10.1371/journal.pone.0212778

Natural language processing and machine learning algorithm to identify brain MRI reports with acute ischemic stroke
Cited by: 53
Author(s): Chulho Kim, Vivienne J. Zhu, Jihad S. Obeid, Leslie A. Lenert
Software Mentions: 5
Published: over 7 years ago

10.3390/metabo11090626

Metabolic Reprogramming of Mammary Epithelial Cells during TGF-β-Induced Epithelial-to-Mesenchymal Transition
Cited by: 5
Author(s): Hua Wang, Sarantos Kostidis, Oleg A. Mayboroda, Martin Giera, Marten Hornsveld, Peter ten Dijke
Software Mentions: 5
Published: almost 5 years ago

10.1093/gigascience/giy052

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
Cited by: 3
Author(s): Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G. Burchard, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes, Fusheng Wang, Zhaohui S. Qin
Software Mentions: 5
Published: about 8 years ago

10.3389/fimmu.2019.00527

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome
Cited by: 37
Author(s): Fergal J. Duffy, January Weiner, Scott G. Hansen, David L. Tabb, Sara Suliman, Ethan Thompson, Jeroen Maertzdorf, Steven G. Smith, Gerard Tromp, Shreemanta K. Parida, Drew Dover, Michael K. Axthelm, Jayne S. Sutherland, Hazel M. Dockrell, Tom H. M. Ottenhoff, Thomas J. Scriba, Louis J. Picker, Gerhard Walzl, Stefan H. E. Kaufmann, Daniel E. Zak
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.9644

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters
Cited by: 26
Author(s): Giulia M. Marchioro, Bettina Glasl, Aschwin H. Engelen, Ester Á. Serrão, David G. Bourne, Nicole S. Webster, Pedro R. Frade
Software Mentions: 5
Published: almost 6 years ago

10.1111/gcb.14945

Investigating the relationship between climate, stand age, and temporal trends in masting behavior of European forest trees
Cited by: 45
Author(s): Mario B. Pesendorfer, Michał Bogdziewicz, Jakub Szymkowiak, Zbigniew Borowski, Władysław Kantorowicz, Josep María Espelta, Marcos Fernández‐Martínez
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-76289-7

Plant functional traits are correlated with species persistence in the herb layer of old-growth beech forests
Cited by: 14
Author(s): Giandiego Campetella, Stefano Chelli, Enrico Simonetti, Claudia Damiani, Sándor Bartha, Camilla Wellstein, Daniele Giorgini, Nicola Puletti, Ladislav Mucina, Marco Cervellini, Roberto Canullo
Software Mentions: 5
Published: over 5 years ago

10.1002/advs.201902880

ImmuCellAI: A Unique Method for Comprehensive T‐Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy
Cited by: 479
Author(s): Ya-Ru Miao, Qiong Zhang, Qian Lei, Mei Luo, Gui-Yan Xie, Hongxiang Wang, An‐Yuan Guo
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.12125

Identification of immune related cells and crucial genes in the peripheral blood of ankylosing spondylitis by integrated bioinformatics analysis
Cited by: 12
Author(s): Yang Zheng, Bingbing Cai, Conglin Ren, Haipeng Xu, Weibin Du, Yinglong Wu, Fei-Jan Lin, Helou Zhang, Renfu Quan
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12859-015-0574-4

Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease
Cited by: 42
Author(s): Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama
Software Mentions: 5
Published: about 11 years ago

10.3389/fimmu.2018.01868

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Cited by: 11
Author(s): Friederike Ebner, Mathias Kuhring, Aleksandar Radonić, Ankur Midha, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 5
Published: almost 8 years ago

10.3390/toxics9090215

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice
Cited by: 4
Author(s): Karen Chiu, Shah Tauseef Bashir, Lei Gao, Jessica Gutiérrez, María R C de Godoy, Jenny Drnevich, Christopher J. Fields, Isaac Cann, Jodi A. Flaws, Romana A. Nowak
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2020.01138

Bioinformatics Analysis of Gut Microbiota and CNS Transcriptome in Virus-Induced Acute Myelitis and Chronic Inflammatory Demyelination; Potential Association of Distinct Bacteria With CNS IgA Upregulation
Cited by: 11
Author(s): Seiichi Omura, Fumitaka Sato, Ah-Mee Park, Mitsugu Fujita, Sundar Khadka, Yumina Nakamura, Aoshi Katsuki, Kenji Nishio, Felicity N. E. Gavins, Ikuo Tsunoda
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0078316

Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes
Cited by: 15
Author(s): Lydia Smith, Arpit Tandon, Ruchir Shah, Deepak Mav, Alyson B. Scoltock, John A. Cidlowski
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pcbi.0030026

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
Cited by: 56
Author(s): Rachel Karchin, Alvaro N.A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej S̆ali
Software Mentions: 5
Published: over 19 years ago

10.3389/fonc.2021.637733

Low Expression of ADCY4 Predicts Worse Survival of Lung Squamous Cell Carcinoma Based on Integrated Analysis and Immunohistochemical Verification
Cited by: 3
Author(s): Zhicong Liu, Lixin Ru, Zhenchao Ma
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2021.640837

Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy
Cited by: 1
Author(s): Khushboo Singh, Hai Fang, Graham Davies, Benjamin Wright, Helen Lockstone, Richard O. Williams, Daniela Čiháková, Julian C. Knight, Shoumo Bhattacharya
Software Mentions: 5
Published: over 5 years ago

10.3390/nu12092570

Diet, Perceived Intestinal Well-Being and Compositions of Fecal Microbiota and Short Chain Fatty Acids in Oat-Using Subjects with Celiac Disease or Gluten Sensitivity
Cited by: 8
Author(s): Lotta Nylund, Salla Hakkola, Leo Lahti, Seppo Salminen, Marko Kalliomäki, Baoru Yang, Kaisa M. Linderborg
Software Mentions: 5
Published: almost 6 years ago

10.1007/s00125-021-05527-y

MAIT cell alterations in adults with recent-onset and long-term type 1 diabetes
Cited by: 5
Author(s): Isabelle Nel, Lucie Beaudoin, Zouriatou Gouda, Camille Rousseau, Pauline Soulard, Matthieu Rouland, Léo Bertrand, Christian Boîtard, Étienne Larger, Agnès Lehuen
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: over 10 years ago

10.3389/fphys.2019.01305

The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen Barriers
Cited by: 28
Author(s): Hong Shen, Zhihui Xu, Zanming Shen, Zhongyan Lu
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2021.744799

Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis
Cited by: 11
Author(s): Giuseppe Gianini Figueirêdo Leite, Bianca Lima Ferreira, Alexandre Keiji Tashima, Erika Sayuri Nishiduka, Edécio Cunha‐Neto, Milena Karina Coló Brunialti, Murillo Santucci César de Assunção, Luciano César Pontes Azevedo, Flávio Geraldo Resende Freitas, Tom van der Poll, Brendon P. Scicluna, Reinaldo Salomão
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0237412

The impact of different negative training data on regulatory sequence predictions
Cited by: 3
Author(s): Louisa-Marie Krützfeldt, Max Schubach, Martin Kircher
Software Mentions: 5
Published: over 5 years ago

10.1186/s12885-019-5537-0

Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma
Cited by: 8
Author(s): Karsten Kleo, Lora Dimitrova, Elisabeth Oker, Nancy Tomaszewski, Erika Gebel Berg, Franziska Taruttis, Julia C. Engelmann, Philipp Schwarzfischer, Jörg Reinders, Rainer Spang, Wolfram Gronwald, Peter J. Oefner, Michael Hummel
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0169115

Field-Evolved Resistance in Corn Earworm to Cry Proteins Expressed by Transgenic Sweet Corn
Cited by: 133
Author(s): Galen P. Dively, P. Dilip Venugopal, Chad Finkenbinder
Software Mentions: 5
Published: over 9 years ago

10.3389/fpls.2021.681962

Why More Leaflets? The Role of Natural Selection in Shaping the Spatial Pattern of Leaf-Shape Variation in Oxytropis diversifolia (Fabaceae) and Two Close Relatives
Cited by: 4
Author(s): Hui Wang, Peiliang Liu, Jian Li, Han Yang, Qin Li, Zhao‐Yang Chang
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2021.711359

Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat
Cited by: 67
Author(s): Ana Nogal, Panayiotis Louca, Mengjie Zhang, Philippa M Wells, Claire J. Steves, Tim D. Spector, Mario Falchi, Ana M. Valdes, Cristina Menni
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0069666

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data
Cited by: 21
Author(s): Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Maria Simi, Rita Shaknovich, Fabien Campagne
Software Mentions: 5
Published: almost 13 years ago

