10.3390/cancers12020470

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

10.1371/journal.pgen.1005457

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
Cited by: 65
Author(s): Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner
Software Mentions: 4
Published: almost 11 years ago

10.1093/brain/awaa334

Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex
Cited by: 86
Author(s): Gemma Shireby, Jonathan Davies, Paul T. Francis, Joe Burrage, Emma Walker, Grant W. A. Neilson, Aisha Dahir, Alan Thomas, Seth Love, Rebecca Smith, Katie Lunnon, Meena Kumari, Leonard C Schalkwyk, Kevin Morgan, Keeley Brookes, Eilís Hannon, Jonathan Mill
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1006449

Genomic Characterization of Metformin Hepatic Response
Cited by: 38
Author(s): Marcelo R. Luizon, Walter L. Eckalbar, Yao Wang, Stacy L. Jones, Robin P. Smith, Laurance Megan, Lawrence Lin, Paul J. Gallins, Amy S. Etheridge, Fred A. Wright, Yifeng Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.10211

The neuropsychological profile of professional action video game players
Cited by: 11
Author(s): Julie Justine Benoit, Eugenie Roudaia, Taylor Johnson, Trevor Love, Jocelyn Faubert
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1008501

The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor
Cited by: 51
Author(s): Elizabeth A. Coe, Jennifer Y. Tan, Michael Shapiro, Pakavarin Louphrasitthiphol, Andrew Bassett, Ana C. Marques, Colin R. Goding, Keith W. Vance
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0007603

Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi
Cited by: 12
Author(s): Kelita Kamoto, Harry Noyes, Peter Nambala, Edward Senga, Janelisa Musaya, Benjamin Kumwenda, Bruno Bucheton, Annette MacLeod, Anneli Cooper, Caroline Clucas, Christiane Herz-Fowler, Enock Matove, Arthur Chiwaya, John Chisi
Software Mentions: 4
Published: almost 7 years ago

10.1128/mBio.00824-21

<i>Drosophila</i> Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance
Cited by: 52
Author(s): Alice Marra, Mark A. Hanson, Shu Kondo, Berra Erkoşar, Bruno Lemaître
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSphere.01255-20

The Majority of Typhoid Toxin-Positive <i>Salmonella</i> Serovars Encode ArtB, an Alternate Binding Subunit
Cited by: 9
Author(s): Ahmed Gaballa, Rachel A. Cheng, Anna Sophia Harrand, Alexa R. Cohn, Martin Wiedmann
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227193

Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth
Cited by: 22
Author(s): Aishwarya P. Yadama, Hooman Mirzakhani, Thomas F. McElrath, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008647

Independent component analysis recovers consistent regulatory signals from disparate datasets
Cited by: 24
Author(s): Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2017.00351

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function
Cited by: 68
Author(s): Sachia J. Traving, Owen Rowe, Nina Munkholt Jakobsen, Helle Sørensen, Julie Dinasquet, Colin A. Stedmon, Agneta Andersson, Lasse Riemann
Software Mentions: 4
Published: over 9 years ago

10.3389/fnins.2020.00887

Does Osteopathic Manipulative Treatment Induce Autonomic Changes in Healthy Participants? A Thermal Imaging Study
Cited by: 22
Author(s): Francesco Cerritelli, Daniela Cardone, Alessio Pirino, Arcangelo Merla, Fabio Scoppa
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2021.693887

Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola
Cited by: 14
Author(s): Ramona Mihaela Ciubotaru, Pietro Franceschi, L. Zulini, M. Stefanini, Domen Škrab, Márcia Denise Rossarolla, Peter Robatscher, Michael Oberhuber, Urška Vrhovšek, Giulia Chitarrini
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0140885

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease
Cited by: 18
Author(s): Lela Lackey, Evonne McArthur, Alain Laederach
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13229-021-00450-w

Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts
Cited by: 4
Author(s): Brooke G. McKenna, Yongchao Huang, Kévin Vervier, Dabney Hofammann, Mary Cafferata, Seima Al-Momani, Florencia Lowenthal, Angela Zhang, Joanna Koh, Savantha Thenuwara, Leo Brueggeman, Ethan Bahl, Tanner Koomar, Natalie R. Pottschmidt, Taylor Kalmus, Lucas Casten, Taylor Thomas, Jacob J. Michaelson
Software Mentions: 4
Published: about 5 years ago

