10.1038/s41598-020-80165-9
Multi-level remodelling of chromatin underlying activation of human T cellsCited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: over 5 years ago
10.1371/journal.pgen.1008405
Causal relationships between obesity and the leading causes of death in women and menCited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: over 6 years ago
10.1038/s41598-021-97071-3
Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditionsCited by: 10
Author(s): Ankit T. Hinsu, Ketankumar Panchal, Ramesh Pandit, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 14
Published: almost 5 years ago
10.7554/eLife.55913
An image-based data-driven analysis of cellular architecture in a developing tissueCited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: almost 6 years ago
10.3390/microorganisms7120680
EpiExploreR: A Shiny Web Application for the Analysis of Animal Disease DataCited by: 4
Author(s): Lara Savini, Luca Candeloro, Samuel Perticara, Annamaria Conte
Software Mentions: 14
Published: over 6 years ago
10.3389/fonc.2020.573295
Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal CancerCited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: over 5 years ago
10.7150/jca.55970
Characteristics of Infiltrating Immune Cells and a Predictive Immune Model for Cervical CancerCited by: 11
Author(s): Ruanmin Zou, Ruihong Gu, Xinbing Yu, Yingying Hu, Ji Hee Yu, Xiangyang Xue, Xueqiong Zhu
Software Mentions: 14
Published: over 5 years ago
10.1186/s13742-016-0147-0
2015 Brainhack ProceedingsCited by: 6
Author(s): R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel J. Clark, Krzysztof J. Gorgolewski, Daniel J. Clark, Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades, Sébastien Déry, Weiran Deng, Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ružić, Nick Ketz, Andrew E. Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez‐Castillo, Caroline Froehlich, Gil Dekel, Daniel S. Margulies, Ben D. Fulcher, Tristan Glatard, Reza Adalat, Natacha Beck, R. Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans, Yaroslav Halchenko, Matteo Visconti di Oleggio Castello, Raúl Hernández-Pérez, Edgar Abarca Morales, Laura V. Cuaya, Kaori Ito, Sook‐Lei Liew, Hans J. Johnson, Erik Kan, Julia Anglin, Michael R. Borich, Neda Jahanshad, Paul Thompson, Marcel Falkiewicz, Julia M. Huntenburg, David O’Connor, Michael P. Milham, Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre R. Franco, Augusto Buchweitz, Felipe Meneguzzi, Rickson C. Mesquita, Luis C. T. Herrera, Daniela Dentico, Vanessa Sochat, Julio E. Villalon‐Reina, Eleftherios Garyfallidis
Software Mentions: 14
Published: over 9 years ago
10.1093/molbev/msab063
Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte GenusCited by: 42
Author(s): Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, C. Schluechter, P. Lamkowski, Jeremy Schmutz, Adam Healey, Bryan Piatkowski, A. Jonathan Shaw, David J. Weston, Kjell Ivar Flatberg, Péter Szövényi, Kristian Hassel, Hans K. Stenøien
Software Mentions: 14
Published: over 5 years ago
10.3390/cancers13174348
Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression DataCited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: almost 5 years ago
10.1186/s12916-020-01686-8
In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in childrenCited by: 19
Author(s): Marta Vives-Usano, Carles Hernández-Ferrer, Léa Maitre, Carlos Ruiz‐Arenas, Sandra Andrušaitytė, Eva Borràs, Ángel Carracedo, Maribel Casas, Leda Chatzi, Muireann Coen, Xavier Estivill, Juan R. González, Kristine B. Gützkow, Hector C. Keun, Chung-Ho E Lau, Solène Cadiou, Johanna Lepeule, Dan Mason, Inés Quintela, Oliver Robinson, Eduard Sabidó, Gillian Santorelli, Per E. Schwarze, Alexandros P. Siskos, Rémy Slama, Marina Vafeiadi, Eulàlia Martı́, Martine Vrijheid, Mariona Bustamante
Software Mentions: 14
Published: almost 6 years ago
10.3389/fgene.2021.702072
Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic CancerCited by: 5
Author(s): Kun Fang, Hairong Qu, Jiapei Wang, Desheng Tang, Changsheng Yan, Jiamin Ma, Lei Gao
Software Mentions: 14
Published: over 4 years ago