10.1371/journal.pone.0174461

Abnormal expression of mRNA, microRNA alteration and aberrant DNA methylation patterns in rectal adenocarcinoma
Cited by: 21
Author(s): Hua Yang, Xiukun Ma, Xianglong Liu, Xia Yuan, Hai Qin, Xipeng Zhang
Software Mentions: 5
Published: over 9 years ago

10.1186/s13046-021-02031-4

Elesclomol-induced increase of mitochondrial reactive oxygen species impairs glioblastoma stem-like cell survival and tumor growth
Cited by: 35
Author(s): Mariachiara Buccarelli, Quintino Giorgio D’Alessandris, Paola Matarrese, Cristiana Mollinari, Michele Signore, Andrea Cappannini, Maurizio Martini, Pierluigi D’Aliberti, Gabriele De Luca, Francesca Pedini, Alessandra Boe, Mauro Biffoni, Roberto Pallini, Lucia Ricci‐Vitiani
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.56474

A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission
Cited by: 42
Author(s): Aurélia C. Balestra, Mohammad Zeeshan, Edward Rea, Carla Pasquarello, Lorenzo Brusini, Tobias Mourier, Amit Kumar Subudhi, Natacha Klages, Patrizia Arboit, Rajan Kumar Pandey, Declan Brady, Sue Vaughan, Anthony A. Holder, Arnab Pain, David Ferguson, Alexandre Hainard, Rita Tewari, Mathieu Brochet
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-86002-x

Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway
Cited by: 102
Author(s): Andrea R. Daamen, Prathyusha Bachali, Katherine A. Owen, Kathryn M. Kingsmore, Erika L. Hubbard, Adam C. Labonte, Robert Robl, Sneha Shrotri, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 5
Published: over 5 years ago

10.1534/g3.117.300125

Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen
Cited by: 4
Author(s): Priyanka Surana, Ruo Xu, Greg Fuerst, Antony V. E. Chapman, Dan Nettleton, Roger P. Wise
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-018-31882-9

Investigating the genetic profile of dopaminergic neurons in the VTA in response to perinatal nicotine exposure using mRNA-miRNA analyses
Cited by: 14
Author(s): Renee F. Keller, Andrei Dragomir, Yonggang Fan, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12870-016-0860-y

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors
Cited by: 16
Author(s): Saurabh Gayali, Shankar Acharya, Nilesh Vikram Lande, Ashish Pandey, Subhra Chakraborty, Niranjan Chakraborty
Software Mentions: 5
Published: almost 10 years ago

10.1038/s41598-018-37098-1

Comparison between dopaminergic and non-dopaminergic neurons in the VTA following chronic nicotine exposure during pregnancy
Cited by: 9
Author(s): Renee F. Keller, Tina Kazemi, Andrei Dragomir, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: over 7 years ago

10.3390/foods8080332

Influence of Kiwifruit Extract Infusion on Consumer Sensory Outcomes of Striploin (M. longissimus lumborum) and Outside Flat (M. biceps femoris) from Beef Carcasses
Cited by: 7
Author(s): A. M. Lees, Małgorzata Konarska, Garth Tarr, Rod Polkinghorne, P. McGilchrist
Software Mentions: 5
Published: almost 7 years ago

10.1136/bmj.l440

Duration of antibiotic treatment for common infections in English primary care: cross sectional analysis and comparison with guidelines
Cited by: 73
Author(s): Koen B Pouwels, Susan Hopkins, Martin J. Llewelyn, A Sarah Walker, Cliodna McNulty, Julie V. Robotham
Software Mentions: 5
Published: over 7 years ago

10.3390/ijerph18105435

Depressive Mood Assessment Method Based on Emotion Level Derived from Voice: Comparison of Voice Features of Individuals with Major Depressive Disorders and Healthy Controls
Cited by: 9
Author(s): Shuji Shinohara, Mitsuteru Nakamura, Yasuhiro Omiya, Masakazu Higuchi, Naoki Hagiwara, Shunji Mitsuyoshi, Hiroyuki Toda, Taku Saito, Masaaki Tanichi, Aihide Yoshino, Shinichi Tokuno
Software Mentions: 5
Published: about 5 years ago

