10.1038/s41598-018-34162-8

Remotely-sensed productivity clusters capture global biodiversity patterns
Cited by: 16
Author(s): Nicholas C. Coops, Sean P. Kearney, Douglas K. Bolton, Volker C. Radeloff
Software Mentions: 4
Published: over 7 years ago

10.1155/2021/7264623

A Simple-to-Use Nomogram for Predicting Survival in Children with Acute Myeloid Leukemia
Cited by: 8
Author(s): Feng Jiang, Xiang Yu, Chuyan Wu, Ming Wang, Ke Wei, Jimei Wang, Guoping Zhou
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13102389

Mutation Profile of Aggressive Pheochromocytoma and Paraganglioma with Comparison of TCGA Data
Cited by: 5
Author(s): Yun Mi Choi, Jinyeong Lim, Min Ji Jeon, Yu‐Mi Lee, Tae‐Yon Sung, Eun‐Gyoung Hong, Jiyoung Lee, Se Jin Jang, Won Gu Kim, Dong Eun Song, Sung-Min Chun
Software Mentions: 4
Published: about 5 years ago

10.1016/j.gpb.2018.08.002

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Cited by: 19
Author(s): Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0194521

Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota
Cited by: 32
Author(s): Guillaume Minard, Florence‐Hélène Tran, Van Trân Van, Corentin Fournier, Patrick Potier, David Roiz, Patrick Mavingui, Claire Valiente Moro
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0017476

Functional Structure of Biological Communities Predicts Ecosystem Multifunctionality
Cited by: 341
Author(s): David Mouillot, Sébastien Villéger, Michael Scherer‐Lorenzen, Norman W. H. Mason
Software Mentions: 4
Published: over 15 years ago

10.1530/REP-19-0293

Blastocyst transfer in mice alters the placental transcriptome and growth
Cited by: 4
Author(s): Katerina Menelaou, Malwina Prater, Simon James Tunster, Georgina E T Blake, Colleen Geary Joo, James C. Cross, Russell S. Hamilton, Erica D. Watson
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0251262

Predictors for inpatient mortality during the first wave of the SARS-CoV-2 pandemic: A retrospective analysis
Cited by: 6
Author(s): Daniel E. Sammartino, Farrukh N Jafri, Brennan Cook, Lisa La, Hye Min Kim, John Cardasis, Joshua P. Raff
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-6142-y

DNA methylation profiles capturing breast cancer heterogeneity
Cited by: 19
Author(s): Xiao Chen, Jianying Zhang, Xiaofeng Dai
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-020-02052-7

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae
Cited by: 6
Author(s): Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet E. Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou, Paul Turner
Software Mentions: 4
Published: over 5 years ago

10.1186/s12903-018-0591-6

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach
Cited by: 24
Author(s): Yoshio Nakano, Nao Suzuki, Fumiyuki Kuwata
Software Mentions: 4
Published: about 8 years ago

10.1093/bib/bbaa014

Regression on imperfect class labels derived by unsupervised clustering
Cited by: 1
Author(s): Rasmus Froberg Brøndum, Thomas Yssing Michaelsen, Martin Bøgsted
Software Mentions: 4
Published: over 6 years ago

10.3758/s13415-020-00857-7

Effects of trait empathy and expectation on the processing of observed actions
Cited by: 3
Author(s): Christine Albrecht, Christian Bellebaum
Software Mentions: 4
Published: over 5 years ago

10.1038/s41597-019-0205-4

The Personal Genome Project-UK, an open access resource of human multi-omics data
Cited by: 18
Author(s): Olga Chervova, Lucía Conde, José Afonso Guerra-Assunção, Ismail Moghul, A. D. B. Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan Tian, Vitaly Voloshin, Tiago S. Jesus, Rifat Hamoudi, Javier Herrero, Stephan Beck
Software Mentions: 4
Published: almost 7 years ago

