan Symons, Kay Nieselt
Software Mentions: 2
Published: over 16 years ago

10.1155/2012/373506

Detecting Cancer Outlier Genes with Potential Rearrangement Using Gene Expression Data and Biological Networks
Cited by: 12
Author(s): Mohammed Alshalalfa, Tarek A. Bismar, Reda Alhajj
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-7-33

Tests for differential gene expression using weights in oligonucleotide microarray experiments
Cited by: 9
Author(s): Pingzhao Hu, Joseph Beyene, Celia M.T. Greenwood
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pcbi.1000207

Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development
Cited by: 171
Author(s): Szymon Stoma, Mikaël Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas, Christophe Godin
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2105-11-351

Identifying differentially regulated subnetworks from phosphoproteomic data
Cited by: 31
Author(s): Martin Klammer, Klaus Godl, Andreas Tebbe, Christoph Schaab
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pcbi.1004924

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT
Cited by: 40
Author(s): Kumari Sonal Choudhary, Neha Rohatgi, Skarphéđinn Halldórsson, Eiríkur Briem, Thorarinn Gudjonsson, Steinn Guðmundsson, Óttar Rolfsson
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2020.01467

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses
Cited by: 19
Author(s): Leticia Botella, Jan Janoušek, Cristiana Maia, Marília Horta Jung, Milica Raco, Thomas S. Jung
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1004077

GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells
Cited by: 96
Author(s): Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein
Software Mentions: 2
Published: over 11 years ago

10.3389/fonc.2021.631056

Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm
Cited by: 10
Author(s): Han-Ching Chan, Amrita Chattopadhyay, Eric Y. Chuang, Tzu-Pin Lu
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-14-S2-S7

Discovery and analysis of consistent active sub-networks in cancers
Cited by: 12
Author(s): Raj Gaire, Lorey Smith, Patrick O. Humbert, James E. Bailey, Peter J. Stuckey, Izhak Haviv
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-019-2791-8

DNAscan: personal computer compatible NGS analysis, annotation and visualisation
Cited by: 15
Author(s): Alfredo Iacoangeli, Ahmad Al Khleifat, William Sproviero, Aleksey Shatunov, Ashley Jones, Sarah Morgan, Alan Pittman, Richard Dobson, Stephen J. Newhouse, Ammar Al‐Chalabi
Software Mentions: 2
Published: over 7 years ago

10.1111/anec.12840

Young and early‐onset dilated cardiomyopathy with malignant ventricular arrhythmia and sudden cardiac death induced by the heterozygous LDB3, MYH6, and SYNE1 missense mutations
Cited by: 9
Author(s): Ting Zhao, Yuting Ma, Zuoquan Zhang, Jing Xian, Xiaojing Geng, Feng Wang, Jiana Huang, Zhe Yang, Yi Luo, Yenn‐Jiang Lin
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2014.00530

Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus
Cited by: 44
Author(s): Philipp Wiemann, Beatrix E. Lechner, Joshua A. Baccile, Thomas Velk, Wen‐Bing Yin, Jin Woo Bok, Suman B. Pakala, Liliana Losada, William C. Nierman, Frank C. Schroeder, Hubertus Haas, Nancy P. Keller
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2105-10-264

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
Cited by: 4
Author(s): Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2105-13-S15-S4

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Cited by: 12
Author(s): Joseph S. Reddy, Ranjit Kumar, James Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: almost 14 years ago

10.3389/fmicb.2020.00202

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Cited by: 11
Author(s): José Manuel Rubio-Gómez, Carlos Molina-Santiago, Zulema Udaondo, Mireia Tena-Garitaonaindia, Tino Krell, Juan L. Ramos, Abdelali Daddaoua
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.00863

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes
Cited by: 14
Author(s): Nan Song, Yuehua Geng, Xinghao Li
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1000160

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
Cited by: 90
Author(s): Marco Punta, Yishai Ofran
Software Mentions: 2
Published: over 17 years ago

10.2196/mental.4984

Mental Health Smartphone Apps: Review and Evidence-Based Recommendations for Future Developments
Cited by: 619
Author(s): David Bakker, Nikolaos Kazantzis, Debra Rickwood, Nikki Rickard
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-016-3030-6

Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler
Cited by: 125
Author(s): Samuel S. Shepard, Sarah Meno, Justin Bahl, Malania M. Wilson, John Barnes, Elizabeth B. Neuhaus
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-14-S11-S3

Efficient digest of high-throughput sequencing data in a reproducible report
Cited by: 4
Author(s): Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C. Perín, Hongbo Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pcbi.1002256