10.1177/0379572120973908

Changes in Retinol Binding Protein 4 Level in Undernourished Children After a Nutrition Intervention Are Positively Associated With Mother’s Weight but Negatively With Mother’s Height, Intake of Whole Milk, and Markers of Systemic Inflammation: Results From a Community-Based Intervention Study
Cited by: 0
Author(s): Subhasish Das, Amran Gazi, Mehedi Hasan, Shah Mohammad Fahim, Ashraful Alam, Md. Shabab Hossain, Mustafa Mahfuz, Tahmeed Ahmed
Software Mentions: 5
Published: over 5 years ago

10.1093/femsec/fiy225

Highly competitive fungi manipulate bacterial communities in decomposing beech wood (<i>Fagus sylvatica</i>)
Cited by: 29
Author(s): Sarah Johnston, Jennifer Hiscox, Melanie Savoury, Lynne Boddy, Andrew J. Weightman
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2105-7-64

HotSwap for bioinformatics: A STRAP tutorial
Cited by: 8
Author(s): Christoph Gille, Peter N. Robinson
Software Mentions: 5
Published: over 20 years ago

10.3389/fgene.2019.00888

Genome-Wide Homozygosity Mapping Reveals Genes Associated With Cognitive Ability in Children From Saudi Arabia
Cited by: 5
Author(s): Sergey A. Kornilov, Mei Tan, Abdullah Aljughaiman, O. Yu. Naumova, Elena L. Grigorenko
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2021.662239

Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution
Cited by: 5
Author(s): Vladimir Jovanović, Melanie Sarfert, Carlos S. Reyna-Blanco, Henrike Indrischek, Dulce I. Valdivia, Ekaterina Shelest, Katja Nowick
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2020.00559

The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies
Cited by: 22
Author(s): Roberta Amoriello, Victor Greiff, Alessandra Aldinucci, Elena Bonechi, Alberto Carnasciali, Benedetta Peruzzi, Anna Maria Repice, Alice Mariottini, Riccardo Saccardi, Benedetta Mazzanti, Luca Massacesi, Clara Ballerini
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.572504

Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid
Cited by: 13
Author(s): Montserrat Saladié, José A. Caparrós-Martín, Ana Patrícia, Peter Wark, Stephen M. Stick, Fergal O’Gara
Software Mentions: 5
Published: almost 6 years ago

10.1016/S2589-7500(21)00022-4

Performance of intensive care unit severity scoring systems across different ethnicities in the USA: a retrospective observational study
Cited by: 28
Author(s): Rik Sarkar, Christopher S. Martin, Heather Mattie, Judy Wawira Gichoya, David J. Stone, Leo Anthony Celi
Software Mentions: 5
Published: over 5 years ago

10.3389/fpsyg.2017.01764

Effects of Noise on English Listening Comprehension among Chinese College Students with Different Learning Styles
Cited by: 4
Author(s): Xiu-yu Yang, Jie Meng, Yong Sheng Zhao
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0201483

HSRA: Hadoop-based spliced read aligner for RNA sequencing data
Cited by: 11
Author(s): Roberto R. Expósito, Jorge González-Domínguez, Juan Touriño
Software Mentions: 5
Published: almost 8 years ago

10.3389/fmicb.2019.01961

Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs
Cited by: 19
Author(s): Marta Turon, Joan Cáliz, Xavier Triadó–Margarit, Emilio O. Casamayor, María Jesús Uriz
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.12067

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
Cited by: 2
Author(s): Rehema Liyai, Kimita Gathii, Clement Masakhwe, David Abuom, Beth Mutai, David Miruka Onyango, John N. Waitumbi
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.7171

Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples
Cited by: 10
Author(s): Huimei Wang, Mingwei Zhang, Qiqi Xie, Yu Jin, Qi Yan, Qiuyuan Yue
Software Mentions: 5
Published: about 7 years ago

10.1186/s42523-021-00080-w

The skin microbiome of Xenopus laevis and the effects of husbandry conditions
Cited by: 7
Author(s): Maya Z. Piccinni, Joy E. M. Watts, Marie Fourny, Matthew Guille, Samuel Robson
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0129323

Microclimatic Divergence in a Mediterranean Canyon Affects Richness, Composition, and Body Size in Saproxylic Beetle Assemblages
Cited by: 4
Author(s): Jörn Buse, Samuel Fassbender, Martin H. Entling, Tomáš Pavlı́ček
Software Mentions: 5
Published: about 11 years ago

10.3389/fcvm.2020.615161

Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic Hearts
Cited by: 21
Author(s): Lingfang Zhuang, Lin Lü, Ruiyan Zhang, Kang Chen, Xiaoxiang Yan
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-018-4763-1