10.1093/conphys/cow049

The use of α- or β-blockers to ameliorate the chronic stress of captivity in the house sparrow (Passer domesticus)
Cited by: 9
Author(s): Clare Parker Fischer, L. Michael Romero
Software Mentions: 4
Published: over 10 years ago

10.1093/conphys/cou056

Efficacy of a sensory deterrent and pipe modifications in decreasing entrainment of juvenile green sturgeon (Acipenser medirostris) at unscreened water diversions
Cited by: 8
Author(s): Jamilynn B. Poletto, Dennis E. Cocherell, Timothy D. Mussen, Ali Ercan, Hossein Bandeh, M. L. Kavvas, Joseph J. Cech, Nann A. Fangue
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0118808

Prediction of Chemical Respiratory Sensitizers Using GARD, a Novel In Vitro Assay Based on a Genomic Biomarker Signature
Cited by: 31
Author(s): Andy Forreryd, Henrik Johansson, Ann-Sofie Albrekt, Carl Borrebaeck, Malin Lindstedt
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-017-3745-z

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model
Cited by: 20
Author(s): Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon‐Mom, Perry D. Moerland, Pernette J. Verschure
Software Mentions: 4
Published: about 9 years ago

10.7150/thno.49451

An immune cell infiltration-based immune score model predicts prognosis and chemotherapy effects in breast cancer
Cited by: 75
Author(s): Silei Sui, Xin An, Caiming Xu, Zongjuan Li, Yi-Jun Hua, Geya Huang, Sibei Sui, Long Qian, Yanxia Sui, Yuqing Xiong, Michael Ntim, Wei Guo, Miao Chen, Wu Deng, Xia Xiao, Man Li
Software Mentions: 4
Published: over 6 years ago

10.1093/conphys/coy076

Sensitivities of an endemic, endangered California smelt and two non-native fishes to serial increases in temperature and salinity: implications for shifting community structure with climate change
Cited by: 19
Author(s): Brian A. Davis, Dennis E. Cocherell, Ted Sommer, Randall D. Baxter, Tien‐Chieh Hung, Anne E. Todgham, Nann A. Fangue
Software Mentions: 4
Published: over 7 years ago

10.1186/s40168-017-0363-6

Pancreatic cyst fluid harbors a unique microbiome
Cited by: 53
Author(s): Shan Li, Gwenny M. Fuhler, Nahush Bn, Tony Jose, Marco J. Bruno, Maikel P. Peppelenbosch, Sergey R. Konstantinov
Software Mentions: 4
Published: over 8 years ago

10.3390/ijerph18031202

Latent Variables Quantifying Neighborhood Characteristics and Their Associations with Poor Mental Health
Cited by: 5
Author(s): Katherine L. Forthman, Janna Colaizzi, Hung‐Wen Yeh, Rayus Kuplicki, Martin P. Paulus
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.6278

Enhancing pollination is more effective than increased conventional agriculture inputs for improving watermelon yields
Cited by: 11
Author(s): Thomas Sawe, Katrine Eldegard, Ørjan Totland, Samora A. Macrice, Anders Nielsen
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.6035

Maternal predator‐exposure affects offspring size at birth but not telomere length in a live‐bearing fish
Cited by: 14
Author(s): Stefano Monteforte, Silvia Cattelan, Chiara Morosinotto, Andrea Pilastro, Alessandro Grapputo
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.4601

Rainforest trees respond to drought by modifying their hydraulic architecture
Cited by: 30
Author(s): David Y. P. Tng, Deborah M. G. Apgaua, Yoko Ishida, Maurizio Mencuccini, J. Lloyd, William F. Laurance, Susan G. Laurance
Software Mentions: 4
Published: over 7 years ago

10.1111/ele.13365

Spatial insurance in multi‐trophic metacommunities
Cited by: 12
Author(s): Romana Limberger, Alexandra Pitt, Martin W. Hahn, Stephen A. Wickham
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40001-017-0284-7

