10.3389/fvets.2020.00126

Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest
Cited by: 12
Author(s): Augusta Zannoni, Marco Pietra, Alba Gaspardo, Pier Attilio Accorsi, Monica Barone, Silvia Turroni, Luca Laghi, Chenglin Zhu, Patrizia Brigidi, Monica Forni
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.7037

FastD: Fast detection of insecticide target‐site mutations and overexpressed detoxification genes in insect populations from RNA‐Seq data
Cited by: 1
Author(s): Longfei Chen, Kun Lang, Mei Yang, Zhanghong Shi, Kang He, Fei Li, Huamei Xiao, Gōngyín Yè, Zhaojun Han
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.00820

Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank
Cited by: 36
Author(s): Steffen Leth Jørgensen, Rui Zhao
Software Mentions: 4
Published: about 10 years ago

10.1186/s13071-021-04787-2

Ecology, seasonality and host preferences of Austrian Phlebotomus (Transphlebotomus) mascittii Grassi, 1908, populations
Cited by: 5
Author(s): Edwin Kniha, Markus Milchram, Vít Dvořák, Petr Halada, Adelheid G. Obwaller, Wolfgang Poeppl, Gerhard Mooseder, Petr Volf, Julia Walochnik
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.5424

Soil and forest structure predicts large-scale patterns of occurrence and local abundance of a widespread Amazonian frog
Cited by: 9
Author(s): Anthony Santana Ferreira, Robert Jehle, Adam J. Stow, Albertina P. Lima
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2021.675798

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts
Cited by: 4
Author(s): Emily N. Junkins, Bradley S. Stevenson
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.6931

Metabarcoding reveals a high diversity of woody host-associated<i>Phytophthora</i>spp. in soils at public gardens and amenity woodlands in Britain
Cited by: 36
Author(s): Carolyn Riddell, Debbie Frederickson-Matika, April C. Armstrong, Matthew Elliot, Jack Forster, Pete E. Hedley, Jenny Morris, Peter Thorpe, D. E. L. Cooke, Leighton Pritchard, Paul M. Sharp, Sarah Green
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2020.590212

Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf (Canis rufus)
Cited by: 19
Author(s): Morgan Bragg, Elizabeth W. Freeman, Haw Chuan Lim, Nucharin Songsasen, Carly R. Muletz‐Wolz
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms7090315

Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts
Cited by: 17
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma Theodora Steenkamp, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.10799

The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies
Cited by: 23
Author(s): Daniel Marquina, Mateusz Buczek, Fredrik Ronquist, Piotr Łukasik
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01721

Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia
Cited by: 19
Author(s): Kurt M. Yakimovich, Casey B. Engstrom, Lynne M. Quarmby
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-020-03591-6

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
Cited by: 1
Author(s): Yulia Kondratenko, Anton Korobeynikov, Alla Lapidus
Software Mentions: 4
Published: about 6 years ago

10.3390/microorganisms9051069

Study of the Vaginal Microbiota in Healthy Women of Reproductive Age
Cited by: 7
Author(s): Melanie Cristine Alonzo Martínez, Eduardo Cazorla, Esther Cánovas, Juan F. Martínez-Blanch, Empar Chenoll, Eric Climent, Vicente Navarro-López
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms7070209

Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment
Cited by: 25
Author(s): Juline M. Walter, Andrea Bagi, Daniela M. Pampanin
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.45450

Positive and negative incentive contrasts lead to relative value perception in ants
Cited by: 21
Author(s): Stephanie Wendt, Kim Strunk, Jürgen Heınze, Andreas Roider, Tomer J. Czaczkes
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.60287

Formicine ants swallow their highly acidic poison for gut microbial selection and control
Cited by: 19
Author(s): Simon Tragust, Claudia Herrmann, Jane Häfner, Ronja Braasch, Christina Tilgen, Maria Hoock, Margarita Artemis Milidakis, Roy Gross, Heike Feldhaar
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0237715

Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties
Cited by: 4
Author(s): Stephanie A. Bruggeman, David P. Horvath, Anne Fennell, Jose L. Gonzalez-Hernandez, Sharon A. Clay
Software Mentions: 4
Published: almost 6 years ago

10.3390/ani11051372

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs
Cited by: 0
Author(s): Emily Van Syoc, Natália Carrillo Gaeta, Erika Ganda
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0074396