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
Cited by: 36
Author(s): Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint‐Jean, Grégory Carrier
Software Mentions: 5
Published: about 8 years ago

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0034560

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments
Cited by: 37
Author(s): David Hysom, Pejman Naraghi-Arani, Maher Elsheikh, A.C. Carrillo, Peter Williams, Shea N. Gardner
Software Mentions: 5
Published: over 14 years ago

10.3390/ani11071860

Vacuum Dynamics as an Alternative Method for Detection of Bimodal Milk Ejection in Dairy Cows
Cited by: 0
Author(s): Matthias Wieland, C.M. Geary, G. Gioia, K. L. Case, P. Moroni, Anja Sipka
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-5504-9

Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data
Cited by: 5
Author(s): Carlos Farkas, Francisco Fuentes-Villalobos, Boris Rebolledo‐Jaramillo, Fernando Benavides, Ariel F. Castro, Roxana Pincheira
Software Mentions: 5
Published: over 7 years ago

10.1016/j.celrep.2019.11.066

Molecular Basis for Autosomal-Dominant Renal Fanconi Syndrome Caused by HNF4A
Cited by: 28
Author(s): Valentina Marchesin, Albert Pérez-Martí, G. Le Meur, Roman Pichler, Kelli Grand, Enriko Klootwijk, Anne Kesselheim, Robert Kleta, Soeren S. Lienkamp, Matias Simons
Software Mentions: 5
Published: over 6 years ago

10.1186/s12879-021-06331-0

A novel CT-based radiomics in the distinction of severity of coronavirus disease 2019 (COVID-19) pneumonia
Cited by: 9
Author(s): Zongyu Xie, Haitao Sun, Jian Wang, He Xu, Shuhua Li, Cancan Zhao, Yuqing Gao, Xiaolei Wang, Tongtong Zhao, Shaofeng Duan, Chunhong Hu, Weiqun Ao
Software Mentions: 5
Published: about 5 years ago

10.12688/f1000research.17706.3

Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia
Cited by: 5
Author(s): Li-Fang Yeo, Farhang Aghakhanian, J. Tan, Han Ming Gan, Maude E. Phipps
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pgen.1009726

The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
Cited by: 8
Author(s): Erik Axelsson, Ingrid Ljungvall, Priyasma Bhoumik, Laura Bas Conn, Eva Murén, Åsa Ohlsson, Lisbeth H. Olsen, Karolina Engdahl, Ragnvi Hagman, Jeanette Hanson, Dmytro Kryvokhyzha, Mats E. Pettersson, Olivier Grenet, Jonathan G. Moggs, Alberto Del Río-Espínola, Christian Epe, Bruce E. Taillon, Nilesh R. Tawari, Shrinivas Mane, Troy Hawkins, Åke Hedhammar, Philippe Gruet, Jens Häggström, Kerstin Lindblad‐Toh
Software Mentions: 5
Published: almost 5 years ago

10.1128/mBio.01500-19

Dissecting the Gene Expression, Localization, Membrane Topology, and Function of the Plasmodium falciparum STEVOR Protein Family
Cited by: 38
Author(s): Jan Stephan Wichers, Jochen Scholz, Jan Strauss, Susanne Witt, Andrés Lill, Laura-Isabell Ehnold, Niklas Neupert, Benjamin Liffner, Renke Lühken, Michaela Petter, Stephan Lorenzen, Danny W. Wilson, Christian Löw, Catherine Lavazec, Iris Bruchhaus, Egbert Tannich, Tim‐Wolf Gilberger, Anna Bachmann
Software Mentions: 5
Published: almost 7 years ago

10.1111/eva.12278

Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tracts
Cited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: about 11 years ago

10.1186/s12864-020-07002-1

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking
Cited by: 13
Author(s): Clemens Falker‐Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, W. Bessei, Jörn Bennewitz, Jens Tetens
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms17060956

Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes
Cited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: about 10 years ago

10.1186/s40168-021-01056-3

Anna Karenina and the subgingival microbiome associated with periodontitis
Cited by: 15
Author(s): Khaled Altabtbaei, Pooja Maney, Sukirth M. Ganesan, Shareef M Dabdoub, Haikady N. Nagaraja, Purnima Kumar
Software Mentions: 5
Published: about 5 years ago