10.1371/journal.pcbi.1009317
Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndromeCited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: over 4 years ago
10.1007/s00401-021-02343-x
Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseasesCited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: almost 5 years ago
10.1371/journal.pone.0237368
Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities?Cited by: 9
Author(s): Gian Maria Niccolò Benucci, Bryan Rennick, Gregory Bonito
Software Mentions: 14
Published: almost 6 years ago
10.1186/s12864-016-3038-y
A full-body transcriptome and proteome resource for the European common carpCited by: 33
Author(s): Iris Kolder, Suzanne J. van der Plas-Duivesteijn, Ge Tan, G.F. Wiegertjes, Maria Forlenza, Arzu Güler, Dmitrii Y. Travin, Minoru Nakao, Tadaaki Moritomo, Ilgiz Irnazarow, Johan T. den Dunnen, Seyed Yahya Anvar, Hans J. Jansen, Ron P. Dirks, Magnus Palmblad, Boris Lenhard, Christiaan V. Henkel, Herman P. Spaink
Software Mentions: 14
Published: over 9 years ago
10.12688/f1000research.12223.1
recount workflow: Accessing over 70,000 human RNA-seq samples with BioconductorCited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: almost 9 years ago
10.1186/s13072-020-00342-y
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretationCited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: about 6 years ago
10.1016/j.celrep.2019.06.037
Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during SpermatogenesisCited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: almost 7 years ago
10.3389/fonc.2020.575422
A Novel Model Based on CXCL8-Derived Radiomics for Prognosis Prediction in Colorectal CancerCited by: 8
Author(s): Yanpeng Chu, Jie Li, Zong Yuan Zeng, Bin Huang, Jiaojiao Zhao, Qin Liu, Huaping Wu, Jiangping Fu, Zheng Yin, Yefan Zhang, Jianqiang Cai, Fanxin Zeng
Software Mentions: 14
Published: over 5 years ago
10.3389/fmicb.2019.01775
Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect SeasonalityCited by: 23
Author(s): Hannah E. Epstein, Hillary A. Smith, Neal E. Cantin, Véronique J. L. Mocellin, Gergely Torda, Madeleine J. H. van Oppen
Software Mentions: 14
Published: almost 7 years ago
10.1186/s13148-021-01173-8
Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolismCited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: over 4 years ago
10.3390/ijms22073681
Circulating miRNAs as Biomarkers for Mitochondrial Neuro-Gastrointestinal EncephalomyopathyCited by: 4
Author(s): Mark Mencias, Michelle Levene, Kevin Blighe, Bridget E. Bax
Software Mentions: 14
Published: about 5 years ago
10.3389/fcell.2021.657667
Identification of the Prognostic Significance of Somatic Mutation-Derived LncRNA Signatures of Genomic Instability in Lung AdenocarcinomaCited by: 31
Author(s): Geng Wang, Zhi Lv, Jinshuo Fan, Jing Xu, Kaimin Mao, Zhengrong Yin, Wanlu Qing, Yang Jin
Software Mentions: 14
Published: about 5 years ago
10.1186/s12859-016-0884-1
Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysisCited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: over 10 years ago
10.1371/journal.pcbi.1003118
Software for Computing and Annotating Genomic RangesCited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: almost 13 years ago
10.3390/pathogens9100841
Diverse Epidemiology of Leptospira Serovars Notified in New Zealand, 1999–2017Cited by: 12
Author(s): Shahista Nisa, David A. Wilkinson, Olivia Angelin‐Bonnet, Shevaun Paine, Karen Weber Cullen, Jackie Wight, Michael G Baker, Jackie Benschop
Software Mentions: 14
Published: over 5 years ago
10.3389/fcell.2020.592490
Transcriptome Sequencing Reveals Potential Roles of ICOS in Primary Sjögren’s SyndromeCited by: 19
Author(s): Jing Luo, Xin Liao, Lihe Zhang, Xin Xu, Senhong Ying, Mengjiao Yu, Lixia Zhu, Suxian Lin, Xiaobing Wang
Software Mentions: 14
Published: over 5 years ago
10.1186/s13059-021-02349-4
PEPPRO: quality control and processing of nascent RNA profiling dataCited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: about 5 years ago
10.1186/s42523-020-00027-7
Domesticated equine species and their derived hybrids differ in their fecal microbiotaCited by: 18