Lock, Stock and Two Different Barrels: Comparing the Genetic Composition of Morphotypes of the Indo-Pacific Sponge Xestospongia testudinaria
Cited by: 28
Author(s): Thomas Swierts, Katja T. C. A. Peijnenburg, Christiaan de Leeuw, Daniel F. R. Cleary, Christine Hörnlein, Edwin Setiawan, Gert Wörheide, Dirk Erpenbeck, Nicole J. de Voogd
Software Mentions: 4
Published: almost 13 years ago

10.3390/microorganisms8091377

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization
Cited by: 13
Author(s): Martina Kracmarova, Jana Karpíšková, Ondřej Uhlík, Michal Strejcek, Jiřina Száková, J. Balík, Kateřina Demnerova, Hana Stiborová
Software Mentions: 4
Published: almost 6 years ago

10.1080/20013078.2018.1461450

ISEV2018 abstract book
Cited by: 157
Author(s): Clotilde Théry, Kenneth W. Witwer
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-021-04067-x

CytoGLMM: conditional differential analysis for flow and mass cytometry experiments
Cited by: 13
Author(s): Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan Holmes
Software Mentions: 4
Published: over 5 years ago

10.1074/mcp.M115.052860

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data
Cited by: 23
Author(s): Xiaojing Wang, Robbert J.C. Slebos, Matthew Chambers, David L. Tabb, Daniel C. Liebler, Bing Zhang
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0204047

Transcriptomics reveal potential vaccine antigens and a drastic increase of upregulated genes during Theileria parva development from arthropod to bovine infective stages
Cited by: 13
Author(s): Triza Tonui, Pilar Corredor‐Moreno, Esther Kanduma, Joyce Njuguna, Moses Njahira, Steven Ger Nyanjom, Joana C. Silva, Appolinaire Djikeng, Roger Pellé
Software Mentions: 4
Published: almost 8 years ago

10.7150/ijms.36255

Transcriptome Profiling Reveals Distinct Phenotype of Human Bone Marrow Mesenchymal Stem Cell-derived Hepatocyte-like cells
Cited by: 9
Author(s): Dongyan Shi, Jiaojiao Xin, Yingyan Lu, Wenchao Ding, Jing Jiang, Qian Zhou, Suwan Sun, Beibei Guo, Xingping Zhou, Li Jun
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0246901

The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus
Cited by: 6
Author(s): Yamelie A. Martínez, Xianwu Guo, Diana Patricia Portales-Pérez, Gildardo Rivera, Julio Enrique Castañeda-Delgado, Carlos A. García-Pérez, José Antonio Enciso-Moreno, Edgar E. Lara-Ramírez
Software Mentions: 4
Published: over 5 years ago

10.3389/fpsyg.2020.02177

The Anxiety-Buffer Hypothesis in the Time of COVID-19: When Self-Esteem Protects From the Impact of Loneliness and Fear on Anxiety and Depression
Cited by: 111
Author(s): Alessandro Rossi, Anna Panzeri, Giada Pietrabissa, Gian Mauro Manzoni, Gianluca Castelnuovo, Stefania Mannarini
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-53023-6

Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis
Cited by: 42
Author(s): Shivraj Braich, Rebecca C. Baillie, Larry S. Jewell, Germán Spangenberg, Noel O. I. Cogan
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0103441

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: about 12 years ago

10.1038/srep20759

Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Cited by: 10
Author(s): Qian Zhou, Wenchao Ding, Liangliang Jiang, Jiaojiao Xin, Tianzhou Wu, Dongyan Shi, Jing Jiang, Cao H, Lanjuan Li, Jun Li
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2013-14-4-r31

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
Cited by: 368
Author(s): Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D. Uno, Takeshi Imai, Hiroki R. Ueda
Software Mentions: 4
Published: over 13 years ago

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: almost 10 years ago

10.1186/1752-0509-4-159

Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models
Cited by: 6
Author(s): Dietrich Trümbach, Cornelia Graf, Benno Pütz, Claudia Kühne, Marcus Panhuysen, Peter Weber, Florian Holsboer, Wolfgang Wurst, Gerhard Welzl, Jan M. Deussing
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0248956

