10.1371/journal.pone.0158334

Multivariate and Cladistic Analyses of Isolated Teeth Reveal Sympatry of Theropod Dinosaurs in the Late Jurassic of Northern Germany
Cited by: 36
Author(s): Oliver Gerke, Oliver Wings
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0222016

Impact of care provider network characteristics on patient outcomes: Usage of social network analysis and a multi-scale community detection
Cited by: 13
Author(s): Mina Ostovari, Denny Yu
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0159864

Population Structure, Genetic Diversity, Effective Population Size, Demographic History and Regional Connectivity Patterns of the Endangered Dusky Grouper, Epinephelus marginatus (Teleostei: Serranidae), within Malta’s Fisheries Management Zone
Cited by: 17
Author(s): Molly Buchholz-Sørensen, Adriana Vella
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13014-021-01853-y

Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burden
Cited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0237288

First evidence for an aposematic function of a very common color pattern in small insects
Cited by: 0
Author(s): Rebeca Mora-Castro, Marcela Alfaro-Córdoba, Marcela Hernández-Jiménez, Mauricio Fernández Otárola, Michael Méndez-Rivera, Didier Ramírez-Morales, Carlos E. Rodríguez-Rodríguez, Andrés Durán-Rodríguez, Paul Hanson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0208641

Use of a sequential high throughput screening assay to identify novel inhibitors of the eukaryotic SRP-Sec61 targeting/translocation pathway
Cited by: 5
Author(s): W. Klein, Claudia Rutz, Jamina Eckhard, Becky Provinciael, Edgar Specker, Martin Neuenschwander, Gunnar Kleinau, Patrick Scheerer, Jens-Peter von Kries, Marc Nazaré, Kurt Vermeire, Ralf Schülein
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0241889

Comparative genome analysis of test algal strain NIVA-CHL1 (Raphidocelis subcapitata) maintained in microalgal culture collections worldwide
Cited by: 2
Author(s): Takahiro Yamagishi, Haruyo Yamaguchi, Shigekatsu Suzuki, Mayumi Yoshikawa, Ian Jameson, Maike Lorenz, David R. Nobles, Christine Campbell, Masanori Seki, Masanobu Kawachi, Hiroshi Yamamoto
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0203266

Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress
Cited by: 54
Author(s): R.C. Sharma, Garima Singh, Sitangshu Bhattacharya, Ashutosh Singh
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0013169

Gene Expression Signature-Based Screening Identifies New Broadly Effective Influenza A Antivirals
Cited by: 58
Author(s): Laurence Josset, Julien Textoris, Béatrice Loriod, Olivier Ferraris, Vincent Moulès, Bruno Lina, Catherine Nguyen, Jean‐Jacques Diaz, Manuel Rosa‐Calatrava
Software Mentions: 4
Published: almost 16 years ago

10.7150/jca.57225

Integrating 13 Microarrays to Construct a 6 RNA-binding proteins Prognostic Signature for Gastric Cancer patients
Cited by: 0
Author(s): Liqun Zhou, Qi Zhou, You Wu, Lin Xin
Software Mentions: 4
Published: over 5 years ago

10.1093/jas/skaa181

The effect of maternal antibiotic use in sows on intestinal development in offspring
Cited by: 10
Author(s): Astrid de Greeff, Dirkjan Schokker, Petra Roubos-van den Hil, P. Ramaekers, S.A. Vastenhouw, Frank Harders, Alex Bossers, M.A. Smits, Johanna M.J. Rebel
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0141194

Analysis of the Optimal Duration of Behavioral Observations Based on an Automated Continuous Monitoring System in Tree Swallows (Tachycineta bicolor): Is One Hour Good Enough?
Cited by: 27
Author(s): Ádám Z. Lendvai, Çağlar Akçay, Jenny Q. Ouyang, Roslyn Dakin, Alice D. Domalik, Prianka S St John, Mark T. Stanback, Ignacio T. Moore, Frances Bonier
Software Mentions: 4
Published: over 10 years ago