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
Cited by: 9
Author(s): Andrew Tae-Jun Kwon, Alice Chou, David J. Arenillas, Wyeth W. Wasserman
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2019.00107

Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria
Cited by: 19
Author(s): Thi Thu Hao Van, Jake A. Lacey, Ben Vezina, Canh Phung, Arif Anwar, Peter C. Scott, Robert J. Moore
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1008809

Latching dynamics as a basis for short-term recall
Cited by: 7
Author(s): Kwang Il Ryom, Vezha Boboeva, Oleksandra Soldatkina, Alessandro Treves
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1000574

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
Cited by: 47
Author(s): Wolfram Stacklies, Fei Xia, Frauke Gräter
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pcbi.1000718

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
Cited by: 11
Author(s): Bernie J. Daigle, Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald M. Reaven, Philip S. Tsao, Russ B. Altman
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0023204

Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients
Cited by: 45
Author(s): Tim Robinson, Susana Campino, Sarah Auburn, Samuel Assefa, Spencer D. Polley, Magnus Manske, Bronwyn MacInnis, Kirk A. Rockett, G. Maslen, Mandy Sanders, Michael A. Quail, Peter L. Chiodini, Dominic P. Kwiatkowski, Taane G. Clark, Colin J. Sutherland
Software Mentions: 2
Published: almost 15 years ago

10.3389/fvets.2021.732129

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing
Cited by: 49
Author(s): Adriana Higuera, Giovanny Herrera, Paula Andrea Jiménez, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Juan Carlos Pinilla, Darwin A. Moreno-Pérez, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 2
Published: almost 5 years ago

10.1186/1742-9994-10-9

Habitat productivity constrains the distribution of social spiders across continents – case study of the genus Stegodyphus
Cited by: 26
Author(s): Marija Majer, Jens‐Christian Svenning, Trine Bilde
Software Mentions: 2
Published: over 13 years ago

10.3389/fnint.2012.00113

The Interplay between Emotion and Cognition in Autism Spectrum Disorder: Implications for Developmental Theory
Cited by: 91
Author(s): Sebastian Gaigg
Software Mentions: 2
Published: over 14 years ago

10.3390/ijerph10104836

Estimating the Public Health Impact of Setting Targets at the European Level for the Reduction of Zoonotic Salmonella in Certain Poultry Populations
Cited by: 15
Author(s): Winy Messens, Luis Vivas-Alegre, Saghir Bashir, Giusi Amore, Pablo Romero-Barrios, Marta Hugas
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1000081

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Cited by: 94
Author(s): Kevin Kwei, Murali D. Bashyam, Jennifer L. Kao, Raman Ratheesh, E. Chandrakanth Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon La Choi, Sreejata Chatterjee, Collins Karikari, Keyan Salari, Pei Wang, Tina Hernandez‐Boussard, G Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0067142

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles
Cited by: 13
Author(s): Shengjun Fan, Zhenyu Pan, Qiang Geng, Xin Li, Yefan Wang, Yu An, Yan Xu, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2156-15-4

On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis
Cited by: 7
Author(s): A.M. Hidalgo, J.W.M. Bastiaansen, B. Harlizius, Hendrik‐Jan Megens, Ole Madsen, R.P.M.A. Crooijmans, Martien A. M. Groenen
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-8-285

miRAS: a data processing system for miRNA expression profiling study
Cited by: 2
Author(s): Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yuanming Xia, Yiqing Wu, Xiangjun Liu
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pone.0072699

In-Depth Characterization of microRNA Transcriptome in Melanoma
Cited by: 111
Author(s): James Kozubek, Zhihai Ma, Elizabeth Fleming, Tatiana Duggan, Rong Wu, Dong-Guk Shin, Soheil S. Dadras
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1005483

Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish
Cited by: 49
Author(s): Diana Mitchell, Craig B. Stevens, Ruth A. Frey, Samuel S. Hunter, Ryuichi Ashino, Shoji Kawamura, Deborah L. Stenkamp
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1008871

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans
Cited by: 14
Author(s): Shelby Priest, Marco A. Coelho, Verónica Mixão, Shelly Applen Clancey, Yitong Xu, Sheng Sun, Toni Gabaldón, Joseph Heitman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1007092

Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway
Cited by: 12
Author(s): Sara J. Hanson, Kevin Byrne, Kenneth H. Wolfe
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2164-15-801

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
Cited by: 31
Author(s): Matteo Dell’Acqua, Andrea Zuccolo, Metin Tuna, L. Gianfranceschi, Mario Enrico Pè
Software Mentions: 2
Published: almost 12 years ago

