10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: over 5 years ago

10.3390/jcm10184071

Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast Cancer
Cited by: 2
Author(s): Megha Lal, Asgar Hussain Ansari, Anurag Agrawal, Arijit Mukhopadhyay
Software Mentions: 12
Published: almost 5 years ago

10.1186/s40560-021-00531-1

Development and validation of an online model to predict critical COVID-19 with immune-inflammatory parameters
Cited by: 7
Author(s): Yue Gao, Lingxi Chen, Jianhua Chi, Shaoqing Zeng, Xikang Feng, Huayi Li, Dan Liŭ, Xiang Feng, Siyuan Wang, Ya Wang, Rui Yu, Yuan Yuan, Sen Xu, Chunrui Li, Wei Zhang, Shuai Cheng Li, Qinglei Gao
Software Mentions: 12
Published: over 5 years ago

10.1038/srep26340

Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods
Cited by: 41
Author(s): Jérôme Morinière, Matthew H. Van Dam, Oliver Hawlitschek, Johannes Bergsten, Mariano C. Michat, Lars Hendrich, Ignacio Ribera, Emmanuel F. A. Toussaint, Michael Balke
Software Mentions: 12
Published: about 10 years ago

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: over 10 years ago

10.3389/fgene.2021.667610

The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Lugang Deng, Peixi Wang, Zhi Qu, Nan Liu
Software Mentions: 12
Published: almost 5 years ago

10.7554/eLife.55529

Smchd1 is a maternal effect gene required for genomic imprinting
Cited by: 22
Author(s): Iromi Wanigasuriya, Quentin Gouil, Sarah Kinkel, Andrés Tapia del Fierro, Tamara Beck, Ellise A Roper, Kelsey Breslin, Jessica M Stringer, Karla J. Hutt, Heather Lee, Andrew Keniry, Matthew E. Ritchie, Marnie E. Blewitt
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2019.02597

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: over 6 years ago

10.3389/fninf.2018.00092

Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0
Cited by: 96
Author(s): Espen Hagen, Solveig Næss, Torbjørn V. Ness, Gaute T. Einevoll
Software Mentions: 12
Published: over 7 years ago

10.1186/s12859-016-1260-x

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Cited by: 14
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 12
Published: over 9 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: over 6 years ago

10.1038/s42003-021-01941-5

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status
Cited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: about 5 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: over 5 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: over 7 years ago

10.1186/s13073-016-0384-y

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
Cited by: 131
Author(s): Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C. Knight
Software Mentions: 12
Published: over 9 years ago

10.1038/s41598-019-41592-5

A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion
Cited by: 1
Author(s): Robert F. Rudy, Nareerat Charoenvimolphan, Baogang Qian, Annerose Berndt, Robert M. Friedlander, Scott T. Weiss, Rose Du
Software Mentions: 12
Published: about 7 years ago

10.1093/gigascience/giz088

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
Cited by: 5
Author(s): Luis Francisco Hernández Sánchez, Bram Burger, Carlos Horro, Antonio Fabregat, Stefan Johansson, Pål Rasmus Njølstad, Harald Barsnes, Henning Hermjakob, Marc Vaudel
Software Mentions: 12
Published: almost 7 years ago

10.7554/eLife.34409

General decapping activators target different subsets of inefficiently translated mRNAs
Cited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: over 7 years ago

10.1093/gigascience/giaa102

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Cited by: 15
Author(s): Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, D. L. Clements, Fidel Ramírez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Léa Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning
Software Mentions: 12
Published: over 5 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: about 5 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: over 8 years ago

10.1038/s41598-021-85155-z

Validating machine learning approaches for prediction of donor related complication in microsurgical breast reconstruction: a retrospective cohort study
Cited by: 6
Author(s): Yujin Myung, Sungmi Jeon, Chan Yeong Heo, Eun‐Kyu Kim, Eunyoung Kang, Hee-Chul Shin, Eun Joo Yang, Jae Hoon Jeong
Software Mentions: 12
Published: over 5 years ago