10.3389/fphys.2021.651690

Identification of VCAN as Hub Gene for Diabetic Kidney Disease Immune Injury Using Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Qiannan Xu, Binjue Li, Yucheng Wang, Cuili Wang, Shi Feng, Xue Lü, Jianghua Chen, Hong Jiang
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.120.401166

DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in<i>Caenorhabditis elegans</i>
Cited by: 14
Author(s): Daniel R. McHugh, Elena Koumis, Paul Jacob, Jennifer Goldfarb, Michelle Schlaubitz-Garcia, Safae Bennani, Paul Regan, Prem Patel, Matthew J. Youngman
Software Mentions: 4
Published: about 6 years ago

10.1002/ece3.5555

Collinearity in ecological niche modeling: Confusions and challenges
Cited by: 160
Author(s): Xiaohui Feng, Daniel Park, Ye Liang, Ranjit Pandey, Monica Papeş
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0030388

A Triple-Isotope Approach to Predict the Breeding Origins of European Bats
Cited by: 53
Author(s): Ana G. Popa‐Lisseanu, Karin Sörgel, Anja Luckner, Leonard I. Wassenaar, Carlos Ibáñez, Stephanie Kramer‐Schadt, Mateusz Ciechanowski, Tamás Görföl, Ivo Niermann, Grégory Beuneux, Robert W. Mysłajek, Javier Juste, Jocelyn Fonderflick, Detlev H. Kelm, Christian C. Voigt
Software Mentions: 4
Published: over 14 years ago

10.3390/brainsci11080996

The Kinematics of Social Action: Visual Signals Provide Cues for What Interlocutors Do in Conversation
Cited by: 6
Author(s): James P. Trujillo, Judith Holler
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12885-021-08536-7

SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target
Cited by: 26
Author(s): Shaokun Wang, Li Pang, Zuolong Liu, Xiangchuan Meng
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0231083

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla
Cited by: 4
Author(s): Yakshi Ortiz, Carla Restrepo, Brayan Vilanova-Cuevas, Eugenio Santiago‐Valentín, Susannah G. Tringe, Filipa Godoy-Vitorino
Software Mentions: 4
Published: over 6 years ago

10.3389/fmolb.2020.605623

Long Non-coding RNA BTG3-7:1 and JUND Co-regulate C21ORF91 to Promote Triple-Negative Breast Cancer Progress
Cited by: 0
Author(s): Dan Zheng, Xiujing He, Ting Luo, Xiaorong Zhong, Hong Zheng, Jiqiao Yang, Yanchu Li, Jing Jing
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-021-01784-0

A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus
Cited by: 36
Author(s): Alison J. Hardcastle, Petra Lišková, Yelena Bykhovskaya, Bennet J McComish, Alice E. Davidson, Chris F. Inglehearn, Xiaohui Li, Hélène Choquet, Mahmoud Habeeb, Sionne E. M. Lucas, Srujana Sahebjada, Nikolas Pontikos, Karla E. Rojas López, Anthony P Khawaja, Manir Ali, Ľubica Ďuďáková, Pavlína Skalická, Bart T. H. van Dooren, Annette J M Geerards, Christoph Haudum, Valeria Lo Faro, Abi Tenen, Mark James Simcoe, Karina Patasova, Darioush Yarrand, Jie Yin, Salina Siddiqui, Anthony J. Rice, Layal Abi Farraj, Yii Der Ida Chen, Jugnoo S Rahi, Ronald M. Krauss, Elizabeth Theusch, Jac Charlesworth, Loretta Szczotka-Flynn, Carmel Toomes, Magda A. Meester-Smoor, Andrea J. Richardson, Paul Mitchell, Kent D. Taylor, Ronald B. Melles, Anthony J. Aldave, Richard A. Mills, Ke Cao, Elsie Chan, Mark Daniell, Jie Jin Wang, Jerome I. Rotter, Alex W. Hewitt, Stuart MacGregor, Caroline C W Klaver, Wishal D. Ramdas, Jamie E Craig, Sudha K. Iyengar, David O’Brart, Eric Jorgenson, Paul N. Baird, Yaron S. Rabinowitz, Kathryn P. Burdon, Chris Hammond, Stephen Tuft, Pirro G. Hysi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0232120

Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen
Cited by: 2
Author(s): E. Wróbel, Alexandra B. Bentz, W. Walter Lorenz, Steven T. Gardner, Mary T. Mendonça, Kristen J. Navara
Software Mentions: 4
Published: about 6 years ago

10.3389/fphys.2018.00399

Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis
Cited by: 55
Author(s): Chen Liang, Lushun Yuan, Kaiyu Qian, Guofeng Qian, Yuan Zhu, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: over 8 years ago

10.7759/cureus.12518

Validity of TIMI Score for Predicting 14-Day Mortality of Non-ST Elevation Myocardial Infarction Patients
Cited by: 0
Author(s): Dileep Kumar, Tahir Saghir, Maham Zahid, Arti Ashok, Mukesh Kumar, Asad Hussain Shah, Izza Shahid, Sajjad Ali, Ayema Haque, Musa Karim
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: almost 13 years ago

10.1007/978-1-4939-9074-0_25

Sharing Programming Resources Between Bio* Projects
Cited by: 4
Author(s): Raoul Jean Pierre Bonnal, Andy Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher J. Fields, Toshiaki Katayama, Pjotr Prins
Software Mentions: 4
Published: over 7 years ago

10.3390/nu13010201

Genistein Reduces the Risk of Local Mammary Cancer Recurrence and Ameliorates Alterations in the Gut Microbiota in the Offspring of Obese Dams
Cited by: 15
Author(s): Fábia de Oliveira Andrade, Fang Liu, Xiyuan Zhang, Mariana Rosim, Caroline Dani, Idalia M. Cruz, Thomas T.Y. Wang, William G. Helferich, Robert W. Li, Leena Hilakivi‐Clarke
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3766

The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants
Cited by: 0
Author(s): Warangkhana Songsungthong, Supasak Kulawonganunchai, Alisa Wilantho, Sissades Tongsima, Pongpisid Koonyosying, Chairat Uthaipibull, Sumalee Kamchonwongpaisan, Philip Shaw
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13148-021-01132-3

Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs
Cited by: 10
Author(s): Saara Marttila, Leena E. Viiri, Pashupati P. Mishra, Brigitte Kühnel, Pamela R. Matías‐García, Leo-Pekka Lyytikäinen, Tiina Ceder, Nina Mononen, Wolfgang Rathmann, Juliane Winkelmann, Annette Peters, Mika Kähönen, Nina Hutri‐Kähönen, Markus Juonala, Katriina Aalto‐Setälä, Olli T. Raitakari, Terho Lehtimäki, Mélanie Waldenberger, Emma Raitoharju
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-27376-3

Transcriptional analysis of adipose tissue during development reveals depot-specific responsiveness to maternal dietary supplementation
Cited by: 16
Author(s): Hernan P. Fainberg, Mark Birtwistle, Reham I. Alagal, Ahmad Alhaddad, Mark Pope, Graeme R. Davies, Rachel Woods, Marcos Castellanos, Sean May, Catharine A. Ortori, David A. Barrett, V.E.A. Perry, Frank Wiens, Bernd Stahl, Eline van der Beek, Harold S. Sacks, Helen Budge, Michael Symonds
Software Mentions: 4
Published: about 8 years ago

10.3390/pathogens10080980

In Vitro Testing of Alternative Synthetic and Natural Antiparasitic Compounds against the Monogenean Sparicotyle chrysophrii
Cited by: 9
Author(s): Ivona Mladineo, Željka Trumbić, Adrián Ormad-García, Oswaldo Palenzuela, Ariadna Sitjà‐Bobadilla, Simona Manuguerra, Cristóbal Espinosa, Concetta María Messina
Software Mentions: 4
Published: almost 5 years ago

