10.7554/eLife.54186
Epigenetic inheritance of circadian period in clonal cellsCited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: about 6 years ago
10.1186/s13227-020-0147-0
Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurusCited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: over 6 years ago
10.3389/fonc.2021.643104
TRIM68, PIKFYVE, and DYNLL2: The Possible Novel Autophagy- and Immunity-Associated Gene Biomarkers for Osteosarcoma PrognosisCited by: 10
Author(s): Jie Jiang, Dachang Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Yuanlin Yao, Wu‐Hua Chen, Hao Guo, Chong Liu, Xinli Zhan
Software Mentions: 13
Published: over 5 years ago
10.1186/s13059-020-02071-7
Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq dataCited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: about 6 years ago
10.12688/f1000research.8967.2
An end to end workflow for differential gene expression using Affymetrix microarraysCited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: about 8 years ago
10.1534/g3.119.400728
Efficient Estimation of Marker Effects in Plant BreedingCited by: 10
Author(s): Alencar Xavier
Software Mentions: 13
Published: over 6 years ago
10.12688/f1000research.10742.2
haploR: an R package for querying web-based annotation toolsCited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: about 9 years ago
10.1038/s42003-021-02335-3
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissuesCited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: about 5 years ago
10.3390/nu12123626
Trajectories of Body Composition during Advanced Aging in Consideration of Diet and Physical Activity: A 20-Year Longitudinal StudyCited by: 6
Author(s): Alexandra Jungert, Gerrit Eichner, Monika Neuhäuser‐Berthold
Software Mentions: 13
Published: over 5 years ago
10.1002/ece3.6520
Growth and survival of the superorganism: Ant colony macronutrient intake and investmentCited by: 3
Author(s): Yeisson Gutiérrez, Tung Phung, Harald Mumma, Arden Ambrose‐Winters, Christoph Scherber, Chris R. Smith
Software Mentions: 13
Published: about 6 years ago
10.1093/bioinformatics/bty713
Bigmelon: tools for analysing large DNA methylation datasetsCited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: almost 8 years ago
10.3389/fonc.2021.639013
Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL PrognosisCited by: 3
Author(s): Liang Wu, Mingming Jiang, Ping Yu, Jianfeng Li, Wen Ouyang, Chong Feng, Wei Zhao, Yuting Dai, Jinyan Huang
Software Mentions: 13
Published: over 5 years ago
10.1186/s12859-020-03922-7
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusionsCited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: over 5 years ago
10.1186/s12859-021-04142-3
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analysesCited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: about 5 years ago
10.1371/journal.pone.0193437
Delineating modern variation from extinct morphology in the fossil record using shells of the Eastern Box Turtle (Terrapene carolina)Cited by: 8
Author(s): Natasha Vitek
Software Mentions: 13
Published: over 8 years ago
10.1128/AEM.01225-21
Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One WorkweekCited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: almost 5 years ago
10.3390/microorganisms9010092
Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot SystemsCited by: 23
Author(s): Joel F. Swift, Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, Allison J. Miller
Software Mentions: 13
Published: over 5 years ago
10.1038/s41598-019-49160-7
Early life determinants induce sustainable changes in the gut microbiome of six-year-old childrenCited by: 27
Author(s): Silvia Gschwendtner, Hani Kang, Elisabeth Thiering, Susanne Kublik, Bärbel U. Foesel, Holger Schulz, Susanne Krauss‐Etschmann, Joachim Heinrich, Anne Schöler, Michael Schloter, Marie Standl
Software Mentions: 13
Published: almost 7 years ago
