10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited 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

10.3389/fmicb.2020.02028

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis
Cited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: almost 6 years ago

10.3389/fmicb.2020.02033

Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations
Cited by: 24
Author(s): João Alves Gama, Rita Zilhão, Francisco Dionísio
Software Mentions: 13
Published: almost 6 years ago

10.1371/journal.pone.0159046

Accuracy and Calibration of Computational Approaches for Inpatient Mortality Predictive Modeling
Cited by: 13
Author(s): Christos T. Nakas, Narayan Schütz, Marcus Werners, Alexander Benedikt Leichtle
Software Mentions: 13
Published: about 10 years ago

10.1093/bioinformatics/bty713

Bigmelon: tools for analysing large DNA methylation datasets
Cited 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

10.1186/s13023-020-01520-7

Identification of risk features for complication in Gaucher’s disease patients: a machine learning analysis of the Spanish registry of Gaucher disease
Cited by: 11
Author(s): Marcio Andrade‐Campos, Laura López de Frutos, Jorge J. Cebolla, Irene Serrano-Gonzalo, Blanca Medrano-Engay, Mercedes Roca-Espiau, Beatriz Gomez-Barrera, Jorge Pérez-Heredia, D. Íñiguez, Pilar Giraldo
Software Mentions: 13
Published: almost 6 years ago

10.1007/s41114-018-0015-6

Computer algebra in gravity research
Cited by: 20
Author(s): Malcolm MacCallum
Software Mentions: 13
Published: almost 8 years ago

10.1186/s13059-020-02151-8

Alignment and mapping methodology influence transcript abundance estimation
Cited 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

10.1186/s40168-020-00861-6

Reservoirs of antimicrobial resistance genes in retail raw milk
Cited by: 41
Author(s): Jinxin Liu, Yongxu Zhu, Michele Jay-Russell, Danielle G. Lemay, David A. Mills
Software Mentions: 13
Published: about 6 years ago

10.1186/s12859-021-04210-8

Contrastive self-supervised clustering of scRNA-seq data
Cited by: 28
Author(s): Madalina Ciortan, Matthieu Defrance
Software Mentions: 13
Published: about 5 years ago

10.7554/eLife.62587

Selfing is the safest sex for Caenorhabditis tropicalis
Cited by: 30
Author(s): Luke M. Noble, John G Yuen, Lewis Stevens, Nicolas Moya, Riaad Persaud, Marc Moscatelli, Jacqueline L. Jackson, Gaotian Zhang, Rojin Chitrakar, L. Ryan Baugh, Christian Braendle, Erik C. Andersen, Hannah S. Seidel, Matthew V. Rockman
Software Mentions: 13
Published: over 5 years ago

10.3389/fninf.2020.572068

Rxnat: An Open-Source R Package for XNAT-Based Repositories
Cited by: 0
Author(s): Adrian Gherman, John Muschelli, Brian Caffo, Ciprian M. Crainiceanu
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: about 8 years ago

10.3390/ijms21134674

The Inflammasome Adaptor Protein ASC in Mild Cognitive Impairment and Alzheimer’s Disease
Cited by: 37
Author(s): Xavier O. Scott, Marisa E. Stephens, Marie C. Desir, W. Dalton Dietrich, Robert W. Keane, Juan Pablo de Rivero Vaccari
Software Mentions: 13
Published: about 6 years ago

10.1186/s13073-020-00823-5

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Cited by: 169
Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna Gemünd, Nikoletta Rovina, Shobhit Agrawal, K. Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Abebe Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon J Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M.B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos‐Bourboulis, Thomas Ulas
Software Mentions: 13
Published: over 5 years ago

10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species
Cited by: 31
Author(s): Joan E. Edwards, Sudarshan A. Shetty, Pim van den Berg, Faith Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Hauke Smidt
Software Mentions: 13
Published: over 6 years ago

10.3389/fmicb.2019.00665

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front
Cited by: 31
Author(s): Gilda Varliero, Christina Bienhold, Florian Schmid, Antje Boetius, Massimiliano Molari
Software Mentions: 13
Published: over 7 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: over 6 years ago

10.18632/aging.202831

Seven interferon gamma response genes serve as a prognostic risk signature that correlates with immune infiltration in lung adenocarcinoma
Cited 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

10.1186/s12859-020-03774-1

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Cited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: almost 6 years ago

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited 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.2020.01317

The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study
Cited by: 17
Author(s): Hao Gu, Lu-Lu Lin, Zhang Chao, Min Yang, Hongshan Zhong, Renxiong Wei
Software Mentions: 13
Published: about 6 years ago