Fully digital data processing during cardiovascular implantable electronic device follow-up in a high-volume tertiary center
Cited by: 0
Author(s): Ingo Staudacher, Asha Roy Nalpathamkalam, Lorenz Uhlmann, Claudius Illg, Sebastian Seehausen, Mohammadreza Akhavanpoor, Anke Buchauer, Nicolas Geis, Patrick Lugenbiel, Patrick Schweizer, Panagiotis Xynogalos, Maura M. Zylla, Eberhard Scholz, Edgar Zitron, Hugo A. Katus, Dierk Thomas
Software Mentions: 4
Published: almost 9 years ago

10.1111/eva.12605

Transgenerational interactions between pesticide exposure and warming in a vector mosquito
Cited by: 36
Author(s): Tam T. Tran, Lizanne Janssens, Khuong Van Dinh, Robby Stoks
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.8042

How index selection, compression, and recording schedule impact the description of ecological soundscapes
Cited by: 3
Author(s): Becky E. Heath, Sarab S. Sethi, C. David L. Orme, Robert M. Ewers, Lorenzo Picinali
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13059-018-1416-2

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Cited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.8584

Iroki: automatic customization and visualization of phylogenetic trees
Cited by: 73
Author(s): Moore Rm, Amelia O. Harrison, Sean M. McAllister, Shawn W. Polson, K. Eric Wommack
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-59016-0

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study
Cited by: 71
Author(s): Zachary M. Burcham, Nicole L. Garneau, Sarah S. Comstock, Robin M. Tucker, Rob Knight, Jessica L. Metcalf
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.5303

Parthenogenetic <i>vs</i>. sexual reproduction in oribatid mite communities
Cited by: 24
Author(s): Mark Maraun, Tancredi Caruso, Jonathan Hense, Ricarda Lehmitz, Levan Mumladze, Maka Murvanidze, Ioana Nae, Julia Schulz, Anna Seniczak, Stefan Scheu
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0080371

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus
Cited by: 33
Author(s): C. Leyrat, Max Renner, K. Harlos, Jonathan M. Grimes
Software Mentions: 4
Published: over 12 years ago

10.3389/fcell.2021.649168

Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers
Cited by: 3
Author(s): Gang Liu, Zhenhao Liu, Xiaomeng Sun, Xiaoqiong Xia, Yunhe Liu, Lei Liu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-53892-x

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Cited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00340-20

Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic
Cited by: 5
Author(s): Alison Vrbanac, Kathryn A. Patras, Alan K. Jarmusch, Robert H. Mills, Samuel R. Shing, Robert A. Quinn, Fernando Vargas, Kyung E. Rhee, Pieter C. Dorrestein, Rob Knight, Victor Nizet
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.56969

Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Cited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pbio.3000891

Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio
Cited by: 19
Author(s): I. Strong, Xianfu Lei, Fang Chen, Kai Yuan, Patrick H. O’Farrell
Software Mentions: 4
Published: almost 6 years ago

10.1107/S139900471400087X

Anomalies in the refinement of isoleucine
Cited by: 3
Author(s): Karen R. M. Berntsen, Gert Vriend
Software Mentions: 4
Published: over 12 years ago

10.1007/s10295-019-02189-z

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
Cited by: 6
Author(s): Jesus F. Barajas, R.P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, J.H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, Jay D. Keasling
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12862-018-1212-3

A North American stem turaco, and the complex biogeographic history of modern birds
Cited by: 26
Author(s): Daniel J. Field, Allison Y. Hsiang
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.6952

Different landscape effects on the genetic structure of two broadly distributed woody legumes,<i>Acacia salicina</i>and<i>A. stenophylla</i>(Fabaceae)
Cited by: 2
Author(s): Francisco Encinas‐Viso, Christiana McDonald‐Spicer, Nunzio Knerr, Peter H. Thrall, Linda Broadhurst
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.3042

Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora
Cited by: 9
Author(s): Áki J. Láruson
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: over 5 years ago