10.1186/s12885-021-08442-y

Genetic expression and mutational profile analysis in different pathologic stages of hepatocellular carcinoma patients
Cited by: 9
Author(s): Xingjie Gao, Chunyan Zhao, Nan Zhang, Xiaoteng Cui, Yuanyuan Ren, Chao Su, Shaoyuan Wu, Zhi Yao, Jie Yang
Software Mentions: 12
Published: almost 5 years ago

10.3390/insects12020180

Unexpected Effects of Local Management and Landscape Composition on Predatory Mites and Their Food Resources in Vineyards
Cited by: 16
Author(s): Stefan Möth, Andreas Walzer, Markus Redl, Božana Petrović, Christoph Hoffmann, Silvia Winter
Software Mentions: 12
Published: over 5 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 7 years ago

10.1186/s12974-021-02235-7

Sex differences and similarities in the neuroimmune response to central administration of poly I:C
Cited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: almost 5 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 8 years ago

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 9 years ago

10.1371/journal.pone.0219698

Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns
Cited by: 11
Author(s): Alexander Platzer, Thomas Nußbaumer, Thomas Karonitsch, Josef S. Smolen, Daniel Aletaha
Software Mentions: 12
Published: almost 7 years ago

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: about 6 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: almost 8 years ago

10.12688/f1000research.22969.2

clustifyr: an R package for automated single-cell RNA sequencing cluster classification
Cited by: 58
Author(s): Rui Fu, Austin E. Gillen, Ryan M. Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R. Hesselberth, Kent Riemondy
Software Mentions: 12
Published: almost 6 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: over 8 years ago

10.1371/journal.pone.0202824

Allometry predicts trabecular bone structural properties in the carnivoran jaw joint
Cited by: 6
Author(s): Matthew Wysocki, Z. Jack Tseng
Software Mentions: 12
Published: almost 8 years ago

10.1371/journal.pone.0184652

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems
Cited by: 48
Author(s): Ana Hranilović, Marina Bely, Isabelle Masneuf‐Pomarède, Vladimir Jiranek, Warren Albertin
Software Mentions: 12
Published: almost 9 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 system
Cited by: 23
Author(s): Steen Harsted, Anders Holsgaard-Larsen, Lise Hestbæk, Eleanor Boyle, Henrik Hein Lauridsen
Software Mentions: 12
Published: almost 7 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: over 5 years ago

10.3389/fpls.2020.01132

Intra and Inter-specific Variability of Salt Tolerance Mechanisms in Diospyros Genus
Cited by: 3
Author(s): Francisco Gil-Muñoz, Juan G. Pérez-Pérez, Ana Quiñones, María del Mar Naval, M. L. Badenes
Software Mentions: 11
Published: almost 6 years ago

10.3390/microorganisms8101619

Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica
Cited by: 6
Author(s): Edisa García Hernández, Elena Baraza, Christian Smit, Matty P. Berg, Joana Falcão Salles
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: over 9 years ago

10.3389/fbioe.2020.00101

The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic Pain
Cited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: over 7 years ago

10.12688/f1000research.18458.2

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: about 7 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: almost 5 years ago

10.3390/jcm9082591

Risk of Adverse Drug Events Following the Virtual Addition of COVID-19 Repurposed Drugs to Drug Regimens of Frail Older Adults with Polypharmacy
Cited by: 14
Author(s): Sweilem B. Al Rihani, Matt K. Smith, Ravil Bikmetov, Malavika Deodhar, Pamela Dow, Jacques Turgeon, Véronique Michaud
Software Mentions: 11
Published: almost 6 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: over 6 years ago

10.3390/ijerph18041816

Academic Achievement in Spanish Secondary School Students: The Inter-Related Role of Executive Functions, Physical Activity and Gender
Cited by: 7
Author(s): Elena Escolano Pérez, Marta Bestué
Software Mentions: 11
Published: over 5 years ago

10.1186/s12859-020-03786-x

IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
Cited by: 32
Author(s): Dandan Liang, Quan Liu, Kejun Zhou, Jia Wang, Guoxiang Xie, Tianlu Chen
Software Mentions: 11
Published: over 5 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: almost 10 years ago

10.3389/fgene.2019.01380

Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme
Cited by: 6
Author(s): Runzhi Huang, Zhenyu Li, Chen Li, Guanghua Wang, Penghui Yan, Li P, Jiaqi Wang, Xiaolong Zhu, Peng Hu, Junfang Zhang, Zhengyan Chang, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.1038/s41598-019-48495-5

Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitors
Cited by: 9
Author(s): Carlos Gutiérrez González, Stephanie Tankou, Laura M. Cox, Ellen P. Casavant, Howard L. Weiner, Joshua E. Elias
Software Mentions: 11
Published: almost 7 years ago

10.1242/dev.177428

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
Cited by: 182
Author(s): Sandra Ruiz García, Marie Deprez, Kévin Lebrigand, Amélie Cavard, Agnès Paquet, Marie-Jeanne Arguel, Virginie Magnone, Marin Truchi, Ignacio Caballero, Sylvie Leroy, Charles‐Hugo Marquette, Brice Marcet, Pascal Barbry, Laure‐Emmanuelle Zaragosi
Software Mentions: 11
Published: over 6 years ago

10.3389/fonc.2021.646060

Immune-Related Gene SERPINE1 Is a Novel Biomarker for Diffuse Lower-Grade Gliomas via Large-Scale Analysis
Cited by: 20
Author(s): Xiaoming Huang, Fenglin Zhang, Dong He, Xiaoshuai Ji, Jiajia Gao, Wenqing Liu, Yunda Wang, Qian Liu, Tao Xin
Software Mentions: 11
Published: about 5 years ago

10.3389/fpsyg.2018.02251

Disabled or Cyborg? How Bionics Affect Stereotypes Toward People With Physical Disabilities
Cited by: 28
Author(s): Bertolt Meyer, Frank Asbrock
Software Mentions: 11
Published: over 7 years ago

10.1038/s41598-020-66107-5

Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations
Cited by: 5
Author(s): Petra Villette, Eve Afonso, Geoffroy Couval, Aurélien Levret, Maxime Galan, A.-C. Goydadin, Jean-François Cosson, Patrick Giraudoux
Software Mentions: 11
Published: about 6 years ago

10.1002/ece3.6044

Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies
Cited by: 21
Author(s): Ombeline Sculfort, Érika Cristina Pinheiro de Castro, Krzysztof M. Kozak, Søren Bak, Marianne Élias, Bastien Nay, Violaine Llaurens
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0151959

Physiological Limits along an Elevational Gradient in a Radiation of Montane Ground Beetles
Cited by: 28
Author(s): R. O. Slatyer, Sean D. Schoville
Software Mentions: 11
Published: about 10 years ago

10.1111/mec.13636

Escape from the cryptic species trap: lichen evolution on both sides of a cyanobacterial acquisition event
Cited by: 34
Author(s): Kevin Schneider, Philipp Resl, Toby Spribille
Software Mentions: 11
Published: about 10 years ago

10.1093/bioinformatics/btz889

<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methods
Cited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: over 6 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 5 years ago

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 6 years ago

10.3389/fcell.2021.707143

The Prognosis and Immune Checkpoint Blockade Efficacy Prediction of Tumor-Infiltrating Immune Cells in Lung Cancer
Cited by: 11
Author(s): Xiangzheng Liu, Xueqian Shang, Jian Li, Shijie Zhang
Software Mentions: 11
Published: almost 5 years ago

10.3390/foods10010143

Intramuscular Fat Prediction Using Color and Image Analysis of Bísaro Pork Breed
Cited by: 7
Author(s): Alfredo Teixeira, Severiano Silva, Marianne Hasse, José Almeida, Luís G. Dias
Software Mentions: 11
Published: over 5 years ago

10.3390/cancers12123800

Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis
Cited by: 14
Author(s): Gi-Ung Kang, Da-Ryung Jung, Yoon Hee Lee, Se Young Jeon, Hyung Soo Han, Gun Oh Chong, Jae‐Ho Shin
Software Mentions: 11
Published: over 5 years ago

10.15252/emmm.201911900

Epigenetic gene expression links heart failure to memory impairment
Cited by: 13
Author(s): Rezaul Islam, Dawid Lbik, M. Sadman Sakib, Raoul Maximilian Hofmann, Tea Berulava, Martí Jiménez Mausbach, Julia Cha, Maria Amélia Azevêdo Goldberg, Elerdashvili Vakhtang, Christian Schiffmann, Anke Zieseniß, Dörthe M. Katschinski, Farahnaz Sananbenesi, Karl Toischer, André Fischer
Software Mentions: 11
Published: over 5 years ago