10.1371/journal.pone.0140989

The Increase in Animal Mortality Risk following Exposure to Sparsely Ionizing Radiation Is Not Linear Quadratic with Dose
Cited by: 35
Author(s): Benjamin Haley, Tatjana Paunesku, David J. Grdina, Gayle E. Woloschak
Software Mentions: 13
Published: over 10 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: over 10 years ago

10.1371/journal.pone.0199277

Predictive performance of six mortality risk scores and the development of a novel model in a prospective cohort of patients undergoing valve surgery secondary to rheumatic fever
Cited by: 13
Author(s): Omar Asdrúbal Vilca Mejía, Manuel J. Antunes, Maxim Goncharov, Luís Alberto Oliveira Dallan, Elinthon Tavares Veronese, Gisele Aparecida Lapenna, Luiz Augusto Ferreira Lisboa, Carlos Manuel de Almeida Brandão, Jorge P. Zubelli, Flávio Tarasoutchi, Pablo Maria Alberto Pomerantzeff, Fábio Biscegli Jatene
Software Mentions: 13
Published: about 8 years ago

10.2196/16810

Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study
Cited by: 29
Author(s): Benjamin S. Glicksberg, Shohei Burns, R. Currie, A. Clark Griffin, Zhen Jane Wang, David Haussler, Theodore C. Goldstein, Eric A. Collisson
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pone.0253546

Tone and genes: New cross-linguistic data and methods support the weak negative effect of the “derived” allele of ASPM on tone, but not of Microcephalin
Cited by: 1
Author(s): Dan Dediu
Software Mentions: 13
Published: about 5 years ago

10.1002/ece3.6520

Growth and survival of the superorganism: Ant colony macronutrient intake and investment
Cited 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

10.1002/ece3.7657

Disentangling demographic effects of red deer on chamois population dynamics
Cited by: 9
Author(s): Valerio Donini, Luca Pedrotti, Francesco Ferretti, Luca Corlatti
Software Mentions: 13
Published: about 5 years ago

10.1186/s13072-020-00380-6

Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling
Cited by: 7
Author(s): Jamie Grit, Benjamin K. Johnson, Patrick S. Dischinger, Curt J. Essenburg, Marie Adams, Stacy Campbell, Kai Pollard, Christine A. Pratilas, Tim Triche, Carrie R. Graveel, Matthew R. Steensma
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.7082.3

EvolQG - An R package for evolutionary quantitative genetics
Cited by: 31
Author(s): Diogo Melo, Guilherme Garcia, Alex Hubbe, Ana Paula A. Assis, Gabriel Marroig
Software Mentions: 13
Published: over 9 years ago

10.3389/fonc.2021.639013

Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL Prognosis
Cited 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

10.3389/fgene.2021.690530

Predicting the Survival and Immune Landscape of Colorectal Cancer Patients Using an Immune-Related lncRNA Pair Model
Cited by: 3
Author(s): Chi Ma, Xin Zhang, Xudong Zhao, Nan Zhang, Sixin Zhou, Yonghui Zhang, Peiyu Li
Software Mentions: 13
Published: almost 5 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: about 9 years ago

10.3389/fonc.2020.629909

Identification of an Immune Gene-Associated Prognostic Signature and Its Association With a Poor Prognosis in Gastric Cancer Patients
Cited by: 15
Author(s): Xiaoqing Guan, Zhiyuan Xu, Runzhe Chen, Jiang‐Jiang Qin, Xiangdong Cheng
Software Mentions: 13
Published: over 5 years ago

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: about 5 years ago

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited 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

10.1128/AEM.01225-21

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited 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

10.1002/jgh3.12451

Presence and type of decompensation affects outcomes in autoimmune hepatitis upon treatment with corticosteroids
Cited by: 1
Author(s): Sanchit Sharma, Samagra Agarwal, Kanica Kaushal, Abhinav Anand, Deepak Gunjan, Rajni Yadav, Sanchit Sharma
Software Mentions: 13
Published: over 5 years ago

10.1016/j.mbplus.2019.04.001

Pan-Cancer analysis of the expression and regulation of matrisome genes across 32 tumor types
Cited by: 37
Author(s): Valerio Izzi, Juho Lakkala, Raman Devarajan, Anni Kääriäinen, Jarkko Koivunen, Ritva Heljasvaara, Taina Pihlajaniemi
Software Mentions: 13
Published: over 7 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: almost 5 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