10.1186/s12935-020-01362-0
Immune-related long non-coding RNA signature identified prognosis and immunotherapeutic efficiency in bladder cancer (BLCA)Cited by: 40
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Ye Tian
Software Mentions: 13
Published: about 6 years ago
10.3389/fpls.2021.633651
Improving Wheat Yield Prediction Using Secondary Traits and High-Density Phenotyping Under Heat-Stressed EnvironmentsCited by: 6
Author(s): Mohammad Zillur Rahman, Jared Crain, Atena Haghighattalab, Ravi P. Singh, Jesse Poland
Software Mentions: 13
Published: almost 5 years ago
10.3390/e22020203
An Analysis of Smart Contracts Security Threats Alongside Existing SolutionsCited by: 18
Author(s): Antonio López Vivar, Alberto Turégano Castedo, Ana Lucila Sandoval Orozco, Luis Javier García Villalba
Software Mentions: 13
Published: over 6 years ago
10.1186/s13059-017-1305-0
Splatter: simulation of single-cell RNA sequencing dataCited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: almost 9 years ago
10.1186/s12868-019-0538-0
28th Annual Computational Neuroscience Meeting: CNS*2019Cited by: 3
Author(s):
Software Mentions: 13
Published: over 6 years ago
10.3389/fonc.2020.629909
Identification of an Immune Gene-Associated Prognostic Signature and Its Association With a Poor Prognosis in Gastric Cancer PatientsCited by: 15
Author(s): Xiaoqing Guan, Zhiyuan Xu, Runzhe Chen, Jiang‐Jiang Qin, Xiangdong Cheng
Software Mentions: 13
Published: over 5 years ago
10.1186/s12859-015-0453-z
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysisCited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: over 11 years ago
10.1128/AEM.01096-17
Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing DataCited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: almost 9 years ago
10.1038/s41398-021-01596-0
Autoantibody profiles associated with clinical features in psychotic disordersCited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: almost 5 years ago
10.1371/journal.pone.0178783
Pharmacokinetics of caspofungin acetate to guide optimal dosing in catsCited by: 8
Author(s): Jana Leshinsky, Andrew J. McLachlan, David J. R. Foster, Ross Norris, Vanessa R. Barrs
Software Mentions: 13
Published: about 9 years ago
10.12688/f1000research.17548.2
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and PythonCited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: over 7 years ago
10.3389/fonc.2020.01767
Ovarian Blood Sampling Identifies Junction Plakoglobin as a Novel Biomarker of Early Ovarian CancerCited by: 6
Author(s): Florian Weiland, Noor A. Lokman, Manuela Klingler‐Hoffmann, Thomas W. Jobling, Andrew N. Stephens, Karin Sundfeldt, Peter Hoffmann, Martin K. Oehler
Software Mentions: 13
Published: almost 6 years ago
10.3390/cancers13163922
Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and DormancyCited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: almost 5 years ago
10.12688/f1000research.6379.2
regionReport: Interactive reports for region-level and feature-level genomic analysesCited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: about 10 years ago
10.1186/s12859-021-04268-4
A comprehensive database for integrated analysis of omics data in autoimmune diseasesCited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: about 5 years ago
10.18632/oncotarget.6716
Integrative bioinformatic analyses of an oncogenomic profile reveal the biology of endometrial cancer and guide drug discoveryCited by: 5
Author(s): Henry Sung Ching Wong, Yung‐Shun Juan, Mei-Shin Wu, Yan Feng Zhang, Yi‐Hsiang Hsu, Huang-Hui Chen, Weimin Liu, Wei Chiao Chang
Software Mentions: 13
Published: over 10 years ago
10.3389/fgene.2019.00317
Single-Cell RNA-Seq Technologies and Related Computational Data AnalysisCited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: over 7 years ago
10.1002/bjs5.50138
Global variation in anastomosis and end colostomy formation following left‐sided colorectal resectionCited by: 16