10.3389/fimmu.2018.03017

A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers
Cited by: 8
Author(s): Malini Manoharan, Nitin Mandloi, Sushri Priyadarshini, Ashwini Patil, Rohit Gupta, Laxman Iyer, Ravi Gupta, Amitabha Chaudhuri
Software Mentions: 11
Published: over 7 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: over 9 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 8 years ago

10.1007/s11214-018-0576-4

The Space Physics Environment Data Analysis System (SPEDAS)
Cited by: 295
Author(s): V. Angelopoulos, P. Cruce, Alexander Drozdov, E. W. Grimes, Nick Hatzigeorgiu, David A. King, D. E. Larson, James W. Lewis, J. M. McTiernan, D. A. Roberts, Chuck Russell, Tomoaki Hori, Yoshiya Kasahara, Atsushi Kumamoto, A. Matsuoka, Yukinaga Miyashita, Yoshizumi Miyoshi, I. Shinohara, Masaaki Teramoto, J. Faden, A. J. Halford, Michael McCarthy, R. M. Millan, J. G. Sample, David M. Smith, L. A. Woodger, A. Masson, Ayris Narock, Kazushi Asamura, T. F. Chang, Che‐Ming Chiang, Y. Kazama, K. Keika, Shoya Matsuda, Takehiko Segawa, K. Seki, Shoji Motomizu, Sunny Wing-Yee Tam, Norio Umemura, B. J. Wang, S. Y. Wang, R. J. Redmon, J. V. Rodriguez, H. J. Singer, J. D. Vandegriff, Shuji Abe, M. Nosé, Atsuki Shinbori, Yoshimasa Tanaka, S. Ueno, L. Andersson, P. Dunn, Christopher Fowler, J. S. Halekas, Takuya Hara, Yuki Harada, C. O. Lee, R. J. Lillis, D. L. Mitchell, M. R. Argall, K. R. Bromund, J. L. Burch, I. J. Cohen, Michael Galloy, B. L. Giles, A. N. Jaynes, O. Le Contel, M. Oka, T. D. Phan, Brian M. Walsh, J. H. Westlake, F. D. Wilder, S. D. Bale, R. Livi, M. Pulupa, P. L. Whittlesey, A. W. DeWolfe, B. Harter, Edson Mello Lucas, U. Auster, J. W. Bonnell, C. M. Cully, E. Donovan, R. E. Ergun, H. U. Frey, B. J. Jackel, A. Keiling, H. Korth, J. P. McFadden, Yoshihiro Nishimura, Ferdinand Plaschke, P. Robert, D. L. Turner, J. M. Weygand, R. M. Candey, Russell D. Johnson, T. J. Kovalick, M. H. Liu, R. E. McGuire, A. W. Breneman, K. Kersten, P. Schroeder
Software Mentions: 11
Published: over 7 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: over 11 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: almost 7 years ago

10.3390/ani11040961

Grumpy Dogs Are Smart Learners—The Association between Dog–Owner Relationship and Dogs’ Performance in a Social Learning Task
Cited by: 8
Author(s): Péter Pongrácz, Gabriella Rieger, Kata Vékony
Software Mentions: 11
Published: about 5 years ago

10.3390/jfmk6020036

Predicting Adaptations to Resistance Training Plus Overfeeding Using Bayesian Regression: A Preliminary Investigation
Cited by: 4
Author(s): R. Scott Smith, Patrick S. Harty, Matthew T. Stratton, Zad Rafi, Christian Rodriguez, Jacob R. Dellinger, Marqui L. Benavides, Baylor A Johnson, Sarah J. White, Abegale D Williams, Grant M. Tinsley
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0144134

Personality and Situation Predictors of Consistent Eating Patterns
Cited by: 15
Author(s): Uku Vainik, Laurette Dubé, Jianjun Lu, Lesley K. Fellows
Software Mentions: 11
Published: over 10 years ago