10.1186/s13567-021-00925-x

Prediction of Johne’s disease state based on quantification of T cell markers and their interaction with macrophages in the bovine intestine
Cited by: 2
Author(s): Caitlin J. Jenvey, Adrienne L. Shircliff, Elsa Obando Marrero, Judith R. Stabel
Software Mentions: 5
Published: over 5 years ago

10.1155/2021/6641838

Analysis of Molecular Mechanism of Erxian Decoction in Treating Osteoporosis Based on Formula Optimization Model
Cited by: 22
Author(s): Lang Yang, Liuyi Fan, Kexin Wang, Yu-peng Chen, Liuqin Liang, Xuemei Qin, Aiping Lü, Peng Cao, Bin Yu, Daogang Guan, Junxiang Peng
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1005711

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
Cited by: 16
Author(s): Wesley M. Botello‐Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jérôme J. Lacroix, Jijun Hao, Yang Luo
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2105-10-S6-S10

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
Cited by: 15
Author(s): Ernesto Picardi, Flavio Mignone, Graziano Pesole
Software Mentions: 5
Published: about 17 years ago

10.1186/s12916-020-01806-4

ADAM22/LGI1 complex as a new actionable target for breast cancer brain metastasis
Cited by: 7
Author(s): Sara Charmsaz, Ben Doherty, Sinéad Cocchiglia, Damir Varešlija, Attilio Marino, Nicola Cosgrove, Ricardo Marques, Nolan Priedigkeit, Siobhan Purcell, Fiona T. Bane, Jarlath Bolger, Christopher Byrne, Philip J. O’Halloran, Francesca Brett, Katherine M. Sheehan, Kieran Brennan, Ann M. Hopkins, Stephen Keelan, Petra Jagušt, Stephen F. Madden, Chiara Martinelli, Matteo Battaglini, Steffi Oesterreich, Adrian V. Lee, Gianni Ciofani, Arnold D. Hill, Leonie S. Young
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-555

piRNAQuest: searching the piRNAome for silencers
Cited by: 49
Author(s): Arijita Sarkar, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 5
Published: about 12 years ago

10.1002/ece3.5267

Macroevolution of arboreality in salamanders
Cited by: 18
Author(s): Erica K. Baken, Dean C. Adams
Software Mentions: 5
Published: about 7 years ago

10.1186/s40168-018-0417-4

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota
Cited by: 56
Author(s): Jane A. Mullaney, J. Stephens, Mary Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown, Emma E. Hamilton‐Williams
Software Mentions: 5
Published: over 8 years ago

10.1186/s40168-018-0586-1

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation
Cited by: 34
Author(s): Hooman Derakhshani, J.C. Plaizier, Jeroen De Buck, Herman W. Barkema, Ehsan Khafipour
Software Mentions: 5
Published: over 7 years ago

10.1038/srep39002

Phenotypic plasticity in sex pheromone production in Bicyclus anynana butterflies
Cited by: 28
Author(s): Emilie Dion, Antónia Monteiro, Joanne Y. Yew
Software Mentions: 5
Published: over 9 years ago

10.1093/gigascience/giz071

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)
Cited by: 35
Author(s): Liang Qiang, Huayang Li, Shouke Li, Fuling Yuan, Jiantong Sun, Qicheng Duan, Qingyun Li, Rui Zhang, Ya Lin Sang, Nian Wang, Xiangwen Hou, Ke Yang, Jian Ning Liu, Long Yang
Software Mentions: 5
Published: about 7 years ago

10.1007/s11356-020-07660-4

Transcriptional and biochemical biomarker responses in a freshwater mussel (Anodonta anatina) under environmentally relevant Cu exposure
Cited by: 7
Author(s): Gustaf Ekelund Ugge, Annie Jonsson, Björn Olsson, Robert Sjöback, Olof Berglund
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0250568

NMR analysis of the correlation of metabolic changes in blood and cerebrospinal fluid in Alzheimer model male and female mice
Cited by: 2
Author(s): Filip Stojanovic, Mariam Taktek, Nam Huan Khieu, Junzhou Huang, Shuxian Jiang, Kerry Rennie, Balu Chakravarthy, Willard J. Costain, Miroslava Čuperlović-Culf
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.pone.0105097

Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: almost 12 years ago

10.3390/nu12072067

Novel Essential Amino Acid Supplements Following Resistance Exercise Induce Aminoacidemia and Enhance Anabolic Signaling Irrespective of Age: A Proof-of-Concept Trial
Cited by: 6
Author(s): Matthew Lees, Oliver J. Wilson, Erin K. Webb, Daniel A. Traylor, Todd Prior, Antonis Elia, Paul Harlow, Alistair Black, Paul Parker, N. Harris, M. Cooke, Christopher Balchin, Mathew Butterworth, Stuart M. Phillips, Theocharis Ispoglou
Software Mentions: 5
Published: about 6 years ago

10.1016/j.celrep.2019.09.082

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data
Cited by: 120
Author(s): Erica A. K. DePasquale, Daniel Schnell, Pieter-Jan Van Camp, Íñigo Valiente-Alandí, Burns C. Blaxall, H. Leighton Grimes, Harinder Singh, Nathan Salomonis
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0236796

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management
Cited by: 9
Author(s): Antonio J. Fernández‐González, Nuria M. Wentzien, Pablo J. Villadas, Antonio Valverde-Corredor, Ana V. Lasa, Carmen Gómez-Lama Cabanás, Jesús Mercado‐Blanco, Manuel Fernández‐López
Software Mentions: 5
Published: almost 6 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-019-5887-7

Refinement of breast cancer molecular classification by miRNA expression profiles
Cited by: 59
Author(s): Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao H. Saal, Åke Borg, Johan Vallon-Christerson, Carlos Rovira
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-019-40479-9

Egg-laying decisions based on olfactory cues enhance offspring fitness in Stomoxys calcitrans L. (Diptera: Muscidae)
Cited by: 21
Author(s): Steve B. S. Baleba, Baldwyn Torto, Daniel K. Masiga, Christopher W. Weldon, Merid N. Getahun
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-020-65329-x

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase
Cited by: 9
Author(s): Max‐Bernhard Ballhausen, Rebecca E. Hewitt, Matthias C. Rillig
Software Mentions: 5
Published: about 6 years ago

10.3390/microorganisms7120598

Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China
Cited by: 24
Author(s): Anyi Hu, Hongjie Wang, Meixian Cao, Abbas Rashid, Mingfeng Li, Chang‐Ping Yu
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-021-02372-y

Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Cited by: 9
Author(s): Fatemeh Ostadhossein, Parikshit Moitra, Esra Altun, Debapriya Dutta, Dinabandhu Sar, Indu Tripathi, Shih Hsuan Hsiao, Valeriya Kravchuk, Shuming Nie, Dipanjan Pan
Software Mentions: 5
Published: about 5 years ago

10.1186/s12967-020-02695-0

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2
Cited by: 39
Author(s): Abul B.M.M.K. Islam, A. A. Khan, Rasel Ahmed, Md. Sabbir Hossain, Shah Md. Tamim Kabir, Md Shahidul Islam, Amam Zonaed Siddiki
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.01943

Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Cited by: 4
Author(s): Felix Laguna-Teno, María Suárez-Diez, Juan Antonio Tamayo-Ramos
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-20471-5

Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer
Cited by: 104
Author(s): Chad Tang, Brian P. Hobbs, Ahmed M. Amer, Li Xiao, Carmen Behrens, Jaime Rodriguez Canales, Edwin Parra Cuentas, Pamela Villalobos, David Fried, Joe Y. Chang, David S. Hong, James Welsh, Boris Sepesi, Laurence Edward Court, Ignacio I. Wistuba, Eugene J. Koay
Software Mentions: 5
Published: over 8 years ago

10.1111/eva.13269

Rapid evolution of knockdown resistance haplotypes in response to pyrethroid selection in <i>Aedes aegypti</i>
Cited by: 13
Author(s): Jennifer Baltzegar, Michael R. Vella, Christian E. Gunning, Gissella M. Vásquez, Helvio Astete, Fred Stell, Michael L. Fisher, Thomas W. Scott, Audrey Lenhart, Alun L. Lloyd, Amy C. Morrison, Fred Gould
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.579709

Potential of Immune-Related Genes as Biomarkers for Diagnosis and Subtype Classification of Preeclampsia
Cited by: 8
Author(s): Ying Wang, Zhen Li, Guanhua Song, Jun Wang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12920-021-00928-9

Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of esophageal squamous cell carcinoma
Cited by: 8
Author(s): Mingdi Liu, Faping Li, Bin Liu, Yong‐Ping Jian, Dan Zhang, Honglan Zhou, Yishu Wang, Zhixiang Xu
Software Mentions: 5
Published: over 5 years ago