Author(s): GlobalSurg Collaborative
Software Mentions: 13
Published: over 7 years ago
10.1111/eva.12965
Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster <i>Crassostrea gigas</i> throughout the Northern HemisphereCited by: 11
Author(s): Ben J. G. Sutherland, Claire Rycroft, Anne‐Laure Ferchaud, Rob Saunders, Li Li, Sheng Liu, Amy M. Chan, Sarah P. Otto, Curtis A. Suttle, Kristina M. Miller
Software Mentions: 13
Published: over 6 years ago
10.1177/0271678X17713901
Modified structural network backbone in the contralesional hemisphere chronically after stroke in rat brainCited by: 21
Author(s): Michel R.T. Sinke, Willem M. Otte, Maurits Pa van Meer, Annette van der Toorn, Rick M. Dijkhuizen
Software Mentions: 13
Published: about 9 years ago
10.1186/s12859-015-0794-7
Evaluation of methods for differential expression analysis on multi-group RNA-seq count dataCited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: over 10 years ago
10.1186/s12859-020-03774-1
Hypercluster: a flexible tool for parallelized unsupervised clustering optimizationCited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: almost 6 years ago
10.3389/fimmu.2020.620716
Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell HelpCited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: over 5 years ago
10.1128/mBio.02275-17
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <i>Puccinia striiformis</i> f. sp. <i>tritici</i> Reveals High Interhaplotype DiversityCited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 8 years ago
10.1007/s00248-020-01635-1
Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral CompositionCited by: 12
Author(s): Irina Tanuwidjaja, Cordula Vogel, Geertje Johanna Pronk, Anne Schöler, Susanne Kublik, Gisle Vestergaard, Ingrid Kögel‐Knabner, Mirna Mrkonjić Fuka, Michael Schloter, Stefanie Schulz
Software Mentions: 13
Published: over 5 years ago
10.18632/aging.202976
Development and validation of epithelial mesenchymal transition-related prognostic model for hepatocellular carcinomaCited by: 7
Author(s): Xuequan Wang, Ziming Xing, Huihui Xu, Haihua Yang, Tongjing Xing
Software Mentions: 13
Published: about 5 years ago
10.1371/journal.pone.0212956
Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentationCited by: 24
Author(s): Colin Lischik, Leonie Adelmann, Joachim Wittbrodt
Software Mentions: 13
Published: over 7 years ago
10.1186/s12861-018-0163-7
Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cellsCited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: over 8 years ago
10.18632/aging.202831
Seven interferon gamma response genes serve as a prognostic risk signature that correlates with immune infiltration in lung adenocarcinomaCited by: 11
Author(s): Boyang Yao, Lixin Wang, Heyong Wang, Jinxia Bao, Qiwen Li, Fengzhi Yu, Wenjing Zhu, Li Zhang, Wang Li, Gu Zhan, Ke Fei, Peng Zhang, Fan Zhang, Xiaoying Huang
Software Mentions: 13
Published: over 5 years ago
10.1038/srep42130
Dissecting the brown adipogenic regulatory network using integrative genomicsCited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: over 9 years ago
10.1186/s12885-020-07695-3
Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancerCited by: 18
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 13
Published: over 5 years ago
10.1007/s10875-020-00908-1
Targeted Proteomics Reveals Inflammatory Pathways that Classify Immune Dysregulation in Common Variable ImmunodeficiencyCited by: 13
Author(s): Roos-Marijn Berbers, Julia Drylewicz, Pauline M. Ellerbroek, Joris M. van Montfrans, Virgil A. S. H. Dalm, P. Martin van Hagen, Baerbel Keller, Klaus Warnatz, Annick van de Ven, J.M. van Laar, Stefan Nierkens, Helen L. Leavis
Software Mentions: 13
Published: over 5 years ago
10.1186/1748-7188-4-7
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificityCited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 17 years ago
