10.1371/journal.pone.0242158

Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro
Cited by: 7
Author(s): Yoshibumi Sato, Keiko Tominaga, Hirotatsu Aoki, Masayuki Murayama, Kazato Oishi, Hiroyuki Hirooka, Takashi Yoshida, Hajime Kumagai
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006636

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Cited by: 69
Author(s): Hannah Seberg, Eric Van Otterloo, Stacie K. Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek Gildea, Juan Francisco de Paz Santana, J. Robert Manak, William J. Pavan, Trevor Williams, Robert A. Cornell
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.634554

Molecular Mapping of Water-Stress Responsive Genomic Loci in Lettuce (Lactuca spp.) Using Kinetics Chlorophyll Fluorescence, Hyperspectral Imaging and Machine Learning
Cited by: 9
Author(s): Pawan Kumar, Renée L. Eriksen, Ivan Šimko, Beiquan Mou
Software Mentions: 4
Published: over 5 years ago

10.1016/j.tine.2019.02.004

Whole-brain white matter organization, intelligence, and educational attainment
Cited by: 33
Author(s): Joe Bathelt, Gaia Scerif, Anna C. Nobre, Duncan E. Astle
Software Mentions: 4
Published: about 7 years ago

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-49829-z

Adenovirus infection is associated with altered gut microbial communities in a non-human primate
Cited by: 27
Author(s): . Wasimuddin, Victor M. Corman, Jörg U. Ganzhorn, Jacques Rakotondranary, Yedidya R. Ratovonamana, Christian Drosten, Simone Sommer
Software Mentions: 4
Published: almost 7 years ago

10.1007/s11135-016-0401-7

Partial least squares path modeling using ordinal categorical indicators
Cited by: 78
Author(s): Florian Schuberth, Jörg Henseler, Theo K. Dijkstra
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.celrep.2019.08.077

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis
Cited by: 129
Author(s): Damien Arnol, Denis Schapiro, Bernd Bodenmiller, Julio Sáez-Rodríguez, Oliver Stegle
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep11671

Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer
Cited by: 27
Author(s): Ji‐Ye Yin, Chenyue Qian, Xiangping Li, Yu Zhang, Huijuan He, Jingjing Wang, Juan Chen, Jiajia Cui, Rongrong Liu, Hui Zhou, Xiao Lin, Xiaojing Xu, Yi Zheng, Yilan Fu, Zi-Yu Chen, Xiang Chen, Wei Zhang, Cheng-Cheng Ye, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 4
Published: about 11 years ago

10.5334/joc.188

Investigating Reading Comprehension in Adolescents with Intellectual Disabilities: Evaluating the Simple View of Reading
Cited by: 3
Author(s): Karin Nilsson, Henrik Danielsson, Åsa Elwér, David Messer, Lucy A. Henry, Stefan Samuelsson
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00547-19

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
Cited by: 31
Author(s): Quinten R Ducarmon, Bastian Hornung, A. R. Geelen, E. Kuijper, Romy D. Zwittink
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-85909-9

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq
Cited by: 7
Author(s): Maddumage Dona Ginushika Priyadarshani Premarathne, Nami Fukutome, Kazuaki Yamasaki, Fumiyo Hayakawa, Atsushi J. Nagano, Hisataka Mizuno, Nobuo Ibaragi, Yukio Nagano
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-11-465

Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Cited by: 4
Author(s): Wayne Xu, Clay J. Carter
Software Mentions: 4
Published: almost 16 years ago

10.1186/1471-2164-11-701

DNA methylation in glioblastoma: impact on gene expression and clinical outcome
Cited by: 176
Author(s): Amandine Etcheverry, Marc Aubry, Marie de Tayrac, Élodie Vauléon, Rachel Boniface, Frédérique Guénot, Stéphan Saïkali, Abderrahmane Hamlat, Laurent Riffaud, Philippe Menei, Véronique Quillien, Jean Mosser
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0256471

Radiology- and gene-based risk stratification in small renal cell carcinoma: A preliminary study
Cited by: 0
Author(s): Takao Sugiyama, Yasuhiro Ushijima, Yuki Motomura, Katsumi Sakamoto, Masakazu Hirakawa, Akihiro Nishie, Koshi Mimori, Yasuo Yamashita, Takashi Tsutsumi, Kousei Ishigami
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00786-20