10.3389/fphys.2018.00019

Comparison of Fatty Acid and Gene Profiles in Skeletal Muscle in Normal and Obese C57BL/6J Mice before and after Blunt Muscle Injury
Cited by: 6
Author(s): Jens-Uwe Werner, Klaus Tödter, Pengfei Xu, Lydia Lockhart, Markus Jähnert, Pascal Gottmann, Annette Schürmann, Ludger Scheja, Martin Wabitsch, Uwe Knippschild
Software Mentions: 4
Published: over 8 years ago

10.1186/1476-4598-13-241

OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets
Cited by: 22
Author(s): Stephen F. Madden, Colin Clarke, Britta K. Stordal, Mark Carey, Russell Broaddus, William M. Gallagher, John Crown, Gordon B. Mills, Bryan T. Hennessy
Software Mentions: 4
Published: over 12 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

10.3390/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

10.3389/fnins.2018.00236

Computational Testing for Automated Preprocessing 2: Practical Demonstration of a System for Scientific Data-Processing Workflow Management for High-Volume EEG
Cited by: 8
Author(s): Benjamin Ultan Cowley, Jussi Korpela
Software Mentions: 4
Published: over 8 years ago

10.3390/ijerph17031111

Short-Term Associations of Fine Particulate Matter and Synoptic Weather Types with Cardiovascular Mortality: An Ecological Time-Series Study in Shanghai, China
Cited by: 11
Author(s): Tian Qing, Mei Li, Scott Montgomery, Bo Fang, Chunfang Wang, Tian Xia, Yang Cao
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: almost 6 years ago

10.1097/MD.0000000000025008

PLCG2 as a potential indicator of tumor microenvironment remodeling in soft tissue sarcoma
Cited by: 10
Author(s): Zhengtian Li, Rong Zhao, Weibo Yang, Chan Li, Jun Huang, Zhenpei Wen, Gang Du, Lingling Jiang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0137782

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
Cited by: 23
Author(s): Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R. Barnes, Zhigang Luo
Software Mentions: 4
Published: almost 11 years ago

10.7717/peerj.12021

Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains
Cited by: 10
Author(s): Martin Konvička, Tomáš Kuras, Jana Lipárová, Vit Slezak, Dita Horázná, Jan Klečka, Irena Klečková
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-11-138

Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland
Cited by: 114
Author(s): Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, Helmut Blum
Software Mentions: 4
Published: over 16 years ago

10.1093/gigascience/gix109

Genome sequence of the small brown planthopper, Laodelphax striatellus
Cited by: 90
Author(s): Jiachen Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yan-Yuan Bao, Wan Zhao, Wei Wang, Hong Liang, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Luo Li, Jianping Yu, Le Kang, Feng Cui
Software Mentions: 4
Published: over 8 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

10.1371/journal.pone.0256091

Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data
Cited by: 12
Author(s): María Canive, Óscar González-Recio, Almudena Fernández, Patricia Vázquez, Gerard Badia-Bringué, José Luis Lavín, Joseba M. Garrido, Ramón A. Juste, Marta Alonso‐Hearn
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12862-019-1523-z

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages
Cited by: 12
Author(s): Mengxiao Yan, Ruibin Liu, Ying Liu, Andrew L. Hipp, Min Deng, Yanshi Xiong
Software Mentions: 4
Published: over 6 years ago

10.1186/s12874-016-0173-8

Modeling the oxygen uptake kinetics during exercise testing of patients with chronic obstructive pulmonary diseases using nonlinear mixed models
Cited by: 10
Author(s): Florent Baty, Christian Ritz, Arnoldus van Gestel, Martin Brutsche, Daniel Gerhard
Software Mentions: 4
Published: about 10 years ago

10.18632/aging.103624

POC1A acts as a promising prognostic biomarker associated with high tumor immune cell infiltration in gastric cancer
Cited by: 6
Author(s): Jun Q. Lu, Xiaoyan Huang, Yaohui Wang, Jian‐Wei Xie, Jia-Bin Wang, Jiumao Lin, Qi‐Yue Chen, Long‐Long Cao, Ping Li, Chang‐Ming Huang, Chao‐Hui Zheng
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-020-0460-4

Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry
Cited by: 63
Author(s): Colin A. Grambow, Lagnajit Pattanaik, William Green
Software Mentions: 4
Published: about 6 years ago

10.1007/s11302-020-09711-4

High expression levels of pyrimidine metabolic rate–limiting enzymes are adverse prognostic factors in lung adenocarcinoma: a study based on The Cancer Genome Atlas and Gene Expression Omnibus datasets
Cited by: 37
Author(s): Haiwei Wang, Xinrui Wang, Liangpu Xu, Ji Zhang, Hua Cao
Software Mentions: 4
Published: about 6 years ago

10.3390/brainsci10110813

Shedding Light on the Effects of Moderate Acute Exercise on Working Memory Performance in Healthy Older Adults: An fNIRS Study
Cited by: 11
Author(s): Katharina Stute, Nicole Hudl, Robert Stojan, Claudia Voelcker‐Rehage
Software Mentions: 4
Published: over 5 years ago

10.3390/s19224905

Microservice Security Agent Based On API Gateway in Edge Computing
Cited by: 24
Author(s): Rongxu Xu, Wenquan Jin, Do‐Hyeun Kim
Software Mentions: 4
Published: over 6 years ago

10.3390/ph14070662

Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics
Cited by: 11
Author(s): Xiaoyue Zhang, Yihan Liu, Dazhi Liu, Jianing Xu, Qiang Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5669-2

Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships
Cited by: 39
Author(s): Afshin Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey, David B. Lowry
Software Mentions: 4
Published: about 7 years ago

10.1021/acs.jproteome.0c00992

Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics
Cited by: 21
Author(s): Hayley L. Mickleburgh, Ed C. Schwalbe, Andrea Bonicelli, Haruka Mizukami, Federica Sellitto, Sefora Starace, Daniel J. Wescott, David Carter, Noemi Procopio
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj-cs.321

Big data clustering techniques based on Spark: a literature review
Cited by: 14
Author(s): Mozamel M. Saeed, Zaher Al Aghbari, Mohammed Alsharidah
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-015-0466-4

Anoikis-resistant subpopulations of human osteosarcoma display significant chemoresistance and are sensitive to targeted epigenetic therapies predicted by expression profiling
Cited by: 24
Author(s): Jessica Foley, Donald J. Scholten, Noel R. Monks, David Cherba, David J. Monsma, Paula J. Davidson, Dawna Dylewski, Karl Dykema, Mary E. Winn, Matthew R. Steensma
Software Mentions: 4
Published: over 11 years ago

10.3390/brainsci11020230

Sentence Recall in Latent and Anomic Aphasia: An Exploratory Study of Semantics and Syntax
Cited by: 6
Author(s): Christos Salis, Nadine Martin, Laura K. Reinert
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.9812

Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve
Cited by: 6
Author(s): Ruifen He, Zhongying Zhao, Yongxiu Yang, Xiaolei Liang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12936-018-2520-1

Eave ribbons treated with the spatial repellent, transfluthrin, can effectively protect against indoor-biting and outdoor-biting malaria mosquitoes
Cited by: 44
Author(s): Arnold S. Mmbando, Halfan S. Ngowo, Alex J. Limwagu, Masoud Kilalangongono, Khamis Kifungo, Fredros O. Okumu
Software Mentions: 4
Published: almost 8 years ago

10.1155/2021/5169052

Regularized Weighted Nonparametric Likelihood Approach for High-Dimension Sparse Subdistribution Hazards Model for Competing Risk Data
Cited by: 1
Author(s): Leili Tapak, Michael R. Kosorok, Majid Majid Sadeghifar, Omid Hamidi, Saeid Afshar, Hassan Doosti
Software Mentions: 4
Published: almost 5 years ago