10.1371/journal.pone.0243241
CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysisCited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: over 5 years ago
10.7717/peerj.1668
Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolutionCited by: 26
Author(s): Tsung Fei Khang, Oi Yoon Michelle Soo, Wooi Boon Tan, L. H. S. Lim
Software Mentions: 13
Published: over 10 years ago
10.1038/s41598-021-90901-4
Characteristics of preoperative steroid profiles and glucose metabolism in patients with primary aldosteronism developing adrenal insufficiency after adrenalectomyCited by: 3
Author(s): Xiao Wang, Daniel A. Heinrich, Sonja Kunz, Nina Heger, Lisa Sturm, Olaf Uhl, Felix Beuschlein, Martín Reincke, Martin Bidlingmaier
Software Mentions: 13
Published: about 5 years ago
10.12688/f1000research.19236.3
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signaturesCited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: almost 7 years ago
10.3390/ijms22062790
Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in EpilepsyCited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: over 5 years ago
10.1186/s13059-020-02151-8
Alignment and mapping methodology influence transcript abundance estimationCited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: almost 6 years ago
10.1038/srep36460
Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modellingCited by: 28
Author(s): Joana Boavida, Jorge Assis, Inga Silva, Ester A. Serrão
Software Mentions: 13
Published: over 9 years ago
10.1002/ece3.5645
Testing adaptive hypotheses on the evolution of larval life history in acorn and stalked barnaclesCited by: 11
Author(s): Christine Ewers‐Saucedo, Paula Pappalardo
Software Mentions: 13
Published: almost 7 years ago
10.3389/fmicb.2021.713523
Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal PlantCited by: 15
Author(s): Guozhuang Zhang, Guangfei Wei, Fang Wei, Zhongjian Chen, Min He, Shuo Jiao, Yong Wang, Lixin Dong, Shilin Chen
Software Mentions: 13
Published: almost 5 years ago
10.3389/fonc.2021.678694
A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell CarcinomaCited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: about 5 years ago
10.1186/s13068-019-1584-7
A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shockCited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: almost 7 years ago
10.1038/s41598-018-21217-z
Spatially-explicit valuation of coastal wetlands for cyclone mitigation in Australia and ChinaCited by: 32
Author(s): Xiaoguang Ouyang, Joe Lee, Rod M. Connolly, Martin J. Kainz
Software Mentions: 13
Published: over 8 years ago
10.3389/fbioe.2021.614324
One-Time Optimization of Advanced T Cell Culture Media Using a Machine Learning PipelineCited by: 9
Author(s): Paul Grzesik, Sebastian C. Warth
Software Mentions: 13
Published: about 5 years ago
10.1371/journal.pcbi.1007113
Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classesCited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: about 7 years ago
10.1099/mgen.0.000492
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypesCited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: over 5 years ago
10.1371/journal.pcbi.1003000
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-SeqCited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 13 years ago
10.3390/ijms22031075
A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma PatientsCited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: over 5 years ago
10.7554/eLife.50087
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycleCited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: over 6 years ago
10.1186/s12939-016-0350-8
Are health care inequalities unfair? A study on public attitudes in 23 countriesCited by: 25
Author(s): Olaf von dem Knesebeck, Nico Vonneilich, Tae Jun Kim
Software Mentions: 13
Published: over 10 years ago
10.1038/s41422-020-00453-x