10.1140/epjds/s13688-017-0109-5

A roadmap for the computation of persistent homology
Cited by: 416
Author(s): Nina Otter, Mason A. Porter, Ulrike Tillmann, Peter Grindrod, Heather A. Harrington
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12870-021-03057-8

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper
Cited by: 4
Author(s): Myung-Shin Kim, Geun Young Chae, Soohyun Oh, Jihyun Kim, Hyunggon Mang, Seungill Kim, Doil Choi
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: about 11 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0092257

Esterase LpEst1 from Lactobacillus plantarum: A Novel and Atypical Member of the αβ Hydrolase Superfamily of Enzymes
Cited by: 23
Author(s): Y. Álvarez, María Esteban-Torres, Álvaro Cortés-Cabrera, Federico Gago, I. Acebrón, R. Benavente, Karin Mardo, Blanca de las Rivas, Rosario Múñoz, José M. Mancheño
Software Mentions: 4
Published: over 12 years ago

10.1186/1746-1596-8-34

CognitionMaster: an object-based image analysis framework
Cited by: 41
Author(s): Stephan Wienert, Daniel Heim, Manato Kotani, Bjoern Lindequist, Albrecht Stenzinger, Masaru Ishii, Peter Hufnagl, Michael Beil, Manfred Dietel, Carsten Denkert, Frederick Klauschen
Software Mentions: 4
Published: over 13 years ago

10.7554/eLife.05224

Social networks predict gut microbiome composition in wild baboons
Cited by: 384
Author(s): Jenny Tung, Luis B. Barreiro, Michael B. Burns, Jean Grenier, Joshua Lynch, Laura Grieneisen, Jeanne Altmann, Susan C. Alberts, Ran Blekhman, Elizabeth A. Archie
Software Mentions: 4
Published: over 11 years ago

10.1186/s12859-021-04117-4

MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy
Cited by: 3
Author(s): Jesse T. Chao, Calvin D. Roskelley, Christopher Loewen
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/btz470

Scaling tree-based automated machine learning to biomedical big data with a feature set selector
Cited by: 216
Author(s): Trang T. Le, Weixuan Fu, Jason H. Moore
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2021.723350

Identification and Molecular Characterization of a Novel Hordeivirus Associated With Yellow Mosaic Disease of Privet (Ligustrum vulgare) in Europe
Cited by: 4
Author(s): Jean-Sébastien Reynard, Silvia Turco, Justine Brodard, Isabelle Kellenberger, François Maclot, Olivier Schumpp, P. Gugerli, Mikhail M. Pooggin
Software Mentions: 4
Published: almost 5 years ago

10.1002/1878-0261.12364

A drug‐repositioning screen for primary pancreatic ductal adenocarcinoma cells identifies 6‐thioguanine as an effective therapeutic agent for TPMT‐low cancer cells
Cited by: 15
Author(s): Inki Kim, Yong-Sung Choi, Jae Yen Song, Eun A Choi, Sojung Park, Eun Ji Lee, Je-Keun Rhee, Song Cheol Kim, Suhwan Chang
Software Mentions: 4
Published: almost 8 years ago

10.1186/gb-2008-9-1-r11

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships
Cited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: over 18 years ago

10.3390/ijms22010347

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
Cited by: 8
Author(s): Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-021-03826-1

Gata2-L359V impairs primitive and definitive hematopoiesis and blocks cell differentiation in murine chronic myelogenous leukemia model
Cited by: 7
Author(s): Yanbin Fu, Yun Tan, Baichang Wu, Yuting Dai, Xiaoguang Xu, Mengmeng Pan, Zhiwei Chen, Na Qiao, Jing Wu, Lu Jiang, Jing Lu, Bing Chen, Avigail Rein, Shai Izraeli, Xiao Jian Sun, Jinyan Huang, Qiu-Hua Huang, Zhu Chen, Sai‐Juan Chen
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-56631-4