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
Cited by: 26
Author(s): Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
Software Mentions: 4
Published: over 5 years ago

10.1186/s12711-021-00668-5

A near complete genome for goat genetic and genomic research
Cited by: 11
Author(s): Ran Li, Peng Yang, Xuelei Dai, Hojjat Asadollahpour Nanaei, Wenwen Fang, Zhirui Yang, Yi Cai, Zhuqing Zheng, Xihong Wang, Yu Jiang
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0258207

A new phenothiazine derivate is active against Clostridioides difficile and shows low cytotoxicity
Cited by: 3
Author(s): Troels Ronco, Francisca Maria Aragao, Lasse Saaby, Jørn B. Christensen, A. Permin, Andrew R. Williams, Stig Milan Thamsborg, Rikke Heidemann Olsen
Software Mentions: 4
Published: almost 5 years ago

10.1128/mSystems.00834-20

Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States
Cited by: 16
Author(s): Melissa B. Manus, Sahana Kuthyar, Ana Gabriela Perroni‐Marañón, Alejandra Núñez‐de la Mora, Katherine R. Amato
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0188640

Epidemiological and genetic characteristics of EV71 in hand, foot, and mouth disease in Guangxi, southern China, from 2010 to 2015
Cited by: 27
Author(s): Minmei Chen, Yu‐Min Ju, Zhiping Xie, Zhou Kai-jiao, Yi Tan, Mo JianJun
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-016-1146-2

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Cited by: 148
Author(s): Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0157739

Ancient Haplotypes at the 15q24.2 Microdeletion Region Are Linked to Brain Expression of MAN2C1 and Children's Intelligence
Cited by: 2
Author(s): Alejandro Cáceres, Tõnu Esko, Irene Pappa, Armand Gutiérrez, Maria-José Lopez-Espinosa, Sabrina Llop, Mariona Bustamante, Henning Tiemeier, Andres Metspalu, Peter K. Joshi, James F. Wilsonx, Judith Reina-Castillón, Jean Shin, Zdenka Pausová, Tomáš Paus, Jordi Sunyer, Luis A. Pérez‐Jurado, Juan R. González
Software Mentions: 4
Published: about 10 years ago

10.3390/v12090922

Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments
Cited by: 14
Author(s): Mara Elena Heinrichs, Dennis Alexander Tebbe, Bernd Wemheuer, Jutta Niggemann, Bert Engelen
Software Mentions: 4
Published: almost 6 years ago

10.1002/mpr.1803

Comparison of major depression diagnostic classification probability using the SCID, CIDI, and MINI diagnostic interviews among women in pregnancy or postpartum: An individual participant data meta‐analysis
Cited by: 31
Author(s): Brooke Levis, Dean McMillan, Ying Sun, Chen He, Danielle B Rice, Ankur Krishnan, Yin Wu, Marleine Azar, Tatiana A. Sanchez, Matthew J. Chiovitti, Parash Mani Bhandari, Dipika Neupane, Nazanin Saadat, Kira E. Riehm, Mahrukh Imran, Jill Boruff, Pim Cuijpers, Simon Gilbody, John P. A. Ioannidis, . ., Scott B. Patten, Ian Shrier, Roy C. Ziegelstein, Liane Comeau, Nicholas Mitchell, Marcello Tonelli, Simone N. Vigod, Franca Aceti, Rubén Alvarado, Cosme Alvarado‐Esquivel, Muideen O. Bakare, Jacqueline Barnes, Cheryl Tatano Beck, Carola Bindt, Philip Boyce, Adomas Bunevičius, Tiago Castro e Couto, Linda H. Chaudron, Humberto Corrêa, Felipe Pinheiro de Figueiredo, Valsamma Eapen, Michelle Fernandes, Bárbara Figueiredo, Jane Fisher, Lluïsa García-Esteve, Lisa Giardinelli, Nadine Helle, Louise M. Howard, Dina Khalifa, Jane Kohlhoff, Laima Kusminskas, Zoltán Kozinszky, Lorenzo Lelli, Angeliki Leonardou, Beth A. Lewis, Michael Maes, Valentina Meuti, Sandra Nakić Radoš, Purificación Navarro García, Daisuke Nishi, Daniel Okitundu Luwa E-Andjafono, Emma Robertson-Blackmore, Tamsen Rochat, Heather Rowe, Bonnie W.M. Siu, Alkistis Skalkidou, Alan Stein, Robert C. Stewart, Kuan Pin Su, Inger Sundström‐Poromaa, Meri Tadinac, S. Darius Tandon, Iva Alexandra Barbosa Tendais, Pavaani Thiagayson, Annamária Töreki, Anna Torres‐Giménez, Thach Tran, Kylee Trevillion, Katherine Turner, Johann M. Vega‐Dienstmaier, Karen Wynter, Kimberly A. Yonkers, Andrea Benedetti, Brett D. Thombs
Software Mentions: 4
Published: almost 7 years ago