10.1371/journal.pone.0258031

High site-fidelity in common bottlenose dolphins despite low salinity exposure and associated indicators of compromised health
Cited by: 6
Author(s): Ryan Takeshita, Brian C. Balmer, Francesca Messina, Eric S. Zolman, Len Thomas, Randall S. Wells, Cynthia R. Smith, Teresa K. Rowles, Lori H. Schwacke
Software Mentions: 11
Published: over 4 years ago

10.1098/rstb.2018.0303

Origin and evolution of papillomavirus (onco)genes and genomes
Cited by: 35
Author(s): Anouk Willemsen, Ignacio G. Bravo
Software Mentions: 11
Published: about 7 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: almost 6 years ago

10.3389/fphys.2020.00845

Dynamic Courtship Signals and Mate Preferences in Sepia plangon
Cited by: 5
Author(s): Alejandra López Galán, Wen-Sung Chung, N. Justin Marshall
Software Mentions: 11
Published: almost 6 years ago

10.7554/eLife.65372

Image3C, a multimodal image-based and label-independent integrative method for single-cell analysis
Cited by: 6
Author(s): Alice Accorsi, Andrew Box, Robert Peuß, Christopher J. Wood, Alejandro Sánchez Alvarado, Nicolas Rohner
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: over 15 years ago

10.1186/s41235-018-0133-4

App icon similarity and its impact on visual search efficiency on mobile touch devices
Cited by: 5
Author(s): Anna Trapp, Carolin Wienrich
Software Mentions: 11
Published: over 7 years ago

10.1038/srep44348

Major shifts at the range edge of marine forests: the combined effects of climate changes and limited dispersal
Cited by: 70
Author(s): Jorge Assis, Estíbaliz Berecibar, Bruno Claro, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Ester Á. Serrão
Software Mentions: 11
Published: over 9 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: almost 6 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 10 years ago

10.1186/s40064-015-0795-z

Rapid publication-ready MS-Word tables for two-way ANOVA
Cited by: 56
Author(s): Houssein Assaad, Yongqing Hou, Lan Zhou, Raymond J. Carroll, Guoyao Wu
Software Mentions: 11
Published: over 11 years ago

10.3389/fmolb.2021.684050

Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: almost 5 years ago

10.3897/BDJ.6.e20760

spind: an R Package to Account for Spatial Autocorrelation in the Analysis of Lattice Data
Cited by: 7
Author(s): Gudrun Carl, Sam Levin, Ingolf Kühn
Software Mentions: 11
Published: over 8 years ago

10.1186/1756-0500-4-546

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data
Cited by: 20
Author(s): Francesco Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma
Software Mentions: 11
Published: over 14 years ago

10.1038/s41598-020-58111-6

Projected distribution and climate refugia of endangered Kashmir musk deer Moschus cupreus in greater Himalaya, South Asia
Cited by: 19
Author(s): Paras B. Singh, Kumar P. Mainali, Zhigang Jiang, Arjun Thapa, Naresh Subedi, Muhammad Naeem Awan, Orus Ilyas, Himal Luitel, Zhixin Zhou, Huijian Hu
Software Mentions: 11
Published: over 6 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: over 5 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: over 19 years ago

10.1038/s41598-017-02464-y

UROPA: a tool for Universal RObust Peak Annotation
Cited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: about 9 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: over 6 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: almost 5 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: over 7 years ago

10.7717/peerj.10680

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma
Cited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: over 5 years ago

10.1186/s12894-019-0479-z

Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Cited by: 2
Author(s): Anika Kremer, Tobias Kremer, Glen Kristiansen, Yuri Tolkach
Software Mentions: 11
Published: about 7 years ago

10.18632/aging.202957

Integrative analysis identifies key mRNA biomarkers for diagnosis, prognosis, and therapeutic targets of HCV-associated hepatocellular carcinoma
Cited by: 8
Author(s): Yongqiang Zhang, Yuqin Tang, Chengbin Guo, Gen Li
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0256694

Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systems
Cited by: 18
Author(s): Shah Al Emran, Timothy J. Krupnik, Sreejith Aravindakshan, Virender Kumar, Cameron M. Pittelkow
Software Mentions: 11
Published: almost 5 years ago