Establishment of intestinal organoid cultures modeling injury-associated epithelial regenerationCited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: over 5 years ago
10.1016/j.cell.2021.04.048
Integrated analysis of multimodal single-cell dataCited by: 4,423
Author(s): Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline Lee, Aaron J. Wilk, Charlotte A. Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, T.A. Stuart, Lamar M. Fleming, Bertrand Z. Yeung, Angela J. Rogers, Juliana McElrath, Catherine A. Blish, Raphaël Gottardo, Peter Smibert, Rahul Satija
Software Mentions: 13
Published: about 5 years ago
10.3389/fimmu.2021.652677
The Contribution of Serum Complement Component 3 Levels to 90-Day Mortality in Living Donor Liver TransplantationCited by: 2
Author(s): Saeko Fukui, Masaaki Hidaka, Shoichi Fukui, Shimpei Morimoto, Takanobu Hara, Akihiko Soyama, Tomohiko Adachi, Hajime Matsushima, Takayuki Tanaka, Mai Fuchigami, Hiroo Hasegawa, Katsunori Yanagihara, Susumu Eguchi
Software Mentions: 13
Published: about 5 years ago
10.3390/tropicalmed5020064
Disease Ecology of Rickettsial Species: A Data Science ApproachCited by: 6
Author(s): Sergé Morand, Kittipong Chaisiri, Anamika Kritiyakan, Rawadee Kumlert
Software Mentions: 13
Published: over 6 years ago
10.1186/s12864-019-5700-7
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq dataCited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: about 7 years ago
10.3389/fgene.2019.01079
HiCeekR: A Novel Shiny App for Hi-C Data AnalysisCited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: over 6 years ago
10.3389/fnbeh.2021.675994
Resurgence of an Inborn Attraction for Animate Objects via Thyroid Hormone T3Cited by: 8
Author(s): Elena Lorenzi, Bastien S. Lemaire, Elisabetta Versace, Toshiya Matsushima, Giorgio Vallortígara
Software Mentions: 12
Published: over 5 years ago
10.1371/journal.pone.0238835
Analyzing the fine structure of distributionsCited by: 35
Author(s): Michael C. Thrun, Tino Gehlert, Alfred Ultsch
Software Mentions: 12
Published: almost 6 years ago
10.1371/journal.pone.0239197
Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signaturesCited by: 13
Author(s): Weston R. Bodily, Brian H. Shirts, Tom Walsh, Süleyman Gülsüner, Mary‐Claire King, Alyssa Parker, Moom R. Roosan, Stephen R. Piccolo
Software Mentions: 12
Published: almost 6 years ago
10.1186/s12998-019-0261-z
Concurrent validity of lower extremity kinematics and jump characteristics captured in pre-school children by a markerless 3D motion capture systemCited by: 23
Author(s): Steen Harsted, Anders Holsgaard-Larsen, Lise Hestbæk, Eleanor Boyle, Henrik Hein Lauridsen
Software Mentions: 12
Published: almost 7 years ago
10.1371/journal.ppat.1005548
Determinants of Arbovirus Vertical Transmission in MosquitoesCited by: 90
Author(s): Sébastian Lequime, Paul Rácz, Louis Lambrechts
Software Mentions: 12
Published: about 10 years ago
10.3390/ani10101894
Who Is Pulling the Leash? Effects of Human Gender and Dog Sex on Human–Dog Dyads When Walking On-LeashCited by: 10
Author(s): Hao-Yu Shih, Mandy Paterson, Fillipe Georgiou, Nancy A. Pachana, Clive J. C. Phillips
Software Mentions: 12
Published: almost 6 years ago
10.26508/lsa.202000770
In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancerCited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: almost 6 years ago
10.1111/test.12258
Some teaching resources using R with illustrative examples exploring COVID ‐19 dataCited by: 0
Author(s): Arthur Berg, Nour Hawila
Software Mentions: 12
Published: about 5 years ago
10.1371/journal.pone.0244350
Knowledge, attitudes, and practices toward COVID-19 among university students in Japan and associated factors: An online cross-sectional surveyCited by: 82
Author(s): Asuka Hatabu, Xinhua Mao, Yi Zhou, Norihito Kawashita, Zheng Wen, Masao Ueda, Tatsuya Takagi, Yinbao Tian
Software Mentions: 12
Published: over 5 years ago
10.3389/fgene.2020.00968