10.1534/g3.116.028324

Histone H1 Limits DNA Methylation in Neurospora crassa
Cited by: 18
Author(s): Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0217920

Overexpression of PODXL/ITGB1 and BCL7B/ITGB1 accurately predicts unfavorable prognosis compared to the TNM staging system in postoperative pancreatic cancer patients
Cited by: 14
Author(s): Keisuke Taniuchi, Mutsuo Furihata, Seiji Naganuma, Masahiko Sakaguchi, Toshiji Saibara
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2019.03111

Characterization of Ebinur Lake Virus and Its Human Seroprevalence at the China–Kazakhstan Border
Cited by: 11
Author(s): Han Xia, Ran Liu, Lu Zhao, Xiang Dong Sun, Zhong Zheng, Evans Atoni, Xiaomin Hu, Bo Zhang, Guilin Zhang, Zhiming Yuan
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00211-17

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese
Cited by: 55
Author(s): Andrea S. Bertuzzi, Aaron M. Walsh, Jeremiah J. Sheehan, Paul D. Cotter, Fiona Crispie, P.L.H. McSweeney, Kieran N. Kilcawley, Mary C. Rea
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-31618-9

Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.
Cited by: 21
Author(s): Mehdi Soltani Howyzeh, Seyed Ahmad Sadat Noori, Vahid Shariati J, Mahboubeh Amiripour
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00133-16

SSUnique: Detecting Sequence Novelty in Microbiome Surveys
Cited by: 4
Author(s): Michael D. J. Lynch, Josh D. Neufeld
Software Mentions: 4
Published: over 9 years ago

10.1111/hex.12545

Closing the patient experience chasm: A two-level validation of the Consumer Quality Index Inpatient Hospital Care
Cited by: 9
Author(s): Alina Smirnova, Kiki M. J. M. H. Lombarts, Onyebuchi A. Arah, Cees van der Vleuten
Software Mentions: 4
Published: over 9 years ago

10.1128/mSphere.00088-19

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria
Cited by: 18
Author(s): Patricia Lu‐Irving, Julia G. Harenčár, Hailey Sounart, Shana R. Welles, Sarah M. Swope, David A. Baltrus, Katrina M. Dlugosch
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0249424

miRGTF-net: Integrative miRNA-gene-TF network analysis reveals key drivers of breast cancer recurrence
Cited by: 15
Author(s): Stepan Nersisyan, A. V. Galatenko, Vladimir Galatenko, M. Yu. Shkurnikov, Alexander G. Tonevitsky
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.01937-21

Mucosal Bacteria Modulate Candida albicans Virulence in Oropharyngeal Candidiasis
Cited by: 16
Author(s): Martinna Bertolini, Roberto Vázquez-Muñoz, Linda Archambault, Siddharth Shah, João Gabriel Silva Souza, Raphael Cavalcante Costa, Angela Thompson, Yanjiao Zhou, Takanori Sobue, Anna Dongari-Bagtzoglou
Software Mentions: 4
Published: almost 5 years ago

10.1093/gigascience/giz110

Evaluation of computational genotyping of structural variation for clinical diagnoses
Cited by: 34
Author(s): Varuna Chander, Richard A. Gibbs, Fritz J. Sedlazeck
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0194021

Loneliness in schizophrenia: Construct clarification, measurement, and clinical relevance
Cited by: 73
Author(s): Graham M.L. Eglit, Barton W. Palmer, Averria Sirkin Martin, Xin Tu, Dilip V. Jeste
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-57888-w