Author(s): Joan E. Edwards, A. Schennink, Faith Burden, Stuart A. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Edoardo Saccenti, Hauke Smidt
Software Mentions: 14
Published: about 6 years ago
10.1186/1476-072X-11-41
Displaying R spatial statistics on Google dynamic maps with web applications created by RwuiCited by: 2
Author(s): Richard Newton, Andrew Deonarine, Lorenz Wernisch
Software Mentions: 14
Published: over 14 years ago
10.3390/plants10040615
Polyphenol Diversity and Antioxidant Activity of European Cistus creticus L. (Cistaceae) Compared to Six Further, Partly Sympatric Cistus SpeciesCited by: 11
Author(s): Brigitte Lukas, Laura Bragagna, Katharina Starzyk, Klaudia Labedz, Klaus Stolze, Johannes Novak
Software Mentions: 14
Published: about 5 years ago
10.1099/mgen.0.000409
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analysesCited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: almost 6 years ago
10.1186/s12859-018-2486-6
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq dataCited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: over 7 years ago
10.1186/s13059-021-02264-8
GeneWalk identifies relevant gene functions for a biological context using network representation learningCited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: over 5 years ago
10.3389/fimmu.2020.606164
Six Immune Associated Genes Construct Prognostic Model Evaluate Low-Grade GliomaCited by: 32
Author(s): Yin Qiu Tan, Yun Tao Li, Teng Feng Yan, Yang Xu, Bao Hui Liu, Ji An Yang, Yang Xue, Qianxue Chen, Hong Bo Zhang
Software Mentions: 14
Published: over 5 years ago
10.1039/d0sc05337f
A data-driven perspective on the colours of metal–organic frameworksCited by: 14
Author(s): Kevin Maik Jablonka, Seyed Mohamad Moosavi, Mehrdad Asgari, Christopher P. Ireland, Luc Patiny, Berend Smit
Software Mentions: 14
Published: over 5 years ago
10.1186/s12920-019-0578-4
Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patientsCited by: 21
Author(s): Petr V. Nazarov, Anke Wienecke-Baldacchino, Andreï Zinovyev, Urszula Czerwińska, Arnaud Muller, Dorothée Nashan, Gunnar Dittmar, Francisco Azuaje, Stephanie Kreis
Software Mentions: 14
Published: over 6 years ago
10.1371/journal.pone.0242060
The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil typesCited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: over 5 years ago
10.3389/fpsyg.2020.564083
Correlates of Health-Protective Behavior During the Initial Days of the COVID-19 Outbreak in NorwayCited by: 54
Author(s): Janis Zickfeld, Thomas W. Schubert, Anders Kuvaas Herting, Jon Grahe, Kate Faasse
Software Mentions: 14
Published: over 5 years ago
10.1186/s12920-017-0274-1
Quantitative analysis of cryptic splicing associated with TDP-43 depletionCited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: about 9 years ago
10.1186/s40478-020-0880-6
Single-nucleus RNA-seq identifies Huntington disease astrocyte statesCited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: over 6 years ago
10.3390/microorganisms9061222
Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot StudyCited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: almost 5 years ago
10.1038/s42003-019-0554-8
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcomeCited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: almost 7 years ago
10.7717/peerj.11880
Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of <i>NEDD4L</i> in clear-cell renal cell cancerCited by: 6
Author(s): Hui Zhao, Junjun Zhang, Xiaoliang Fu, Dongdong Mao, Xuesen Qi, Shuai Liang, Gang Ma, Zewen Song, Ru Yang, Zhenni Guo, Binghua Tong, Meiqing Sun, Baile Zuo, Guoyin Li
Software Mentions: 14
Published: almost 5 years ago
10.1186/s13059-019-1783-3
AlleleAnalyzer: a tool for personalized and allele-specific sgRNA designCited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: almost 7 years ago
10.1038/srep30325
In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cellsCited by: 72
Author(s): Joke Robijns, Freya Molenberghs, Tom Sieprath, Tobias Corne, Marlies Verschuuren, Winnok H. De Vos