10.2196/15394

Applying Machine Learning Models with An Ensemble Approach for Accurate Real-Time Influenza Forecasting in Taiwan: Development and Validation Study
Cited by: 18
Author(s): Hao-Yuan Cheng, Yu-Chun Wu, Min-Hau Lin, Yu-Lun Liu, Yue-Yang Tsai, Jo-Hua Wu, Ke-Han Pan, Chih-Jung Ke, Chiu-Mei Chen, Liu Ding-ping, I‐Feng Lin, Jen-Hsiang Chuang
Software Mentions: 4
Published: almost 6 years ago

10.1093/bib/bbw130

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
Cited by: 3
Author(s): Bohdan B. Khomtchouk, Edmund Weitz, Peter D. Karp, Claes Wahlestedt
Software Mentions: 4
Published: over 9 years ago

10.1098/rstb.2019.0808

Genetic sexing strains for the population suppression of the mosquito vector <i>Aedes aegypti</i>
Cited by: 22
Author(s): Panagiota Koskinioti, Antonios A. Augustinos, Danilo O. Carvalho, Muhammad Misbah-ul-Haq, Gulizar Pillwax, Lucia Duran de la Fuente, Gustavo Salvador-Herranz, Rafael Argilés Herrero, Kostas Bourtzis
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-021-02499-y

Modeling the effects of EMT-immune dynamics on carcinoma disease progression
Cited by: 2
Author(s): Daniel Bergman, Matthew Karikomi, Min Yu, Qing Nie, Adam L. MacLean
Software Mentions: 4
Published: almost 5 years ago

10.1007/s12032-021-01464-3

Dual inhibition of TGFβ and AXL as a novel therapy for human colorectal adenocarcinoma with mesenchymal phenotype
Cited by: 6
Author(s): Davide Ciardiello, Bernadette Blauensteiner, Nunzia Matrone, Valentina Belli, Thomas Mohr, Pietro Paolo Vitiello, Giulia Martini, L. Poliero, Claudia Cardone, Stefania Napolitano, Vincenzo De Falco, Emilio Francesco Giunta, Vincenza Ciaramella, Carminia Della Corte, Giusi Barra, Francesco Selvaggi, Renato Franco, Federica Zito Marino, Antonio Cuomo, Teresa Troiani, Maria Sibilia, Fortunato Ciardiello, Erika Martinelli
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-020-02279-y

Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease
Cited by: 9
Author(s): Li Ma, Wu Shi, Xiaoyan Ma, Ming‐Hui Zou, Weidan Chen, Wenlei Li, Rongjun Zou, Xinxin Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.03203

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity
Cited by: 61
Author(s): Nicola Vitulo, Wilson José Fernandes Lemos, Matteo Calgaro, Marco Confalone, Giovanna E. Felis, Giacomo Zapparoli, Tiziana Nardi
Software Mentions: 4
Published: over 7 years ago

10.1186/s13048-021-00802-3

Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth
Cited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-3131-2

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22
Cited by: 24
Author(s): Chandra Prakash, S. V. Amitha Mithra, Praveen Singh, Trilochan Mohapatra, Nagendra Singh
Software Mentions: 4
Published: almost 10 years ago

10.3389/fmicb.2018.02581

Structural and Functional Characterization of PA14/Flo5-Like Adhesins From Komagataella pastoris
Cited by: 6
Author(s): Michael D. Kock, Stefan Brückner, Nina Wozniak, M. Maestre-Reyna, M. Veelders, Julia Schlereth, Hans‐Ulrich Mösch, Lars‐Oliver Essen
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms20030606

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields
Cited by: 41
Author(s): Maciej Pawel Ciemny, Aleksandra E. Badaczewska-Dawid, Monika Pikuzinska, Andrzej Koliński, Sebastian Kmiecik
Software Mentions: 4
Published: over 7 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: almost 5 years ago

10.1155/2014/736798

Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA
Cited by: 2
Author(s): Xiaoyong Sun, Simon Lin, Xiaoyan Yan
Software Mentions: 4
Published: over 12 years ago