Helicobacter pylori infection associates with fecal microbiota composition and diversity
Cited by: 41
Author(s): Fabian Frost, Tim Kacprowski, Malte Rühlemann, Corinna Bang, André Franke, Kathrin Zimmermann, Matthias Nauck, Uwe Völker, Henry Völzke, Reiner Biffar, Christian Schulz, Julia Mayerle, Frank Ulrich Weiss, Georg Homuth, Markus M. Lerch
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-6007-4

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
Cited by: 30
Author(s): José Salvatore Leister Patané, Joaquim Martins, Luiz Thibério Rangel, José Belasque, Luciano Antônio Digiampietri, Agda Paula Facincani, Rafael Marini Ferreira, Fabrício José Jaciani, Yunzeng Zhang, Alessandro M. Varani, Nalvo F. Almeida, Nian Wang, Jesus Aparecido Ferro, Leandro Márcio Moreira, João Carlos Setúbal
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms8111679

Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
Cited by: 13
Author(s): Valentina Méndez, Matías A. Valenzuela, Francisco Salvà‐Serra, Daniel Jaén‐Luchoro, Ximena Besoaín, Edward R. B. Moore, Michael Seeger
Software Mentions: 4
Published: almost 6 years ago

10.1038/s42003-021-02166-2

Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease
Cited by: 5
Author(s): Mayar Allam, Thomas Hu, Shuangyi Cai, Krishnan Laxminarayanan, Robert B. Hughley, Ahmet F. Coşkun
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2017.01279

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-018-27650-4

MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides
Cited by: 4
Author(s): Emma Timmins‐Schiffman, Molly P. Mikan, Ying S. Ting, H. Rodger Harvey, Brook L. Nunn
Software Mentions: 4
Published: about 8 years ago

10.1111/gcb.14657

Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants
Cited by: 39
Author(s): Rutger A. Wilschut, Stefan Geisen, Henk Martens, Olga Kostenko, Mattias de Hollander, Freddy C. ten Hooven, Carolin Weser, L. Basten Snoek, J. Bloem, Danka Caković, Tatjana Čelik, Kadri Koorem, Nikos Krigas, Marta Manrubia, Kelly S. Ramirez, Maria A. Tsiafouli, Branko Vreš, Wim H. van der Putten
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.29391

Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites
Cited by: 25
Author(s): Fabien Sindikubwabo, Shibin Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y. Botté, Artur Scherf, Mohamed-Ali Hakimi
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0249174

A panel of 8-lncRNA predicts prognosis of breast cancer patients and migration of breast cancer cells
Cited by: 8
Author(s): Lili Zhu, Kang Cui, Lanling Weng, Yu Pan, Yabing Du, Tengfei Zhang, Hong Liu, Bingjie Li, Wei Ma
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.7237

Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of <i>Sceloporus</i> lizards
Cited by: 6
Author(s): Julio A. Rivera, Heather N. Rich, A. Michelle Lawing, Michael S. Rosenberg, Emilı́a P. Martins
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-918

POMO - Plotting Omics analysis results for Multiple Organisms
Cited by: 3
Author(s): Jake Lin, Richard Kreisberg, Aleksi Kallio, Andrew T. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, Reija Autio
Software Mentions: 4
Published: over 13 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: almost 9 years ago

10.1186/1297-9716-42-60

Estimating front-wave velocity of infectious diseases: a simple, efficient method applied to bluetongue
Cited by: 39
Author(s): Maryline Pioz, Hélène Guis, Didier Calavas, Benoı̂t Durand, David Abrial, Christian Ducrot
Software Mentions: 4
Published: over 15 years ago

10.3389/fncom.2020.580632

DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains
Cited by: 11
Author(s): Xiayu Chen, Ming Zhou, Zhengxin Gong, Wei Xu, Xingyu Liu, Taicheng Huang, Zonglei Zhen, Jia Liu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0201221