Characterizing COVID-19 clinical phenotypes and associated comorbidities and complication profiles
Cited by: 42
Author(s): Elizabeth R. Lusczek, Nicholas E. Ingraham, Basil S. Karam, Jennifer Proper, Lianne Siegel, Erika S. Helgeson, Sahar Lotfi-Emran, Emily Zolfaghari, Emma Jones, Michael Usher, Jeffrey G. Chipman, R. Adams Dudley, Bradley J. Benson, Genevieve B. Melton, Anthony Charles, Monica I. Lupei, Christopher J. Tignanelli
Software Mentions: 4
Published: over 5 years ago

10.1111/cmi.12397

The co‐transcriptome of uropathogenic<scp><i>E</i></scp><i>scherichia coli</i>‐infected mouse macrophages reveals new insights into host–pathogen interactions
Cited by: 62
Author(s): Charalampos Harris Mavromatis, Nilesh J. Bokil, Makrina Totsika, Asha Kakkanat, Kolja Schaale, Carlo Vittorio Cannistraci, Tae Woo Ryu, Scott A. Beatson, Glen C. Ulett, Mark A. Schembri, Matthew J. Sweet, Timothy Ravasi
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0125663

Protein Structure and Evolution: Are They Constrained Globally by a Principle Derived from Information Theory?
Cited by: 5
Author(s): Les Hatton, Gregory W. Warr
Software Mentions: 4
Published: about 11 years ago

10.1186/s40168-019-0695-5

Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area
Cited by: 27
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Julian Gordon, Prasanthi Gandhi, Rachel Reboulet, Jarrad Hampton-Marcell
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0158936

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome
Cited by: 91
Author(s): Alaguraj Veluchamy, Teddy Jégu, Federico Ariel, David Latrasse, Kadarkaraisamy Mariappan, Soon-Kap Kim, Martín Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.ppat.1009804

Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
Cited by: 34
Author(s): Jonathan Youngs, Nicholas M. Provine, Nicholas Lim, Hannah Sharpe, Ali Amini, Yi‐Ling Chen, Jian Luo, Matthew Edmans, Panagiota Zacharopoulou, Wentao Chen, Oliver Sampson, Robert S Paton, William J Hurt, David A. Duncan, Anna L McNaughton, Vincent N. Miao, Susannah Leaver, Duncan Wyncoll, Jonathan Ball, P Hopkins, Donal Skelly, Eleanor Barnes, Susanna Dunachie, Graham Ogg, Teresa Lambe, Ian D. Pavord, Alex K. Shalek, Craig Thompson, Luzheng Xue, Derek C. Macallan, Philip Goulder, Paul Klenerman, Tihana Bicanic
Software Mentions: 4
Published: almost 5 years ago

10.18632/oncotarget.22947

Spatial habitats from multiparametric MR imaging are associated with signaling pathway activities and survival in glioblastoma
Cited by: 19
Author(s): Katherine Dextraze, Abhijoy Saha, Donnie Kim, Shivali Narang, Michael Lehrer, Aroor R. Rao, Saphal Narang, Dinesh Rao, Salmaan Ahmed, Venkatesh S Madhugiri, Clifton D. Fuller, Michelle M. Kim, Sunil Krishnan, Ganesh Rao, Arvind Rao
Software Mentions: 4
Published: over 8 years ago

10.1186/s40168-018-0446-z

Reproducible protocols for metagenomic analysis of human faecal phageomes
Cited by: 127
Author(s): Andrey N. Shkoporov, Feargal J. Ryan, Lorraine A. Draper, Amanda Forde, Stephen R. Stockdale, Karen Daly, Siobhan A. McDonnell, James A. Nolan, Thomas D.S. Sutton, Marion Dalmasso, A. McCann, R. Paul Ross, Colin Hill
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0025851

Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga
Cited by: 200
Author(s): Michael T. Guarnieri, Ambarish Nag, Sharon Smolinski, Al Darzins, Michael Seibert, Philip T. Pienkos
Software Mentions: 4
Published: almost 15 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0220843

Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs
Cited by: 89
Author(s): Donghyun Shin, Sung-Ho Chang, Paul Bogere, KyeongHye Won, Jae-Ho Choi, Yun‐Sang Choi, Hak Kyo Lee, Jin Hur, Byung-Yong Park, Young-Hoon Kim, Jae-Young Heo
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0145031