10.1186/s40168-021-01048-3

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements
Cited by: 28
Author(s): Dieter M. Tourlousse, Koji Narita, Takamasa Miura, Mitsuo Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, Atsushi Yamazoe, Yuichi Uchino, Keishi Kameyama, Shingo Arioka, Jiro Kataoka, Takayoshi Hisada, Kazuyuki Fujii, Shunsuke Takahashi, Miho Kuroiwa, Masatomo Rokushima, Mitsue Nishiyama, Yoshiki Tanaka, Takuya Fuchikami, Hitomi Aoki, Satoshi Kira, Ryo Koyanagi, Takeshi Naito, Morie Nishiwaki, Hirotaka Kumagai, Mikiko Konda, Keiji Kasahara, Moriya Ohkuma, Hiroko Kawasaki, Yuji Sekiguchi, Jun Terauchi
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21176060

Sperm Proteome after Interaction with Reproductive Fluids in Porcine: From the Ejaculation to the Fertilization Site
Cited by: 12
Author(s): Chiara Luongo, Leopoldo González-Brusi, Paula Cots-Rodríguez, M. J. Izquierdo-Rico, Manuel A. Bueno Sánchez, Francisco Alberto García–Vázquez
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12866-019-1500-0

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Cited by: 101
Author(s): Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey, Christian H. Ahrens
Software Mentions: 4
Published: about 7 years ago

10.1002/1878-0261.12073

Stromal SPOCK1 supports invasive pancreatic cancer growth
Cited by: 26
Author(s): Veronique L. Veenstra, Helene Damhofer, Cynthia Waasdorp, Anne Steins, Hemant M. Kocher, Jan Paul Medema, Hanneke W. M. van Laarhoven, Maarten F. Bijlsma
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-019-1827-8

methylCC: technology-independent estimation of cell type composition using differentially methylated regions
Cited by: 12
Author(s): Stephanie Hicks, Rafael A. Irizarry
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: almost 9 years ago

10.3390/ani10061055

Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing
Cited by: 5
Author(s): Arturo Levicán, James S. Fisher, Sandra L. McLellan, Rubén Avendaño‐Herrera
Software Mentions: 4
Published: about 6 years ago

10.3390/s150818613

Scalable and Cost-Effective Assignment of Mobile Crowdsensing Tasks Based on Profiling Trends and Prediction: The ParticipAct Living Lab Experience
Cited by: 28
Author(s): Paolo Bellavista, Antonio Corradi, Luca Foschini, Raffaele Ianniello
Software Mentions: 4
Published: almost 11 years ago

10.3390/s21072430

Time Series Forecasting of Univariate Agrometeorological Data: A Comparative Performance Evaluation via One-Step and Multi-Step Ahead Forecasting Strategies
Cited by: 17
Author(s): Saurabh Suradhaniwar, Soumyashree Kar, Surya S. Durbha, J. Adinarayana
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227667

Redefining transcriptional regulation of the APOE gene and its association with Alzheimer’s disease
Cited by: 25
Author(s): Eun-Gyung Lee, Jessica Tulloch, Sunny Chen, Lesley Leong, Aleen Saxton, Brian C. Kraemer, Martin Darvas, C. Dirk Keene, Andrew Shutes‐David, Kaitlin Todd, Steve Millard, Chang‐En Yu
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.7380

Dhole pack size variation: Assessing the effect of Prey availability and Apex predator
Cited by: 5
Author(s): Aishwarya Bhandari, Pallavi Ghaskadbi, Parag Nigam, Bilal Habib
Software Mentions: 4
Published: over 5 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: about 9 years ago