Beached bachelors: An extensive study on the largest recorded sperm whale Physeter macrocephalus mortality event in the North Sea
Cited by: 15
Author(s): Lonneke L. IJsseldijk, Abbo van Neer, Rob Deaville, Lineke Begeman, Marco van de Bildt, Judith M. A. van den Brand, Andrew Brownlow, Richard Czeck, Willy Dabin, Mariel ten Doeschate, Vanessa Herder, Helena Herr, Jooske IJzer, Thierry Jauniaux, Lasse Fast Jensen, Paul D. Jepson, Wendy K Jo, Jan Lakemeyer, Kristina Lehnert, M.F. Leopold, Albert D. M. E. Osterhaus, Matthew Perkins, Uwe Piatkowski, Ellen Prenger‐Berninghoff, Ralf Pund, P. Wohlsein, Andrea Gröne, Ursula Siebert
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2015.00779

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils
Cited by: 31
Author(s): Kshitij Ranjan, Fabiana S. Paula, Rebecca C. Mueller, Ederson da Conceição Jesus, Karina Cenciani, Brendan J. M. Bohannan, Klaus Nüsslein, Jorge L. M. Rodrigues
Software Mentions: 4
Published: about 11 years ago

10.3390/microorganisms7100475

Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea
Cited by: 6
Author(s): Xiuling Wang, Shunjie Liu, Mingjie Chen, Changxia Yu, Yan Zhao, Haiyan Yang, Zhe Li, Zhengpeng Li
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.60108

Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris
Cited by: 21
Author(s): Brent A. Wilkerson, Heather L Zebroski, Connor Finkbeiner, Alex Chitsazan, Kathy Beach, Nilasha Sen, Renee C Zhang, Olivia Bermingham‐McDonogh
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2021.628437

Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System
Cited by: 8
Author(s): Darren Heenan-Daly, Simone Coughlan, Eileen Dillane, Barbara Doyle Prestwich
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-64570-8

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects
Cited by: 16
Author(s): My Hanh Le, Daryi Wang
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-87635-8

H3K4me2 ChIP-Seq reveals the epigenetic landscape during mushroom formation and novel developmental regulators of Schizophyllum commune
Cited by: 9
Author(s): Peter Jan Vonk, Robin A. Ohm
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0250660

System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study
Cited by: 3
Author(s): Utpala Nanda Chowdhury, Shamim Ahmad, M. Babul Islam, Salem A. Alyami, Julian M.W. Quinn, Valsamma Eapen, Mohammad Ali Moni
Software Mentions: 4
Published: about 5 years ago

10.1002/ece3.660

Investigating sex-specific dynamics using uniparental markers: West New Guinea as a case study
Cited by: 4
Author(s): Stefano Mona, Ernest Mordret, Michel Veuille, Mila Tommaseo-Ponzetta
Software Mentions: 4
Published: about 13 years ago

10.1002/ece3.4481

Genetic diversity and differentiation in narrow versus widespread taxa of<i>Helianthemum</i>(Cistaceae) in a hotspot: The role of geographic range, habitat, and reproductive traits
Cited by: 11
Author(s): Sara Martín‐Hernanz, Sara Martínez‐Sánchez, Rafael G. Albaladejo, Juan Lorite, Juan Arroyo, Abelardo Aparicio
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0232436

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed
Cited by: 9
Author(s): Christos Dadousis, Francesca Cecchi, Michela Ablondi, Maria Chiara Fabbri, Alessandra Stella, Rıccardo Bozzi
Software Mentions: 4
Published: over 5 years ago

10.1007/s00338-017-1561-1

Palaeoecological records of coral community development on a turbid, nearshore reef complex: baselines for assessing ecological change
Cited by: 16
Author(s): Jamie A. Johnson, Chris T. Perry, Scott G. Smithers, Kyle M. Morgan, Nadiezhda Santodomingo, Kenneth G. Johnson
Software Mentions: 4
Published: over 9 years ago