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
Cited by: 27
Author(s): Margaret Staton, Teodora Best, Sudhir Khodwekar, Sandra A. Owusu, Tao Xu, Yi Xu, Tara Jennings, Richard Cronn, Aru K. Arumuganathan, Mark V. Coggeshall, Oliver Gailing, Haiying Liang, Jeanne Romero‐Severson, Scott E. Schlarbaum, John E. Carlson
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2018.01201

Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom
Cited by: 93
Author(s): Jin Zhou, Mindy L. Richlen, Taylor R. Sehein, David M. Kulis, Donald M. Anderson, Zhonghua Cai
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-017-11812-x

Concordant and discordant gene expression patterns in mouse strains identify best-fit animal model for human tuberculosis
Cited by: 32
Author(s): Teresa Domaszewska, Lisa Scheuermann, Karin Hahnke, Hans Mollenkopf, Anca Dorhoi, Stefan H. E. Kaufmann, January Weiner
Software Mentions: 4
Published: almost 9 years ago

10.1186/s40168-018-0537-x

Root exudates drive the soil-borne legacy of aboveground pathogen infection
Cited by: 294
Author(s): Jun Yuan, Jun Zhao, Teng Wen, Mingwen Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen
Software Mentions: 4
Published: almost 8 years ago

10.1186/s40168-020-00997-5

Rhizosphere community selection reveals bacteria associated with reduced root disease
Cited by: 96
Author(s): Chuntao Yin, Juan M. Casa Vargas, Daniel Schlatter, Christina H. Hagerty, Scot H. Hulbert, T. C. Paulitz
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-018-0472-x

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum
Cited by: 252
Author(s): Mie Crusell, Tue H. Hansen, Trine Nielsen, Kristine H. Allin, Malte Rühlemann, Peter Damm, Henrik Vestergaard, Christina Rørbye, Niklas Rye Jørgensen, Ole Bjarne Christiansen, Femke-Anouska Heinsen, André Franke, Jeannet Lauenborg, Oluf Pedersen
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-020-07072-1

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes
Cited by: 18
Author(s): Syed Farhan Ahmad, Maryam Jehangir, Adauto Lima Cardoso, Ivan Rodrigo Wolf, Vladimir Pavan Margarido, Diogo Cavalcanti Cabral-de-Mello, Rachel J. O’Neill, Guilherme Targino Valente, Cesar Martins
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-020-00867-0

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Cited by: 394
Author(s): Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-14-283

Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-019-6131-1

Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies
Cited by: 19
Author(s): Linda Beauclair, Christelle Ramé, Peter Arensburger, Benoît Piégu, Florian Guillou, Joëlle Dupont, Yves Bigot
Software Mentions: 4
Published: almost 7 years ago

10.3389/fnins.2019.01321

Analyzing Neuroimaging Data Through Recurrent Deep Learning Models
Cited by: 63
Author(s): Armin W. Thomas, Hauke R. Heekeren, Klaus Robert Müller, Wojciech Samek
Software Mentions: 4
Published: over 6 years ago

10.1098/rstb.2015.0212

Ochre star mortality during the 2014 wasting disease epizootic: role of population size structure and temperature
Cited by: 100
Author(s): Morgan E. Eisenlord, Maya L. Groner, Reyn Yoshioka, Joel K. Elliott, Jeffrey Maynard, Steven C. Fradkin, Margaret Turner, Katie Pyne, Natalie Rivlin, Ruben van Hooidonk, C. Drew Harvell
Software Mentions: 4
Published: over 10 years ago

10.1016/j.ccell.2018.04.004

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial
Cited by: 136
Author(s): Alan Mackay, Anna Burford, Valeria Molinari, David Jones, Elisa Izquierdo, Jurriaan Brouwer‐Visser, Felice Giangaspero, Christine Haberler, Torsten Pietsch, Thomas S. Jacques, Dominique Figarella‐Branger, Daniel Rodriguez, Paul S. Morgan, Pichai Raman, Angela J. Waanders, Adam Resnick, Maura Massimino, Maria Luisa Garré, Smith Hw, David Capper, Stefan M. Pfister, Thomas Würdinger, Rachel Tam, Josep Garcia, Meghna Das Thakur, Gilles Vassal, Jacques Grill, Tim Jaspan, Pascale Varlet, Chris Jones
Software Mentions: 4
Published: over 8 years ago