10.3389/fpsyg.2020.02177

The Anxiety-Buffer Hypothesis in the Time of COVID-19: When Self-Esteem Protects From the Impact of Loneliness and Fear on Anxiety and Depression
Cited by: 111
Author(s): Alessandro Rossi, Anna Panzeri, Giada Pietrabissa, Gian Mauro Manzoni, Gianluca Castelnuovo, Stefania Mannarini
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSphere.00479-21

Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms
Cited by: 12
Author(s): James T. Van Leuven, Andrés González, Emmanuel C. Ijezie, Alexander Q. Wixom, John L. Clary, Maricris N. Naranjo, Benjamin J. Ridenhour, Craig R. Miller, Tanya A. Miura
Software Mentions: 4
Published: about 5 years ago

10.1073/pnas.1919176117

Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts
Cited by: 203
Author(s): Nardus Mollentze, Daniel G. Streicker
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-36292-5

Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial
Cited by: 39
Author(s): Xuan He, Mariana Parenti, Tove Grip, Magnus Domellöf, Bo Lönnerdal, Olle Hernell, Niklas Timby, Carolyn M. Slupsky
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-53023-6

Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis
Cited by: 42
Author(s): Shivraj Braich, Rebecca C. Baillie, Larry S. Jewell, Germán Spangenberg, Noel O. I. Cogan
Software Mentions: 4
Published: over 6 years ago

10.12688/f1000research.9893.2

exprso: an R-package for the rapid implementation of machine learning algorithms
Cited by: 12
Author(s): Thomas P. Quinn, Daniel S. Tylee, Stephen J. Glatt
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-65883-4

Anguillid eels as a surrogate species for conservation of freshwater biodiversity in Japan
Cited by: 18
Author(s): Hikaru Itakura, Ryoshiro Wakiya, Matthew Gollock, Kenzo Kaifu
Software Mentions: 4
Published: about 6 years ago

10.3389/fchem.2019.00707

A New Genetic Algorithm Approach Applied to Atomic and Molecular Cluster Studies
Cited by: 19
Author(s): Frederico Teixeira Silva, M. X. Silva, Jadson C. Belchior
Software Mentions: 4
Published: almost 7 years ago

10.1002/ece3.7549

Differential reliance on aquatic prey subsidies influences mercury exposure in riparian arachnids and songbirds
Cited by: 10
Author(s): Allyson K. Jackson, Collin A. Eagles‐Smith, W. Douglas Robinson
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-021-01828-5

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories
Cited by: 26
Author(s): Lisa‐Maria Mauerhofer, Sara Zwirtmayr, Patricia Pappenreiter, Sébastien Bernacchi, Arne H. Seifert, Barbara Reischl, Tilman Schmider, Ruth-Sophie Taubner, Christian Paulik, Simon K.-M. R. Rittmann
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10856

Divergent morphological responses to millennia of climate change in two species of bats from Hall’s Cave, Texas, USA
Cited by: 1
Author(s): М. С. Мороз, Illiam S. C. Jackson, Daniel Ramirez, Melissa E. Kemp
Software Mentions: 4
Published: over 5 years ago

10.1002/cti2.1190

BDCA1 ⁺ cDC2s, BDCA2 ⁺ pDCs and BDCA3 ⁺ cDC1s reveal distinct pathophysiologic features and impact on clinical outcomes in melanoma patients
Cited by: 11
Author(s): Eleonora Sosa Cuevas, Laurissa Ouaguia, Stéphane Mouret, J. Charles, Florence de Fraipont, Olivier Manches, Jenny Valladeau‐Guilemond, Nathalie Bendriss‐Vermare, Laurence Chaperot, Caroline Aspord
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.47427

Default mode-visual network hypoconnectivity in an autism subtype with pronounced social visual engagement difficulties
Cited by: 42
Author(s): Michael Lombardo, Lisa T. Eyler, Adrienne Moore, Michael Datko, Cynthia Carter Barnes, Debra Cha, Eric Courchesne, Karen Pierce
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.46418

Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes
Cited by: 20
Author(s): Lauren N. Booth, Travis J. Maures, Robin Yeo, Cindy Tantilert, Anne Brunet
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9081793

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis
Cited by: 3
Author(s): Ho‐Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2016.00075

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions
Cited by: 35
Author(s): Valerio Bianchi, Arnaud Céol, Alessandro G. E. Ogier, Stefano de Pretis, Eugenia Galeota, Kamal Kishore, Pranami Bora, Ottavio Croci, Stefano Campaner, Bruno Amati, Marco J. Morelli, Mattia Pelizzola
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0236548

Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe
Cited by: 16
Author(s): Davide Delpiano, Thorsten Uthmeier
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-79320-z

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)
Cited by: 32
Author(s): Katie Murphy, Joseph Edwards, Katherine Louie, Benjamin P. Bowen, Venkatesan Sundaresan, Trent Northen, Philipp Zerbe
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0094284

Differences in Forage-Acquisition and Fungal Enzyme Activity Contribute to Niche Segregation in Panamanian Leaf-Cutting Ants
Cited by: 21
Author(s): Pepijn W. Kooij, Joanito Liberti, Konstantinos Giampoudakis, Morten Schiøtt, Jacobus J. Boomsma
Software Mentions: 4
Published: over 12 years ago

10.12688/f1000research.26429.2

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
Cited by: 2
Author(s): Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Manjool Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.597877

Identification of a Glycolysis-Related LncRNA Signature to Predict Survival in Diffuse Glioma Patients
Cited by: 11
Author(s): Yangyang Wang, Wenqiang Zhou, Shunchang Ma, Xiudong Guan, Dainan Zhang, Jiayi Peng, Xi Wang, Linhao Yuan, Peiliang Li, Beibei Mao, Kang Peng, Deling Li, Chuanbao Zhang, Wang Jia
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1006937

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder
Cited by: 9
Author(s): Abrar E. Al‐Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan Smith
Software Mentions: 4
Published: over 7 years ago

10.1098/rsos.160820

Social associations between California sea lions influence the use of a novel foraging ground
Cited by: 25
Author(s): Zachary A. Schakner, Matthew B. Petelle, Mathew J. Tennis, Bjorn K. van der Leeuw, Robert T. Stansell, Daniel T. Blumstein
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0244038

Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation
Cited by: 9
Author(s): Manuel Peter, Dominik F. Aschauer, Renata Rose, Anne Sinning, Florian Grössl, Dominic Kargl, Klaus Kraitsy, Thomas R Burkard, Heiko J. Luhmann, Wulf Haubensak, Simon Rumpel
Software Mentions: 4
Published: over 5 years ago

10.1093/g3journal/jkaa061

Gene-level quantitative trait mapping in <i>Caenorhabditis elegans</i>
Cited by: 16
Author(s): Luke M. Noble, Matthew V. Rockman, Henrique Teotónio
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0215767

Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities
Cited by: 11
Author(s): François Thomas, James T. Morris, Cathleen Wigand, Stefan M. Sievert
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-018-0404-9

Commensal microbiota modulate gene expression in the skin
Cited by: 126
Author(s): Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow‐McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis, Elizabeth A. Grice
Software Mentions: 4
Published: over 8 years ago

10.3390/plants9121809

Physico-Chemical Characteristics and Culturable Microbial Communities of Grape Berries Change Strongly during Noble Rot Development
Cited by: 3
Author(s): Júlia Hegyi-Kaló, Ádám István Hegyi, József Geml, Zsolt Zsófi, Xénia Pálfi, Kálmán Zoltán Váczy
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.120.401053

Mutations in a Novel Cadherin Gene Associated with Bt Resistance in <i>Helicoverpa zea</i>
Cited by: 14
Author(s): Megan L. Fritz, Schyler O. Nunziata, Ruifeng Guo, Bruce E. Tabashnik, Yves Carrière
Software Mentions: 4
Published: over 6 years ago

10.1186/s13024-021-00462-3

A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy
Cited by: 4
Author(s): Laura Gutierrez-Quiceno, Eric B. Dammer, Ashlyn G. Johnson, James Webster, Rhythm Shah, Duc M. Duong, Luming Yin, Nicholas T. Seyfried, Victor E. Alvarez, Thor D. Stein, Ann C. McKee, Chadwick M. Hales
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0120385

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize
Cited by: 58
Author(s): Malachy T. Campbell, Christopher A. Proctor, Yongchao Dou, Aaron J. Schmitz, Piyaporn Phansak, Greg R. Kruger, Chi Zhang, Harkamal Walia
Software Mentions: 4
Published: over 11 years ago

10.1534/g3.118.200127

Comparison of the Relative Potential for Epigenetic and Genetic Variation To Contribute to Trait Stability
Cited by: 23
Author(s): Emma Sofie Timm Aller, Lea Møller Jagd, Daniel J. Kliebenstein, Meike Burow
Software Mentions: 4
Published: over 8 years ago