10.1111/eva.12122

Linking genotype, ecotype, and phenotype in an intensively managed large carnivore
Cited by: 13
Author(s): Aaron B. A. Shafer, Scott E. Nielsen, Joseph M. Northrup, Gordon B. Stenhouse
Software Mentions: 4
Published: over 12 years ago

10.3389/fmicb.2018.00169

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil
Cited by: 48
Author(s): Wei Yang, Song Gu, Ying Xin, Ayodeji Bello, Wanqing Sun, Xiuhong Xu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0247556

MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses
Cited by: 4
Author(s): Hongmei Zhu, Siu-wai Leung
Software Mentions: 4
Published: over 5 years ago

10.1093/g3journal/jkab085

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (<i>Hermetia illucens</i> L.)
Cited by: 29
Author(s): Tomas N Generalovic, Shane McCarthy, Ian A. Warren, Jonathan Wood, James Torrance, Ying Sims, Michael A. Quail, Kerstin Howe, Miha Pipan, Richard Durbin, Chris D. Jiggins
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0009425

Profound downregulation of neural transcription factor Npas4 and Nr4a family in fetal mice neurons infected with Zika virus
Cited by: 3
Author(s): Sergio P. Alpuche-Lazcano, James Saliba, Vivian Vasconcelos Costa, Gabriel Henrique Campolina-Silva, Fernanda Martins Marim, Lucas S. Ribeiro, Volker Blank, Andrew J. Mouland, Mauro M. Teixeira, Anne Gatignol
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1007765

Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Cited by: 12
Author(s): Vidya Murthy, Toma Tebaldi, Toshimi Yoshida, Serkan Erdin, Teresa Calzonetti, Ravi Vijayvargia, Takshashila Tripathi, Emanuela Kerschbamer, Ihn Sik Seong, Alessandro Quattrone, Michael E. Talkowski, James F. Gusella, Katia Georgopoulos, Marcy E. MacDonald, Marta Biagioli
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2020.00817

Morphological and Genetic Variation in Monocultures, Forestry Systems and Wild Populations of Agave maximiliana of Western Mexico: Implications for Its Conservation
Cited by: 17
Author(s): Dánae Cabrera-Toledo, Ofelia Vargas‐Ponce, Sabina Ascencio-Ramírez, Luis Mario Valadez-Sandoval, Jessica Pérez‐Alquicira, Judith Morales-Saavedra, Oassis F. Huerta-Galván
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008253

A Cyclin A—Myb-MuvB—Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles
Cited by: 24
Author(s): Michael D. Rotelli, Robert A. Policastro, Anna M. Bolling, Andrew W. Killion, Abraham J. Weinberg, Michael J. Dixon, Gabriel E. Zentner, Claire Walczak, Mary A. Lilly, Brian R. Calvi
Software Mentions: 4
Published: about 7 years ago

10.1136/oemed-2016-103895

Risk factors for leptospirosis seropositivity in slaughterhouse workers in western Kenya
Cited by: 26
Author(s): Elizabeth A. J. Cook, William A. de Glanville, Lian F. Thomas, Samuel Kariuki, Barend M. deC. Bronsvoort, Eric M. Fèvre
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1003130

Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
Cited by: 74
Author(s): Andrew Cron, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder Singh, Cedrik M. Britten, Marij J.P. Welters, Sjoerd H. van der Burg, Mike West, Cliburn Chan
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pgen.1009054

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases
Cited by: 13
Author(s): Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijerph18041370

Anhedonia as a Potential Risk Factor of Alzheimer’s Disease in a Community-Dwelling Elderly Sample: Results from the ZARADEMP Project
Cited by: 2
Author(s): David Vaquero-Puyuelo, Concepción De‐la‐Cámara, Beatriz Olaya, Patricia Gracia-García, António Lobo, Raúl López-Antón, Javier Santabárbara
Software Mentions: 4
Published: over 5 years ago