Describing the fecal metabolome in cryogenically collected samples from healthy participants
Cited by: 9
Author(s): Kajetan Trošt, Linda Ahonen, Tommi Suvitaival, Nicole Christiansen, Trine Nielsen, Maja Thiele, Suganya Jacobsen, Aleksander Krag, Peter Rossing, Torben Hansen, Lars Ove Dragsted, Cristina Legido‐Quigley
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0208054

Agnostic detection of genomic alterations by holistic DNA structural interrogation
Cited by: 1
Author(s): Ryan K. Shultzaberger, Rachel E. Abrams, Challise J. Sullivan, Anthony Schmitt, T. W. Thompson, John Dresios
Software Mentions: 4
Published: over 7 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: almost 5 years ago

10.3390/ani11061762

The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors
Cited by: 17
Author(s): M. J. P. Theelen, Roosmarijn E C Luiken, Jaap A. Wagenaar, Marianne Sloet van Oldruitenborgh-Oosterbaan, John W. A. Rossen, Aldert Zomer
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-60562-w

Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression
Cited by: 19
Author(s): Elvia Ramírez-Carrillo, Osiris Gaona, Javier Nieto, Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Olga A. Rojas-Ramos, Isaac González‐Santoyo
Software Mentions: 4
Published: over 6 years ago

10.1037/xlm0000532

Listeners and readers generalize their experience with word meanings across modalities.
Cited by: 16
Author(s): Rebecca A. Gilbert, Matthew H. Davis, M. Gareth Gaskell, Jennifer M. Rodd
Software Mentions: 4
Published: almost 8 years ago

10.1093/gbe/evaa053

Divergence-Based Introgression Polarization
Cited by: 8
Author(s): Evan S. Forsythe, Daniel B Sloan, Mark A. Beilstein
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-60175-3

The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts
Cited by: 18
Author(s): Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, James N. D. Battey, Athanasios Kondylis, Marja Talikka, Bjoern Titz, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Sonia Ouadi, Rendy Yanuar, Ching Keong Tung, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-61659-y

Short and long period growth markers of enamel formation distinguish European Pleistocene hominins
Cited by: 16
Author(s): Mario Modesto‐Mata, MC Dean, Rodrigo S. Lacruz, Timothy Bromage, Cecilia García‐Campos, Marina Martínez de Pinillos, Laura Martín‐Francés, María Martinón‐Torres, Eudald Carbonell, Juan Luís Arsuaga, José Marı́a Bermúdez de Castro
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0243704

Cyberchondria in the age of COVID-19
Cited by: 53
Author(s): Nataša Jokić‐Begić, Anita Lauri Korajlija, Una Mikac
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0254200

Contextualizing goal preferences in fear-avoidance models. Looking at fatigue as a disabling symptom in fibromyalgia patients
Cited by: 5
Author(s): Cecilia Peñacoba, Irene López‐Gómez, María Ángeles Pastor-Mira, Sofía López-Roig, Carmen Écija
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-11-37

Predicting Bevirimat resistance of HIV-1 from genotype
Cited by: 32
Author(s): Dominik Heider, Jens Verheyen, Daniel Hoffmann
Software Mentions: 4
Published: over 16 years ago

10.1186/s12943-018-0833-x

RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas
Cited by: 57
Author(s): Cheng Hsien Lu, Xi Su, Amanda Y. Wang, Tao Yuan, Zhenxiao Wang, Chaoping Huang, Yuehua Qiao, Hongyi Hu, Liangfa Liu
Software Mentions: 4
Published: about 8 years ago

10.3390/s20071887

Pattern Recognition and Anomaly Detection by Self-Organizing Maps in a Multi Month E-nose Survey at an Industrial Site
Cited by: 11
Author(s): Sabina Licen, Alessia Di Gilio, Jolanda Palmisani, S Petraccone, Gianluigi de Gennaro, Pierluigi Barbieri
Software Mentions: 4
Published: over 6 years ago

10.1016/j.mex.2020.100941

A novel item-allocation procedure for the three-form planned missing data design
Cited by: 2
Author(s): Kyle M. Lang, E. Whitney G. Moore, Elizabeth Grandfield
Software Mentions: 4
Published: over 6 years ago