10.1186/s13063-021-05171-2

Passive Immunity Trial for Our Nation (PassITON): study protocol for a randomized placebo-control clinical trial evaluating COVID-19 convalescent plasma in hospitalized adults
Cited by: 13
Author(s): Wesley H. Self, Thomas G. Stewart, Allison P. Wheeler, Wissam El Atrouni, Amanda J. Bistran-Hall, Jonathan D. Casey, Vince D. Cataldo, James D. Chappell, Claudia S. Cohn, Jessica Collins, Mark R. Denison, Marjolein de Wit, S. Dixon, Abhijit Duggal, Terri Edwards, Magali J. Fontaine, Adit A. Ginde, Michelle Harkins, Thelma Harrington, Estelle S. Harris, Daanish Hoda, Tina S. Ipe, Stuti J. Jaiswal, Nicholas J. Johnson, Alan E. Jones, Maryrose Laguio-Vila, Christopher J. Lindsell, Jason Mallada, Manoj J. Mammen, Ryan A. Metcalf, Elizabeth Middleton, Simon Mucha, Hollis R. O’Neal, Sonal Pannu, Jill M. Pulley, Xinhua Qiao, Jay S. Raval, Jillian P. Rhoads, Harry Schrager, Carl Shanholtz, Nathan I. Shapiro, Stephen Schrantz, Isaac Thomsen, Krista Vermillion, Gordon R. Bernard, Todd W. Rice
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.6848

Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (<i>Danio rerio</i>)
Cited by: 5
Author(s): Matthew Tuttle, Mark Dalman, Qin Liu, Richard L. Londraville
Software Mentions: 4
Published: about 7 years ago

10.1186/s12943-015-0358-5

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Cited by: 198
Author(s): Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter, Christoph Michalski
Software Mentions: 4
Published: about 11 years ago

10.3389/fmicb.2020.549531

The Analysis of Field Strains Isolated From Food, Animal and Clinical Sources Uncovers Natural Mutations in Listeria monocytogenes Nisin Resistance Genes
Cited by: 8
Author(s): Joseph Wambui, Athmanya K. Eshwar, Mariella Aalto-Araneda, Anna K Pöntinen, Marc J. A. Stevens, Patrick Murigu Kamau Njage, Taurai Tasara
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-018-2150-1

Identification of residue pairing in interacting β-strands from a predicted residue contact map
Cited by: 4
Author(s): Wenzhi Mao, Tong Wang, Wenxuan Zhang, H. Gong
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-14-188

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
Cited by: 14
Author(s): George Y. Wu, Hongkai Ji
Software Mentions: 4
Published: about 13 years ago

10.1097/MD.0000000000025715

Mining immune-related genes with prognostic value in the tumor microenvironment of breast invasive ductal carcinoma
Cited by: 1
Author(s): Qiang He, Shuyin Xue, Qingde Wa, Mei He, Feng Shan, Zhibing Chen, Wei Chen, Xinrong Luo
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00393

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health
Cited by: 30
Author(s): Ameen Eetemadi, Navneet Rai, Beatriz Merchel Piovesan Pereira, Minseung Kim, Harold H. Schmitz, Ilias Tagkopoulos
Software Mentions: 4
Published: over 6 years ago

10.1186/s13722-021-00231-z

Alcohol consumption and dependence is linked to the extent that people experience need satisfaction while drinking alcohol in two Aboriginal and Torres Strait Islander communities
Cited by: 5
Author(s): James H. Conigrave, Emma L. Bradshaw, Katherine M. Conigrave, Richard M. Ryan, Scott Wilson, Jimmy Perry, Michael Doyle, K. S. Kylie Lee
Software Mentions: 4
Published: over 5 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

10.1186/1755-8794-7-S1-S5

Derivative component analysis for mass spectral serum proteomic profiles
Cited by: 13
Author(s): Henry Han
Software Mentions: 4
Published: over 12 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

10.1371/journal.pntd.0009425

Profound downregulation of neural transcription factor Npas4 and Nr4a family in fetal mice neurons infected with Zika virus
Cited by: 3
Author(s): Sergio P. Alpuche-Lazcano, James Saliba, Vivian Vasconcelos Costa, Gabriel Henrique Campolina-Silva, Fernanda Martins Marim, Lucas S. Ribeiro, Volker Blank, Andrew J. Mouland, Mauro M. Teixeira, Anne Gatignol
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.ppat.1008154

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