Software Mentions: 14
Published: almost 10 years ago
10.1186/s12864-018-4559-3
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq dataCited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 8 years ago
10.1002/1873-3468.12684
Computational approaches for interpreting sc <scp>RNA</scp> ‐seq dataCited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: almost 9 years ago
10.1038/s41598-020-80365-3
Drivers of spatio-temporal variation in mosquito submissions to the citizen science project ‘Mückenatlas’Cited by: 13
Author(s): Nadja Pernat, Helge Kampen, Florian Ruland, Jonathan M. Jeschke, Doreen Werner
Software Mentions: 14
Published: over 5 years ago
10.1186/s12859-016-1455-1
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integrationCited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: over 9 years ago
10.3389/fgene.2021.723360
Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous ChickensCited by: 7
Author(s): Fasil Getachew Kebede, Hans Komen, Tadelle Dessie, Setegn Worku Alemu, Olivier Hanotte, J.W.M. Bastiaansen
Software Mentions: 14
Published: over 4 years ago
10.1007/s00204-020-02956-3
Human neuronal signaling and communication assays to assess functional neurotoxicityCited by: 13
Author(s): Dominik Loser, Jasmin Schaefer, Timm Danker, Clemens Möller, Markus Brüll, Ilinca Suciu, Anna‐Katharina Ückert, Stefanie Klima, Marcel Leist, Udo Kraushaar
Software Mentions: 14
Published: over 5 years ago
10.3390/ani10071151
Tenebrio molitor Larvae Meal Affects the Cecal Microbiota of Growing PigsCited by: 8
Author(s): Sandra De Meyer, Denise K. Geßner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis, Klaus Eder
Software Mentions: 14
Published: almost 6 years ago
10.1186/s13059-019-1851-8
Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancerCited by: 44
Author(s): Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Software Mentions: 14
Published: over 6 years ago
10.1038/s42003-020-01625-6
Mapping the immune environment in clear cell renal carcinoma by single-cell genomicsCited by: 103
Author(s): Nicholas Borcherding, Ajaykumar Vishwakarma, Andrew P. Voigt, Andrew M. Bellizzi, Jacob Kaplan, Kenneth G. Nepple, Aliasger K. Salem, Russell W. Jenkins, Yousef Zakharia, Weizhou Zhang
Software Mentions: 14
Published: over 5 years ago
10.1080/19490976.2021.1888673
Links between gut microbiome composition and fatty liver disease in a large population sampleCited by: 31
Author(s): Matti O. Ruuskanen, Fredrik Åberg, Ville Männistö, Aki S. Havulinna, Guillaume Méric, Yang Liu, Rohit Loomba, Yoshiki Vázquez-Baeza, Anupriya Tripathi, Liisa Valsta, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Software Mentions: 14
Published: over 5 years ago
10.1186/s40679-016-0031-0
Analyzing microtomography data with Python and the scikit-image libraryCited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: over 9 years ago
10.1038/s41598-020-67753-5
Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samplesCited by: 13
Author(s): Shradha Mukherjee
Software Mentions: 14
Published: almost 6 years ago
10.1371/journal.ppat.1008653
Genome-wide transcriptomics identifies an early preclinical signature of prion infectionCited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: almost 6 years ago
10.1186/s12859-021-04193-6
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencingCited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: about 5 years ago
10.3390/ijms20174162
SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal CancersCited by: 13
Author(s): Fabia Fricke, Malwina Michalak, Uwe Warnken, Ingrid Haußer, Martina Schnölzer, Jürgen Kopitz, Johannes Gebert
Software Mentions: 14
Published: almost 7 years ago
10.1371/journal.pone.0243467
Predicting self-harm within six months after initial presentation to youth mental health services: A machine learning studyCited by: 16
Author(s): Frank Iorfino, Nicholas Ho, Joanne S. Carpenter, Shane Cross, Tracey A Davenport, Daniel F. Hermens, Hannah Yee, Alissa Nichles, Natalia Zmicerevska, Adam J. Guastella, Elizabeth Scott, Ian B. Hickie
Software Mentions: 14
Published: over 5 years ago
10.3390/ijms22115751