10.1186/s12879-020-05135-y

The correlations between Th1 and Th2 cytokines in human alveolar echinococcosis
Cited by: 7
Author(s): Xingming Ma, Xuefei Zhang, Jia Liu, Yufang Liu, Cunzhe Zhao, Huixia Cai, Lei Wen, Jun Ma, Haining Fan, Jianye Zhou, Na Liu, Jingxiao Zhang, Yongshun Wang, Wei Wang, Peizhen Zhan, Xiongying Zhang, Qing Zhang, Kemei Shi, Peiyun Liu
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 9 years ago

10.1186/s13040-015-0059-z

Principal component gene set enrichment (PCGSE)
Cited by: 20
Author(s): H. Robert Frost, Zhigang Li, Jason H. Moore
Software Mentions: 4
Published: about 11 years ago

10.3389/fnmol.2020.00057

Sequences of Reverse Transcribed Brain DNA Are Modified by Learning
Cited by: 2
Author(s): Antonio Giuditta, Joyce Casalino
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0046633

Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection
Cited by: 96
Author(s): Bin Liu, Xiaolong Wang, Qingcai Chen, Qian Dong, Xun Lan
Software Mentions: 4
Published: almost 14 years ago

10.7717/peerj.4458

Characterization of the salivary microbiome in people with obesity
Cited by: 63
Author(s): Yujia Wu, Xiaopei Chi, Qian Zhang, Feng Chen, Xuliang Deng
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0166358

Accelerating Information Retrieval from Profile Hidden Markov Model Databases
Cited by: 0
Author(s): A. Faleh Tamimi, Yaqoub Ashhab, Hashem Tamimi
Software Mentions: 4
Published: over 9 years ago

10.1093/ve/veaa073

Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation
Cited by: 9
Author(s): Jiangbin Fan, Johannes A. Jehle, Jörg T. Wennmann
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms8040513

Relationships between Gut Microbiota, Metabolome, Body Weight, and Glucose Homeostasis of Obese Dogs Fed with Diets Differing in Prebiotic and Protein Content
Cited by: 15
Author(s): Emmanuelle Apper, Lisa Privet, Bernard Taminiau, Cindy Le Bourgot, Ljubica Svilar, Jean‐Charles Martin, Marianne Diez
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-91864-2

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Cited by: 2
Author(s): Parastoo Modarres, Farzaneh Mohamadi Farsani, Amir Abas Nekouie, Sadeq Vallian
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-21553-0

Environmental and anthropogenic factors affecting the increasing occurrence of shark-human interactions around a fast-developing Indian Ocean island
Cited by: 26
Author(s): Erwann Lagabrielle, Agathe Allibert, Jérémy J. Kiszka, Nicolas Loiseau, James P. Kilfoil, Anne Lemahieu
Software Mentions: 4
Published: over 8 years ago

10.1186/s13395-019-0196-z

Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field
Cited by: 8
Author(s): Apostolos Malatras, Stéphanie Duguez, William Duddy
Software Mentions: 4
Published: over 7 years ago

10.3390/s17020403

Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System
Cited by: 27
Author(s): Zhenyu Wu, Yuan Xu, Yunong Yang, Chunhong Zhang, Xinning Zhu, Yang Ji
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0187572

Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles
Cited by: 56
Author(s): Arsen Arakelyan, Lilit Nersisyan, David Poghosyan, Lusine Khondkaryan, Աննա Հակոբյան, Henry Löffler-Wirth, Evie Melanitou, Hans Binder
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0117818

mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer
Cited by: 33
Author(s): Silvia von der Heyde, Sven Wagner, Czerny Alexander, M. Nietert, Fabian Ludewig, Gabriela Salinas-Riester, Dorit Arlt, Tim Beißbarth
Software Mentions: 4
Published: over 11 years ago

10.18632/aging.202400

A DNA methylation age predictor for zebrafish
Cited by: 27
Author(s): Benjamin Mayne, Darren Korbie, Lisa M Kenchington, Ben J Ezzy, Oliver Berry, Simon Jarman
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-12-83

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models
Cited by: 11
Author(s): Juliana Silva Bernardes, Alessandra Carbone, Gerson Zaverucha
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2105-12-275

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information
Cited by: 11
Author(s): Krishnadev Oruganty, Narayanaswamy Srinivasan
Software Mentions: 4
Published: about 15 years ago

10.1186/s12967-019-1851-1

Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia
Cited by: 17
Author(s): Zi‐jun Xu, Ji‐chun Ma, Jing‐Dong Zhou, Xiang‐mei Wen, Dong‐ming Yao, Wei Zhang, Runbi Ji, Dehong Wu, Li‐Juan Tang, Zhaoqun Deng, Jun Qian, Lin Jiang
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.11045

Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis
Cited by: 5
Author(s): Xiao Feng, Lingbin Qi, Xiaoyu Xu, Yun Feng, Xiaoming Gong, Aixingzi Aili, Yu Chen, Zhigang Xue, Jinfeng Xue, Xiaowen Tong
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-018-2401-1

Data integration by multi-tuning parameter elastic net regression
Cited by: 23
Author(s): Jie Liu, Gangning Liang, Kimberly D. Siegmund, Juan Pablo Lewinger
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12859-019-2994-z

An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
Cited by: 29
Author(s): Arezo Torang, Paraag Gupta, David J. Klinke
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-15-300

Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer
Cited by: 81
Author(s): Wei-Chun Chou, An‐Lin Cheng, Marco Brotto, Chun‐Yu Chuang
Software Mentions: 4
Published: over 12 years ago

10.3389/fpsyg.2020.557171

Childhood Adversity and Affective Touch Perception: A Comparison of United Kingdom Care Leavers and Non-care Leavers
Cited by: 21
Author(s): Shaunna L. Devine, Susannah Walker, Adarsh Makdani, Elizabeth R. Stockton, Martyn J. McFarquhar, Francis McGlone, Paula Trotter
Software Mentions: 4
Published: almost 6 years ago

10.1155/2015/605891

Evaluation of Penalized and Nonpenalized Methods for Disease Prediction with Large-Scale Genetic Data
Cited by: 2
Author(s): Sungho Won, Ho Sun Choi, Suyeon Park, Juyoung Lee, Changyi Park, Sunghoon Kwon
Software Mentions: 4
Published: over 11 years ago

10.1186/s12881-020-01005-1

Association between FCGR2A rs1801274 and MUC5B rs35705950 variations and pneumonia susceptibility
Cited by: 6
Author(s): Xueshu Shi, Yaqi Ma, Haiyan Li, Huanxin Yu
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22179566

Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes
Cited by: 6
Author(s): Thatchawan Thanasupawat, Aleksandra Głogowska, Chris D. Pascoe, S Krishnan, Maliha Tabassum Munir, Farhana Begum, Jason Beiko, Jerry Krcek, Marc R. Del Bigio, Marshall Pitz, Yaoqing Shen, Victor Spicer, Kevin M. Coombs, John Wilkins, Sabine Hombach‐Klonisch, Thomas Klonisch
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers7040887

Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics
Cited by: 27
Author(s): Janet Doolittle-Hall, Danielle L. Cunningham Glasspoole, William T. Seaman, Jennifer Webster‐Cyriaque
Software Mentions: 4
Published: almost 11 years ago

10.1093/bioinformatics/btz160

Interoperable and scalable data analysis with microservices: applications in metabolomics
Cited by: 24
Author(s): Payam Emami Khoonsari, Pablo Moreno-Ger, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne Thévenot, Michael Van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0090322

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
Cited by: 29
Author(s): Philipp Schulz, Karel Jansseune, Thomas Degenkolbe, Michaël Méret, Hannes Claeys, Aleksandra Skirycz, Markus Teige, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0106131

Gene Expression Profiling Reveals Epithelial Mesenchymal Transition (EMT) Genes Can Selectively Differentiate Eribulin Sensitive Breast Cancer Cells
Cited by: 47
Author(s): Zoltán Dezső, Judith Oestreicher, Amy Weaver, Stephanie Santiago, Sergei Agoulnik, Jesse C. Chow, Yoshiya Oda, Yasuhiro Funahashi
Software Mentions: 4
Published: almost 12 years ago

10.1002/ece3.6118

A comparison of wetland characteristics between Agricultural Conservation Easement Program and public lands wetlands in West Virginia, USA
Cited by: 4
Author(s): Katharine E. Lewis, Christopher T. Rota, James T. Anderson
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.6222

LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
Cited by: 21
Author(s): Nigel P. Dyer, Vahid Shahrezaei, Daniel Hebenstreit
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0054144

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
Cited by: 139
Author(s): José M. Otero, Donatella Cimini, Kiran Raosaheb Patil, Simon Guldberg Poulsen, Lisbeth Olsson, Jens Nielsen
Software Mentions: 4
Published: over 13 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyg.2021.580684