10.1017/S1352465820000958

Cognitive appraisals of dissociation in psychosis: a new brief measure
Cited by: 7
Author(s): Emma Černis, Jessica C. Bird, Andrew Molodynski, Anke Ehlers, Daniel Freeman
Software Mentions: 4
Published: over 5 years ago

10.3758/s13428-020-01355-x

Two-stage maximum likelihood approach for item-level missing data in regression
Cited by: 7
Author(s): Lihan Chen, Victoria Savalei, Mijke Rhemtulla
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: almost 5 years ago

10.1093/aobpla/plv049

Testing models for the leaf economics spectrum with leaf and whole-plant traits in<i>Arabidopsis thaliana</i>
Cited by: 41
Author(s): Benjamin Blonder, François Vasseur, Cyrille Violle, Bill Shipley, Brian J. Enquist, Denis Vile
Software Mentions: 4
Published: over 11 years ago

10.1186/s12898-019-0271-7

Adaptation of wild boar (Sus scrofa) activity in a human-dominated landscape
Cited by: 52
Author(s): Franz Johann, Markus Handschuh, Peter Linderoth, Carsten F. Dormann, Janosch Arnold
Software Mentions: 4
Published: over 6 years ago

10.1099/acmi.0.000015

Phylogenomics insights into order and families of Lysobacterales
Cited by: 19
Author(s): Sanjeet Kumar, Kanika Bansal, Prashant P. Patil, Prabhu B. Patil
Software Mentions: 4
Published: over 7 years ago

10.1172/jci.insight.145346

Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension
Cited by: 39
Author(s): Connar Westgate, Hannah Botfield, Zerin Alimajstorovic, Andreas Yiangou, Mark D. Walsh, Gabrielle Smith, Rishi Singhal, James Mitchell, Olivia Grech, Keira Markey, Daniel Hebenstreit, Daniel A. Tennant, Jeremy W. Tomlinson, Susan P Mollan, Christian Ludwig, İldem Akerman, Gareth G. Lavery, Alexandra J Sinclair
Software Mentions: 4
Published: about 5 years ago

10.1099/mgen.0.000498

ActDES – a curated Actinobacterial Database for Evolutionary Studies
Cited by: 2
Author(s): Jana Katharina Schniete, Nelly Sélem-Mójica, Anna Sofia Birke, Pablo Cruz-Morales, Iain S. Hunter, Francisco Barona‐Gómez, Paul A. Hoskisson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12913-021-06492-3

Prediction of hospital bed capacity during the COVID− 19 pandemic
Cited by: 27
Author(s): Mieke Deschepper, Kristof Eeckloo, Simon Malfait, Dominique Benoît, Steven Callens, Stijn Vansteelandt
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-10861-6

Small ocean temperature increases elicit stage-dependent changes in DNA methylation and gene expression in a fish, the European sea bass
Cited by: 73
Author(s): Dafni Anastasiadi, Noèlia Díaz, Francesc Piferrer
Software Mentions: 4
Published: almost 9 years ago

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Cited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: about 5 years ago

10.1002/ece3.5577

Site‐specific distribution of oak rhizosphere‐associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
Cited by: 21
Author(s): Melanie Sapp, Nicolas Tyborski, Anja Linstädter, Aida López Sánchez, Tim Mansfeldt, Guido Waldhoff, Georg Bareth, Michael Bonkowski, Laura Rose
Software Mentions: 4
Published: almost 7 years ago

10.1002/ece3.2026

Plant diversity increases spatio-temporal niche complementarity in plant-pollinator interactions
Cited by: 41
Author(s): Christine Venjakob, Alexandra‐Maria Klein, Anne Ebeling, Teja Tscharntke, Christoph Scherber
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0018737

Effect of Acute Ozone Induced Airway Inflammation on Human Sympathetic Nerve Traffic: A Randomized, Placebo Controlled, Crossover Study
Cited by: 19
Author(s): Jens Tank, Heike Biller, Karsten Heusser, Olaf Holz, André Diedrich, Theodor Framke, Armin Koch, Anika Großhennig, Wolfgang Koch, Norbert Krug, Jens Jordan, Jens M. Hohlfeld
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0174067

Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization
Cited by: 14
Author(s): Leonardo Carreira Trevelin, Roberto Leonan Morim Novaes, Paul François Colas-Rosas, Thayse Cristhina Melo Benathar, Carlos A. Peres
Software Mentions: 4
Published: over 9 years ago

10.1099/vir.0.065219-0

Identification of novel anelloviruses with broad diversity in UK rodents
Cited by: 41
Author(s): Shoko Nishiyama, Bernadette M. Dutia, James P. Stewart, Anna Meredith, Darren Shaw, Peter Simmonds, Colin Sharp
Software Mentions: 4
Published: about 12 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.1592

The role of geography and host abundance in the distribution of parasitoids of an alien pest
Cited by: 7
Author(s): Petra Nováková, Jaroslav Holuša, Jakub Horák
Software Mentions: 4
Published: over 10 years ago

10.1534/genetics.118.301482

Diverse Lineages of <i>Candida albicans</i> Live on Old Oaks
Cited by: 54
Author(s): Douda Bensasson, Jo Dicks, John M. Ludwig, Christopher J. Bond, Adam Elliston, Ian N. Roberts, Stephen A. James
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-12-208

NCACO-score: An effective main-chain dependent scoring function for structure modeling
Cited by: 4
Author(s): Liqing Tian, Aiping Wu, Yang Cao, Xiaoxi Dong, Yun Hu, Taijiao Jiang
Software Mentions: 4
Published: about 15 years ago

10.1186/s12859-018-2430-9

A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models
Cited by: 5
Author(s): Michal R. Grzadkowski, Dorota H. Sendorek, Christine P’ng, Vincent Huang, Paul C. Boutros
Software Mentions: 4
Published: over 7 years ago

10.1186/1755-8794-6-S3-S1

A categorical network approach for discovering differentially expressed regulations in cancer
Cited by: 2
Author(s): Nikolay Balov
Software Mentions: 4
Published: over 13 years ago

10.1186/s12862-016-0607-2

Thermal plasticity in farmed, wild and hybrid Atlantic salmon during early development: has domestication caused divergence in low temperature tolerance?
Cited by: 16
Author(s): Monica Favnebøe Solberg, Lise Dyrhovden, Ivar Helge Matre, Kevin A. Glover
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: about 12 years ago

10.3390/genes11050472

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
Cited by: 7
Author(s): Mushtaque Ali, Hongyan Cheng, Mahtab Soomro, Shuyan Li, Muhammad Tufail, Mian Faisal Nazir, Feng Xu, Youping Zhang, Dongyun Zuo, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 4
Published: over 6 years ago

10.3390/genes11060634

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming
Cited by: 7
Author(s): Daria D. Novikova, Pavel Cherenkov, Yana Sizentsova, В. В. Миронова
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-55852-x

Multi-parameter immune profiling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Camila Fernández-Zapata, Stephan Schlickeiser, Désirée Kunkel, Axel Schulz, Henrik E. Mei, Carl Weidinger, René M. Gieß, Susanna Asseyer, Britta Siegmund, Friedemann Paul, Klemens Ruprecht, Josef Priller
Software Mentions: 4
Published: over 6 years ago

10.3390/genes11091066

Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense
Cited by: 6
Author(s): Gongmin Cheng, Longyan Zhang, Hengling Wei, Hantao Wang, Jianhua Lü, Shuxun Yu
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2013-14-2-r15

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Cited by: 217
Author(s): Stephen R. Fairclough, Zehua Chen, Eric M. Kramer, Qiandong Zeng, Sarah Young, Hugh M. Robertson, Emina Begović, Daniel J. Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B. Franz Lang, Brian J. Haas, Chad Nusbaum, Nicole King
Software Mentions: 4
Published: over 13 years ago

10.1038/srep46553

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism
Cited by: 60
Author(s): Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian B. Dry, Huijuan Wu, Jiang Lu
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-7-264

Spatial normalization of array-CGH data
Cited by: 76
Author(s): Pierre Neuvial, Philippe Hupé, Isabel Martínez Brito, Stéphane Liva, Élodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, Emmanuel Barillot
Software Mentions: 4
Published: about 20 years ago