10.1002/ece3.5586

Life history alterations upon oral and hemocoelic bacterial exposure in the butterfly Melitaea cinxia
Cited by: 1
Author(s): Luisa Woestmann, Dimitri Stucki, Marjo Saastamoinen
Software Mentions: 13
Published: almost 7 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited 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

10.4049/immunohorizons.1900097

Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza Vaccination
Cited by: 3
Author(s): Priyanka B. Subrahmanyam, Tyson H. Holmes, Derek Lin, Laura F. Su, Gerlinde Obermoser, Jacques Banchereau, Virginia Pascual, Adolfo Garcı́a-Sastre, Randy A. Albrecht, Karolina Palucka, Mark M. Davis, Holden T. Maecker
Software Mentions: 13
Published: over 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

10.3390/microorganisms9010092

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Cited 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

10.3389/fonc.2021.583547

Alternative Splicing Events in Tumor Immune Infiltration in Colorectal Cancer
Cited by: 5
Author(s): Shi Jian-yu, Yan-yan Bi, Bo Yu, Qingfeng Wang, Teng Dan, WU Dong-ning
Software Mentions: 13
Published: about 5 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited 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*2019
Cited by: 3
Author(s):
Software Mentions: 13
Published: over 6 years ago

10.1126/sciadv.abg6070

Enhancing the heat tolerance of reef-building corals to future warming
Cited by: 36
Author(s): Emily J. Howells, David Abrego, Yi Jin Liew, John A. Burt, Eli Meyer, Manuel Aranda
Software Mentions: 13
Published: almost 5 years ago

10.1371/journal.pone.0018657

Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data
Cited by: 172
Author(s): Heather Piwowar
Software Mentions: 13
Published: about 15 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 platyurus
Cited 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/fgene.2019.00317

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis
Cited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: over 7 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited 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 Data
Cited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: almost 9 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: about 10 years ago

10.1534/g3.119.400728

Efficient Estimation of Marker Effects in Plant Breeding
Cited by: 10
Author(s): Alencar Xavier
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pone.0242502

Timeliness of immunisation with the pentavalent vaccine at different levels of the health care system in the Lao People’s Democratic Republic: A cross-sectional study
Cited by: 3
Author(s): Lisa Hefele, Sengdavanh Syphan, Dalouny Xayavong, Anousin Homsana, Daria Kleine, Phetsavanh Chanthavilay, Phonethipsavanh Nouanthong, Kinnaly Xaydalasouk, Outavong Phathammavong, Somxay Billamay, Anonh Xeuatvongsa, Daniel Reinharz, Antony P. Black, Claude P. Muller
Software Mentions: 13
Published: over 5 years ago

10.3934/mbe.2020007

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis
Cited by: 1
Author(s): Yonghua Zhuang, Kristen J. Wade, Laura Saba, Katerina Kechris
Software Mentions: 13
Published: over 6 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
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 Pipeline
Cited by: 9
Author(s): Paul Grzesik, Sebastian C. Warth
Software Mentions: 13
Published: about 5 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited 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

10.3389/fcimb.2021.688256

Machine Learning Uses Chemo-Transcriptomic Profiles to Stratify Antimalarial Compounds With Similar Mode of Action
Cited by: 1
Author(s): Ashleigh van Heerden, Roelof van Wyk, Lyn-Marié Birkholtz
Software Mentions: 13
Published: about 5 years ago

10.3389/fgene.2020.00620

An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis
Cited by: 13
Author(s): Shu Li, Wei Zhao, Manyi Sun
Software Mentions: 13
Published: about 6 years ago

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited 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

10.1186/s12859-019-2787-4

flowDiv: a new pipeline for analyzing flow cytometric diversity
Cited by: 9
Author(s): Bruno Wanderley, Daniel Araújo, María Victoria Quiroga, André Megali Amado, Adrião Duarte Dória Neto, Hugo Sarmento, Sebastián Metz, Fernando Unrein
Software Mentions: 13
Published: about 7 years ago

10.1111/mec.15422

Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community
Cited by: 21
Author(s): Daniel J. Becker, Kelly A. Speer, Alexis M. Brown, M. Brock Fenton, Alex D. Washburne, Sonia Altizer, Daniel G. Streicker, Raina K. Plowright, Vladimir E. Chizhikov, Nancy B. Simmons, Dmitriy V. Volokhov
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pone.0212956

Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Cited by: 24
Author(s): Colin Lischik, Leonie Adelmann, Joachim Wittbrodt
Software Mentions: 13
Published: over 7 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 Help
Cited 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