Multi-Omics Model Applied to Cancer GeneticsCited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
Software Mentions: 14
Published: about 5 years ago
10.1523/ENEURO.0328-20.2020
Group II Metabotropic Glutamate Receptors Modulate Sound Evoked and Spontaneous Activity in the Mouse Inferior ColliculusCited by: 1
Author(s): Inga Kristaponyte, Nichole L. Beebe, Jesse W. Young, Sharad J. Shanbhag, Brett R. Schofield, Alexander V. Galazyuk
Software Mentions: 14
Published: over 5 years ago
10.3389/fgene.2021.689406
Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA SequencingCited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: almost 5 years ago
10.7717/peerj.3472
Using high-throughput sequencing of ITS2 to describe <i>Symbiodinium</i> metacommunities in St. John, US Virgin IslandsCited by: 50
Author(s): Ross Cunning, Ruth D. Gates, Peter J. Edmunds
Software Mentions: 14
Published: almost 9 years ago
10.1371/journal.pntd.0002045
Drivers of Echinococcus multilocularis Transmission in China: Small Mammal Diversity, Landscape or Climate?Cited by: 65
Author(s): Patrick Giraudoux, Francis Raoul, David Pleydell, Tiaoying Li, Xiuming Han, Jiamin Qiu, Yan Xie, Wang Hu, Akira Itō, Philip S. Craig
Software Mentions: 14
Published: about 13 years ago
10.3758/s13420-020-00446-1
Response of male and female domestic chicks to change in the number (quantity) of imprinting objectsCited by: 5
Author(s): Bastien S. Lemaire, Rosa Rugani, Lucia Regolin, Giorgio Vallortígara
Software Mentions: 14
Published: over 5 years ago
10.12688/f1000research.8900.2
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomicsCited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: over 9 years ago
10.1371/journal.pone.0249268
Outdoor cycling activity affected by COVID-19 related epidemic-control-decisionsCited by: 38
Author(s): Anne-Maria Schweizer, Anna Leiderer, Veronika Mitterwallner, Anna Walentowitz, Gregor Mathes, Manuel J. Steinbauer
Software Mentions: 14
Published: about 5 years ago
10.1186/s12888-020-02645-6
Depression, anxiety, and burnout among medical students and residents of a medical school in Nepal: a cross-sectional studyCited by: 66
Author(s): Nishan Babu Pokhrel, Ramesh Khadayat, P Tulachan
Software Mentions: 14
Published: almost 6 years ago
10.3389/fnins.2014.00067
Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRFCited by: 11
Author(s): Vincent Thomas, Solveig Badillo, Laurent Risser, Lotfi Chaâri, Christine Bakhous, Florence Forbes, Philippe Ciuciu
Software Mentions: 14
Published: about 12 years ago
10.3390/microorganisms9061167
Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in TrinidadCited by: 10
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 14
Published: about 5 years ago
10.3389/fimmu.2020.572924
Differential Skewing of Circulating MR1-Restricted and γδ T Cells in Human Psoriasis VulgarisCited by: 7
Author(s): Vera Plužarić, Mario Štefanić, Martina Mihalj, Maja Tolušić Levak, Ivanka Muršić, Ljubica Glavaš‐Obrovac, Martin Petřek, Péter Balogh, Stana Tokić
Software Mentions: 14
Published: over 5 years ago
10.1038/s41375-018-0360-1
Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALLCited by: 39
Author(s): Helena Hohtari, Oscar Brück, Sami Blom, Riku Turkki, Marjatta Sinisalo, Panu E. Kovanen, Olli Kallioniemi, Teijo Pellinen, Kimmo Porkka, Satu Mustjoki
Software Mentions: 14
Published: over 7 years ago
10.1093/gigascience/giaa039
Biospytial: spatial graph-based computing for ecological Big DataCited by: 5
Author(s): Juan Manuel Escamilla Molgora, Luigi Sedda, Peter M. Atkinson
Software Mentions: 14
Published: about 6 years ago
10.1186/s12859-016-0971-3
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression dataCited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: about 10 years ago
10.1371/journal.pone.0218310
Evaluating health facility access using Bayesian spatial models and location analysis methodsCited by: 8
Author(s): Nicholas Tierney, Antonietta Mira, H Reinhold, Giuseppe Arbia, Samuel Clifford, Angelo Auricchio, Tiziano Moccetti, Stefano Peluso, Kerrie Mengersen
Software Mentions: 14
Published: almost 7 years ago