10.1186/s12862-019-1523-z

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages
Cited by: 12
Author(s): Mengxiao Yan, Ruibin Liu, Ying Liu, Andrew L. Hipp, Min Deng, Yanshi Xiong
Software Mentions: 4
Published: almost 7 years ago

10.3389/fphar.2021.708050

A Comparison of Nine Machine Learning Mutagenicity Models and Their Application for Predicting Pyrrolizidine Alkaloids
Cited by: 5
Author(s): Christoph Helma, Verena Schöning, Jürgen Drewe, Philipp Boss
Software Mentions: 4
Published: about 5 years ago

10.1007/s00401-020-02230-x

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
Cited by: 21
Author(s): Sheila Mansouri, Suganth Suppiah, Yasin Mamatjan, Irene Paganini, Jeffrey Liu, Shirin Karimi, Vikas Patil, Farshad Nassiri, Olivia Singh, Yogi Sundaravadanam, Pramod C. Rath, Roberta Sestini, Francesca Gensini, Sameer Agnihotri, Jaishri O. Blakeley, Kimberly Laskie Ostrow, David A. Largaespada, Scott R. Plotkin, Anat Stemmer‐Rachamimov, Marcela Maria Ferrer, Trevor J. Pugh, Kenneth Aldape, Laura Papi, Gelareh Zadeh
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12862-015-0416-z

A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea
Cited by: 21
Author(s): Carolina Granados Mendoza, Julia Naumann, Marie‐Stéphanie Samain, Paul Goetghebeur, Yannick De Smet, Stefan Wanke
Software Mentions: 4
Published: about 11 years ago

10.1186/s12862-016-0700-6

Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini
Cited by: 40
Author(s): Ilya Borisenko, Marcin Adamski, Alexander Ereskovsky, Maja Adamska
Software Mentions: 4
Published: about 10 years ago

10.3390/v12111290

Highly Pathogenic Avian Influenza (H5N1) Landscape Suitability Varies by Wetland Habitats and the Degree of Interface between Wild Waterfowl and Poultry in India
Cited by: 3
Author(s): Michael Walsh, Siobhan M. Mor, Shaikh Shah Hossain
Software Mentions: 4
Published: over 5 years ago

10.1186/s13071-020-04336-3

High-resolution habitat suitability model for Phlebotomus pedifer, the vector of cutaneous leishmaniasis in southwestern Ethiopia
Cited by: 2
Author(s): Myrthe Pareyn, Anneleen Rutten, Behailu Merdekios, Ronja E. M. Wedegärtner, Nigatu Girma, Leo Regelbrugge, Simon Shibru, Herwig Leirs
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12967-020-02454-1

Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer
Cited by: 11
Author(s): Shanshan Yu, Chuan Hu, Lixiao Liu, Luya Cai, Xuedan Du, Qiongjie Yu, Fan Lin, Jinduo Zhao, Ye Zhao, Cheng Zhang, Xuan Li, Wenfeng Li
Software Mentions: 4
Published: about 6 years ago

10.1186/1756-3305-7-289

Modeling the distribution of the West Nile and Rift Valley Fever vector Culex pipiens in arid and semi-arid regions of the Middle East and North Africa
Cited by: 45
Author(s): Amy K. Conley, Douglas O. Fuller, Nabil Haddad, A. K. Hassan, Ahmed Gad, John C. Beier
Software Mentions: 4
Published: over 12 years ago

10.1186/s12915-019-0697-6

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
Cited by: 39
Author(s): Joel‐Elias Kuon, Weihong Qi, Pascal Schläpfer, Matthias Hirsch‐Hoffmann, Philipp Rogalla von Bieberstein, Andrea Patrignani, Lucy Poveda, Stefan Grob, Miyako Keller, Rie Shimizu‐Inatsugi, Ueli Grossniklaus, Hervé Vanderschuren, Wilhelm Gruissem
Software Mentions: 4
Published: almost 7 years ago

10.1155/2021/9587084

Development of an Individualized Immune Prognostic Signature for Clear Cell Renal Cell Carcinoma through the Identification of Differential Immune Genes
Cited by: 1
Author(s): Jianfeng Wang, Chaozhi Tang, Xiaowu Liu
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-016-1428-4