10.3389/fimmu.2019.00468

CD117 (c-Kit) Is Expressed During CD8+ T Cell Priming and Stratifies Sensitivity to Apoptosis According to Strength of TCR Engagement
Cited by: 19
Author(s): Guido Frumento, Jianmin Zuo, Kriti Verma, Wayne Croft, Pradeep Ramagiri, Frederick Chen, Paul Moss
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-9-348

Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
Cited by: 13
Author(s): Stephen Tanner, Pankaj Agarwal
Software Mentions: 2
Published: almost 18 years ago

10.3390/ijerph15091941

A Hybrid Forecasting Approach to Air Quality Time Series Based on Endpoint Condition and Combined Forecasting Model
Cited by: 27
Author(s): Jiaming Zhu, Peng Wu, Huayou Chen, Ligang Zhou
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1004766

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
Cited by: 155
Author(s): Val F. Lanza, María de Toro, M. Pilar Garcillán-Barcia, Azucena Mora, Jorge Blanco, Teresa M. Coque
Software Mentions: 2
Published: over 11 years ago

10.3389/fimmu.2021.709910

Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture
Cited by: 4
Author(s): Nicole C. Smith, Navaneethaiyer Umasuthan, Surendra Kumar, Nardos Tesfaye Woldemariam, Rune Andreassen, Sherri L. Christian, Matthew L. Rise
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijerph16245102

PM2.5 Pollution: Health and Economic Effect Assessment Based on a Recursive Dynamic Computable General Equilibrium Model
Cited by: 6
Author(s): Keyao Chen, Guizhi Wang, Lingyan Wu, Jibo Chen, Shuai Yuan, Qi Liu, Xiaodong Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2156-10-48

Single-feature polymorphism discovery by computing probe affinity shape powers
Cited by: 11
Author(s): Wayne Xu, Seungho Cho, Sungjin Yang, Yung–Tsi Bolon, Hatice Bilgiç, Haiyan Jia, Yongqiang Xiong, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 17 years ago

10.1534/g3.116.036673

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology
Cited by: 8
Author(s): Bryan T. Welly, Michael R. Miller, Jeffrey L Stott, M Blanchard, Alma Islas–Trejo, Sean O’Rourke, Amy Young, Juan F. Medrano, Alison L. Van Eenennaam
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2017.01288

Helicobacter pylori Affects the Antigen Presentation Activity of Macrophages Modulating the Expression of the Immune Receptor CD300E through miR-4270
Cited by: 34
Author(s): Matteo Pagliari, Fabio Munari, Marta Toffoletto, Silvia Lonardi, Francesco Chemello, Gaia Codolo, Caterina Millino, Chiara Della Bella, Beniamina Pacchioni, William Vermi, Matteo Fassan, Marina de Bernard, Stefano Cagnin
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1761-4

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks
Cited by: 31
Author(s): Shawn J. Cokus, Paul F. Gugger, Victoria L. Sork
Software Mentions: 2
Published: about 11 years ago

10.3389/fimmu.2021.625586

The Effects of Helicobacter pylori Infection on Microbiota Associated With Gastric Mucosa and Immune Factors in Children
Cited by: 9
Author(s): Wei Zheng, Miao Jin, Lingling Luo, Long Gao, Bin Chen, Xiaoli Shu, Weizhong Gu, Kui Peng, Fubang Li, Hong Zhao, Benson O. A. Botchway, Marong Fang, Mizu Jiang
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.118.200134

Programmable Single and Multiplex Base-Editing in <i>Bombyx mori</i> Using RNA-Guided Cytidine Deaminases
Cited by: 14
Author(s): Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao, Qingyou Xia
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-016-3374-y

Potential immunosuppressive effects of Escherichia coli O157:H7 experimental infection on the bovine host
Cited by: 11
Author(s): Evelien Kieckens, Joanna Rybarczyk, RW Li, Daisy Vanrompay, Eric Cox
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.118.200417

Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer (<i>Cervus nippon</i>) and Wapiti (<i>Cervus elaphus</i>)
Cited by: 3
Author(s): Hengxing Ba, Zhipeng Li, Yumei Yang, Chunyi Li
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.118.200171

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Cited by: 28
Author(s): Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijerph17030933

Comparative Analysis of the Reproduction Accuracy of Main Methods for Finding the Mandible Position in the Centric Relation Using Digital Research Method. Comparison between Analog-to-Digital and Digital Methods: A Preliminary Report
Cited by: 3
Author(s): А А Stafeev, A N Ryakhovsky, P Petrov, Sergey Chikunov, A V Khizhuk, Marina Bykova, Nataliya Vuraki
Software Mentions: 2
Published: over 6 years ago