Systematic Transcriptome Analysis of Noise-Induced Hearing Loss Pathogenesis Suggests Inflammatory Activities and Multiple Susceptible Molecules and PathwaysCited by: 6
Author(s): Quan Wang, Yilin Shen, Hongbo Hu, Fan Cui, Andi Zhang, Rui Ding, Bin Ye, Ming Xiang
Software Mentions: 12
Published: almost 6 years ago
10.1186/s12885-021-07788-7
Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinomaCited by: 14
Author(s): Rui Zhang, Qi Li, Jiao Fu, Z C Jin, Jingbo Su, Jian Zhang, Chen Chen, Zhimin Geng, Dong Zhang
Software Mentions: 12
Published: over 5 years ago
10.1186/s12974-021-02235-7
Sex differences and similarities in the neuroimmune response to central administration of poly I:CCited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: almost 5 years ago
10.3389/fpls.2021.651936
Unraveling the Relationship Between Seed Yield and Yield-Related Traits in a Diversity Panel of Brassica juncea Using Multi-Traits Mixed ModelCited by: 13
Author(s): Ranjit Saroj, S. L. Soumya, S. P. Singh, Surya Sankar, Rajat Chaudhary, . Yashpal, Neeru Saini, Sujata Vasudev, Devendra K. Yadava
Software Mentions: 12
Published: about 5 years ago
10.1002/ece3.7992
Using Delaunay triangulation to sample whole‐specimen color from digital imagesCited by: 5
Author(s): Jennifer J Valvo, J. David Aponte, Mitch J Daniel, Kenna Dwinell, Helen Rodd, David Houle, Kimberly A. Hughes
Software Mentions: 12
Published: almost 5 years ago
10.1186/s12915-016-0258-1
The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome modelCited by: 283
Author(s): Philipp Dirksen, Sarah Arnaud Marsh, Ines Braker, Nele Heitland, Sophia Wagner, Rania Nakad, Sebastian Mäder, Carola Petersen, Vienna Kowallik, Philip Rosenstiel, Marie‐Anne Félix, Hinrich Schulenburg
Software Mentions: 12
Published: about 10 years ago
10.3389/fimmu.2021.698236
Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung AdenocarcinomaCited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: almost 5 years ago
10.1002/aps3.1227
Open‐source data reveal how collections‐based fungal diversity is sensitive to global changeCited by: 24
Author(s): Carrie Andrew, Ulf Büntgen, Simon Egli, Béatrice Senn-Irlet, John‐Arvid Grytnes, Jacob Heilmann‐Clausen, Lynne Boddy, Claus Bässler, Alan C. Gange, Einar Heegaard, Klaus Høiland, Paul M. Kirk, Irmgard Krisai‐Greilhuber, Thomas W. Kuyper, Håvard Kauserud
Software Mentions: 12
Published: over 7 years ago
10.3389/fonc.2019.01361
Development and Validation of an RNA-Seq-Based Prognostic Signature in NeuroblastomaCited by: 28
Author(s): Jianguo Zhou, Bo Liang, Sanli Jin, Hui-Ling Liao, Guocheng Du, Long Cheng, Hu Ma, Udo S. Gaipl
Software Mentions: 12
Published: over 6 years ago
10.1002/ece3.6606
Evolution of breeding plumages in birds: A multiple‐step pathway to seasonal dichromatism in New World warblers (Aves: Parulidae)Cited by: 16
Author(s): Ryan S. Terrill, Glenn F. Seeholzer, Jared D. Wolfe
Software Mentions: 12
Published: almost 6 years ago
10.3389/fmolb.2021.681526
Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic AnalysisCited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: about 5 years ago
10.1371/journal.pone.0225900
PyRates—A Python framework for rate-based neural simulationsCited by: 10
Author(s): Richard Gast, Daniel Rose, Christoph Salomon, Harald E. Möller, Nikolaus Weiskopf, Thomas R. Knösche
Software Mentions: 12
Published: over 6 years ago
10.3389/fimmu.2021.647832
Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of InfectionCited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 5 years ago
10.12688/f1000research.12122.1
Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inferenceCited by: 14
Author(s): Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 12
Published: about 9 years ago
10.1186/s13567-021-00981-3
Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogensCited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: almost 5 years ago