10.3389/fneur.2020.00539

Longitudinal Effects of Immediate and Delayed Estradiol on Cognitive Performance in a Spatial Maze and Hippocampal Volume in Menopausal Macaques Under an Obesogenic Diet
Cited by: 6
Author(s): Benjamin Zimmerman, Payel Kundu, Zheng Liu, Henryk F. Urbanski, Christopher D. Kroenke, Steven G. Kohama, Cynthia L. Bethea, Jacob Raber
Software Mentions: 13
Published: about 6 years ago

10.3390/jcm10051089

Prediction of Neurologically Intact Survival in Cardiac Arrest Patients without Pre-Hospital Return of Spontaneous Circulation: Machine Learning Approach
Cited by: 4
Author(s): Dong-Woo Seo, Hahn Yi, Hyun‐Jin Bae, Youn-Jung Kim, Cheol Ho Sohn, Won Young Kim, Kyung-Taek Lim, Namkug Kim, Youn-Jung Kim
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pone.0212669

Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects
Cited by: 3
Author(s): Robin Gradin, Malin Lindstedt, Henrik J. Johansson
Software Mentions: 13
Published: over 7 years ago

10.18632/aging.202976

Development and validation of epithelial mesenchymal transition-related prognostic model for hepatocellular carcinoma
Cited by: 7
Author(s): Xuequan Wang, Ziming Xing, Huihui Xu, Haihua Yang, Tongjing Xing
Software Mentions: 13
Published: about 5 years ago

10.3389/fonc.2020.01767

Ovarian Blood Sampling Identifies Junction Plakoglobin as a Novel Biomarker of Early Ovarian Cancer
Cited 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

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited 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

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: almost 7 years ago

10.1186/s12885-020-07695-3

Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited 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

10.3390/nu12123626

Trajectories of Body Composition during Advanced Aging in Consideration of Diet and Physical Activity: A 20-Year Longitudinal Study
Cited by: 6
Author(s): Alexandra Jungert, Gerrit Eichner, Monika Neuhäuser‐Berthold
Software Mentions: 13
Published: over 5 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: almost 6 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited 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

10.1128/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 Diversity
Cited 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

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited 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

10.3389/fpls.2021.628439

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions
Cited by: 19
Author(s): Marta Liber, Isabel Margarida Duarte, Ana-Teresa Maia, Hugo R. Oliveira
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.19236.3

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Cited 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

10.1186/1471-2164-14-46

Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Cited by: 9
Author(s): Ming Zhao, Xiangdong Liu, Xinyun Li, Hongbo Chen, Hui Jin, Rui Zhou, Mengjin Zhu, Shuhong Zhao
Software Mentions: 13
Published: over 13 years ago

10.1038/srep36460

Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modelling
Cited by: 28
Author(s): Joana Boavida, Jorge Assis, Inga Silva, Ester A. Serrão
Software Mentions: 13
Published: over 9 years ago

10.3390/curroncol28040269

Evaluating the Impact of the COVID-19 Pandemic on New Cancer Diagnoses and Oncology Care in Manitoba
Cited by: 14
Author(s): Kathleen Decker, Pascal Lambert, Allison Feely, Oliver Bucher, Julian O. Kim, Pamela Hebbard, Maclean Thiessen, Tunji Fatoye, Marshall Pitz, Rashmi Koul, Piotr Czaykowski
Software Mentions: 13
Published: almost 5 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited 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

10.1038/s41598-018-21217-z

Spatially-explicit valuation of coastal wetlands for cyclone mitigation in Australia and China
Cited by: 32
Author(s): Xiaoguang Ouyang, Joe Lee, Rod M. Connolly, Martin J. Kainz
Software Mentions: 13
Published: over 8 years ago

10.1186/s12859-019-3251-1

BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
Cited by: 17
Author(s): Venkat Sundar Gadepalli, Hatice Gülçin Özer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb
Software Mentions: 13
Published: over 6 years ago

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: about 5 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 Plant
Cited 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

10.3390/ijms22031075

A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited 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

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited 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

10.3389/fonc.2021.643104

TRIM68, PIKFYVE, and DYNLL2: The Possible Novel Autophagy- and Immunity-Associated Gene Biomarkers for Osteosarcoma Prognosis
Cited 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

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: almost 11 years ago

10.3390/cancers13163922

Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy
Cited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: almost 5 years ago

10.3389/fvets.2019.00045

Exploring Uncertainty in Canine Cancer Data Sources Through Dasymetric Refinement
Cited by: 5
Author(s): Gianluca Boo, Stefan Leyk, Sara Irina Fabrikant, Ricarda Graf, Andreas Pospischil
Software Mentions: 13
Published: over 7 years ago