Reported Affect Changes as a Function of Response Delay: Findings From a Pooled Dataset of Nine Experience Sampling Studies
Cited by: 4
Author(s): Gudrun Eisele, Hugo Vachon, Inez Myin-Germeys, Wolfgang Viechtbauer
Software Mentions: 4
Published: over 5 years ago

10.3390/s21165413

A New Deep Learning-Based Methodology for Video Deepfake Detection Using XGBoost
Cited by: 26
Author(s): Aya Abdelsalam Ismail, Marwa S. Elpeltagy, Mervat S. Zaki, Kamal A. ElDahshan
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0179891

Estimating psychopathological networks: Be careful what you wish for
Cited by: 155
Author(s): Sacha Epskamp, Joost Kruis, Maarten Marsman
Software Mentions: 4
Published: about 9 years ago

10.2196/games.2778

Ecological Validity of Virtual Reality Daily Living Activities Screening for Early Dementia: Longitudinal Study
Cited by: 124
Author(s): Ioannis Tarnanas, Winfried Schlee, Magda Tsolaki, René M. Müri, Urs Peter Mosimann, Tobias Nef
Software Mentions: 4
Published: about 13 years ago

10.7717/peerj.9646

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (<i>Penaeus monodon</i>) with different growth performance
Cited by: 19
Author(s): Tanaporn Uengwetwanit, Umaporn Uawisetwathana, Sopacha Arayamethakorn, Juthatip Khudet, Sage Chaiyapechara, Nitsara Karoonuthaisiri, Wanilada Rungrassamee
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-13-80

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
Cited by: 15
Author(s): Wessel N. van Wieringen, Kristian Unger, Gwenaël G. R. Leday, Oscar Krijgsman, Renée X. de Menezes, Bauke Ylstra, Mark A. van de Wiel
Software Mentions: 4
Published: over 14 years ago

10.1038/srep29434

Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-12-64

Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library
Cited by: 118
Author(s): Pedro López-Romero
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2164-14-643

Integrated genomic analysis of triple-negative breast cancers reveals novel microRNAs associated with clinical and molecular phenotypes and sheds light on the pathways they control
Cited by: 75
Author(s): Emanuele de Rinaldis, Patrycja Gazinska, Anca Mera, Zora Modrušan, Grazyna Fedorowicz, Brian Burford, Cheryl Gillett, Pierfrancesco Marra, Anita Grigoriadis, David Dornan, Lars Holmberg, Sarah Pinder, Andrew Tutt
Software Mentions: 4
Published: over 13 years ago

10.1128/mBio.02302-20

Identification of Zinc-Dependent Mechanisms Used by Group B <i>Streptococcus</i> To Overcome Calprotectin-Mediated Stress
Cited by: 27
Author(s): Lindsey R. Burcham, Yoann Le Breton, Jana N. Radin, Brady L. Spencer, Liwen Deng, Aurélia Hiron, Monica Ransom, Jéssica da C. Mendonça, Ashton T. Belew, Najib M. El-Sayed, Kevin S. McIver, Thomas E. Kehl-Fie, Kelly S. Doran
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.676980

Integrative Multi-Omics Reveals Serum Markers of Tuberculosis in Advanced HIV
Cited by: 9
Author(s): Sonya Krishnan, Artur T. L. Queiroz, Amita Gupta, Nikhil Gupte, Gregory P. Bisson, Johnstone Kumwenda, Kogieleum Naidoo, Lerato Mohapi, Vidya Mave, Rosie Mngqibisa, Javier R. Lama, Mina C. Hosseinipour, Bruno B. Andrade, Petros C. Karakousis
Software Mentions: 4
Published: about 5 years ago

10.1186/s13148-021-01004-w

Profile of copper-associated DNA methylation and its association with incident acute coronary syndrome
Cited by: 15
Author(s): Pinpin Long, Qiuhong Wang, Yizhi Zhang, Xiaoyan Zhu, Kuai Yu, Haijing Jiang, Xuezhen Liu, Min Zhou, Yu Yuan, Kang Liu, Jing Jiang, Xiaomin Zhang, Meian He, Huan Guo, Weihong Chen, Jing Yuan, Long Cheng, Liming Liang, Tangchun Wu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0256148

RNA-sequencing of AVPV and ARH reveals vastly different temporal and transcriptomic responses to estradiol in the female rat hypothalamus
Cited by: 5
Author(s): Margaret A. Mohr, Angela Wong, Gauthaman Sukumar, Clifton L. Dalgard, Weizhe Hong, Tao Wu, Ye Wu, Paul E. Micevych
Software Mentions: 4
Published: almost 5 years ago