10.3390/genes12081258

Systematic Identification of circRNAs in Alzheimer’s Disease
Cited by: 9
Author(s): Kyle R. Cochran, Kirtana Veeraraghavan, Gautam Kundu, Krystyna Mazan-Mamczarz, Christopher Coletta, Madhav Thambisetty, Myriam Gorospe, Supriyo De
Software Mentions: 4
Published: almost 5 years ago

10.3390/e22020153

Selection Consistency of Lasso-Based Procedures for Misspecified High-Dimensional Binary Model and Random Regressors
Cited by: 2
Author(s): Mariusz Kubkowski, Jan Mielniczuk
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-70582-1

Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae)
Cited by: 17
Author(s): Evgenii Baiakhmetov, Arkadiusz Nowak, Polina D. Gudkova, Marcin Nobis
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-92507-2

The in-utero experience of piglets born from sows with lameness shapes their life trajectory
Cited by: 8
Author(s): Marisol Parada Sarmiento, Thiago Bernardino, Patrícia Tatemoto, Gina Polo, Adroaldo José Zanella
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1009302

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin
Cited by: 24
Author(s): Natalie Saini, Camille K. Giacobone, Leszek J. Klimczak, Brian N. Papas, Adam Burkholder, Jianliang Li, David C. Fargo, Re Bai, Kevin Gerrish, Cynthia L. Innes, Shepherd H. Schurman, Dmitry A. Gordenin
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.150203

Genomic and epigenomic evolution of acquired resistance to combination therapy in esophageal squamous cell carcinoma
Cited by: 6
Author(s): Qingjie Min, Yan Wang, Qingnan Wu, Xianfeng Li, Huajing Teng, Jingyuan Fan, Yiren Cao, Pingsheng Fan, Qimin Zhan
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0109870

Intraspecific Trait Variation Driven by Plasticity and Ontogeny in Hypochaeris radicata
Cited by: 41
Author(s): Rachel M. Mitchell, Jonathan D. Bakker
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41598-020-68136-6

Effects of substratum and depth on benthic harmful dinoflagellate assemblages
Cited by: 13
Author(s): Li Keat Lee, Zhen Fei Lim, Haifeng Gu, Leo Lai Chan, R. Wayne Litaker, Patricia A. Tester, Chui Pin Leaw, Po Teen Lim
Software Mentions: 4
Published: about 6 years ago

10.1172/jci.insight.141341

Shear stress associated with cardiopulmonary bypass induces expression of inflammatory cytokines and necroptosis in monocytes
Cited by: 17
Author(s): Lan N. Tu, Lance Hsieh, Masaki Kajimoto, Kevin Charette, Nataliya Kibiryeva, Adriana Forero, Sarah E. Hampson, Jennifer Marshall, James E. O’Brien, Marta Scatena, Michael A. Portman, Ram Savan, Christopher Benner, Alberto Aliseda, Muhammad Nuri, Douglas C. Bittel, Peter Pastuszko, Vishal Nigam
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-021-01431-6

Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders
Cited by: 3
Author(s): Pei‐Fen Kuan, Xiaohua Yang, Ruwei Xu, Chang Che, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-65578-w

Social environment modulates investment in sex trait versus lifespan: red deer produce bigger antlers when facing more rivalry
Cited by: 9
Author(s): Juan Carranza, F. Javier Pérez‐Barbería, Concha Mateos Martín, Susana Alarcos, Jerónimo Torres-Porras, Javier Pérez‐González, Cristina B. Sánchez-Prieto, Juliana Valencia, Leticia Castillo, Eva de la Peña, Isabel Barja, José Manuel Seoane, Manuel M. Reglero, Antonio Flores, A. Membrillo
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.64283

Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs
Cited by: 19
Author(s): Swati Gaikwad, Fardin Ghobakhlou, David J. Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G. Hinnebusch
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-017-2000-6

A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy
Cited by: 53
Author(s): Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers, Matthew E. Hudson
Software Mentions: 4
Published: over 8 years ago

10.3390/s18114029

Sensor Fusion for Recognition of Activities of Daily Living
Cited by: 51
Author(s): Jiaxuan Wu, Yunfei Feng, Peng Sun
Software Mentions: 4
Published: over 7 years ago