10.3389/fgene.2020.522125
Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression ProfilesCited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: over 5 years ago
10.1371/journal.pcbi.1005158
Machine Learning for Characterization of Insect Vector FeedingCited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: over 9 years ago
10.1093/gigascience/giab039
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumenCited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: about 5 years ago
10.1111/jcmm.15705
Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade gliomaCited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: almost 6 years ago
10.1186/s12859-021-04261-x
Machine learning-based prediction of survival prognosis in cervical cancerCited by: 16
Author(s): Dongyan Ding, Tingyuan Lang, Dongling Zou, Jianrong Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma, Qi Zhou
Software Mentions: 14
Published: almost 5 years ago
10.1093/bioinformatics/btx657
heatmaply: an R package for creating interactive cluster heatmaps for online publishingCited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: over 8 years ago
10.15252/msb.20209498
Developmental function and state transitions of a gene expression oscillator in <i>Caenorhabditis elegans</i>Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: almost 6 years ago
10.1186/s12920-017-0261-6
CVE: an R package for interactive variant prioritisation in precision oncologyCited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: about 9 years ago
10.3389/fimmu.2021.557994
Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale AnalysisCited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: almost 5 years ago
10.1186/s12967-021-02894-3
Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responsesCited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: about 5 years ago
10.1186/s12859-021-03970-7
stochprofML: stochastic profiling using maximum likelihood estimation in RCited by: 3
Author(s): Lisa Amrhein, Christiane Fuchs
Software Mentions: 14
Published: about 5 years ago
10.1155/2020/8833972
An Epithelial-Mesenchymal Transition (EMT) Preoperative Nomogram for Prediction of Lymph Node Metastasis in Bladder Cancer (BLCA)Cited by: 5
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 14
Published: over 5 years ago
10.1186/s12859-021-04268-4
A comprehensive database for integrated analysis of omics data in autoimmune diseasesCited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: almost 5 years ago
10.1002/ece3.5645
Testing adaptive hypotheses on the evolution of larval life history in acorn and stalked barnaclesCited by: 11
Author(s): Christine Ewers‐Saucedo, Paula Pappalardo
Software Mentions: 13
Published: over 6 years ago
10.1186/s13068-019-1584-7
A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shockCited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: over 6 years ago
10.1038/s42003-021-01887-8
The impact of locomotion on the brain evolution of squirrels and close relativesCited by: 23
Author(s): Ornella Bertrand, Hans P. Püschel, Julia A. Schwab, Mary Silcox, Stephen L. Brusatte
Software Mentions: 13
Published: about 5 years ago
10.7554/eLife.67784
Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across EuropeCited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: about 5 years ago
10.1186/s42523-020-0023-1
Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)speciesCited 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
10.1371/journal.pone.0206563
Nitrogen addition pulse has minimal effect in big sagebrush (Artemisia tridentata) communities on the Pinedale Anticline, Wyoming (USA)Cited by: 1
Author(s): Christopher W. Beltz, Megan L. Mobley, Ingrid C. Burke
Software Mentions: 13
Published: about 7 years ago
10.3389/fgene.2021.665888
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single CellsCited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: almost 5 years ago
10.1099/mgen.0.000492
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypesCited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: over 5 years ago