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Cited by: 45
Author(s): Roberto A. Barrero, Kathryn R. Napier, J. H. Cunnington, L. W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-019-3115-8

GenGraph: a python module for the simple generation and manipulation of genome graphs
Cited by: 4
Author(s): Jon Ambler, Shandukani Mulaudzi, Nicola Mulder
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2105-10-251

SNAD: sequence name annotation-based designer
Cited by: 6
Author(s): Igor A. Sidorov, Denis A. Reshetov, Alexander E. Gorbalenya
Software Mentions: 4
Published: almost 17 years ago

10.1038/s41389-021-00311-4

Single-cell RNA sequencing reveals that targeting HSP90 suppresses PDAC progression by restraining mitochondrial bioenergetics
Cited by: 8
Author(s): Li-Peng Hu, Kaixia Zhou, Yan‐Miao Huo, Dejun Liu, Qing Li, Minwei Yang, Peng Huang, Chunjie Xu, Guang-Ang Tian, Lishuang Yao, Xueli Zhang, Yahui Wang, Jun Li, Zhigang Zhang, Shu-Heng Jiang, Xin Xing, Xu Wang, Weiting Qin, Qin Yang
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-14-334

Fastphylo: Fast tools for phylogenetics
Cited by: 17
Author(s): Muhammad Alam Zaib Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimerà, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
Software Mentions: 4
Published: over 12 years ago

10.1002/ece3.3847

Untangling climate and water chemistry to predict changes in freshwater macrophyte distributions
Cited by: 18
Author(s): Robin S. Sleith, John D. Wehr, Kenneth G. Karol
Software Mentions: 4
Published: over 8 years ago

10.16966/2380-5536.170

Validity Study of the R-PLA, a Resilience Scale for People Living with HIV
Cited by: 1
Author(s): Jinxiang Hu, Julianne M. Serovich, Monique J. Brown, Judy A. Kimberly, Yi-Hsin Chen
Software Mentions: 4
Published: over 7 years ago

10.1186/s13287-020-01973-4

Development and validation of a novel stem cell subtype for bladder cancer based on stem genomic profiling
Cited by: 11
Author(s): Chaozhi Tang, Jiakang Ma, Xiuli Liu, Zhengchun Liu
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijerph17249271

Spatial and Temporal Analysis of Plasmodium knowlesi Infection in Peninsular Malaysia, 2011 to 2018
Cited by: 16
Author(s): Wei Kit Phang, Mohd Hafizi Abdul Hamid, Jenarun Jelip, Rose Nani Mudin, Ting-Wu Chuang, Yee Ling Lau, Mun Yik Fong
Software Mentions: 4
Published: over 5 years ago

10.1002/cam4.3915

The debatable presence of PIWI‐interacting RNAs in invasive breast cancer
Cited by: 11
Author(s): Elisa Kärkkäinen, Sami Heikkinen, Maria Tengström, Veli‐Matti Kosma, Arto Mannermaa, Jaana M. Hartikainen
Software Mentions: 4
Published: about 5 years ago

10.1002/cam4.2581

Clinical candidate and genistein analogue AXP107‐11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein‐coupled estrogen receptor signaling
Cited by: 11
Author(s): Fahmi Mesmar, Bingbing Dai, Ahmed Atef Ibrahim, Linnea Hases, Mohammed Hakim Jafferali, Jithesh J. Augustine, Sebastian DiLorenzo, Ya’an Kang, Yang Zhao, Jing Wang, Michael Kim, Chin Yo Lin, Anders Berkenstam, Jason B. Fleming, Cecilia Williams
Software Mentions: 4
Published: almost 7 years ago

10.3390/s21072430

Time Series Forecasting of Univariate Agrometeorological Data: A Comparative Performance Evaluation via One-Step and Multi-Step Ahead Forecasting Strategies
Cited by: 17
Author(s): Saurabh Suradhaniwar, Soumyashree Kar, Surya S. Durbha, J. Adinarayana
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-17298-x

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma
Cited by: 59
Author(s): Kevin Brennan, June Ho Shin, Joshua K. Tay, Marcos Prunello, Andrew J. Gentles, John B. Sunwoo, Olivier Gevaert
Software Mentions: 4
Published: over 8 years ago

10.7150/jca.50462

Classification of Clear Cell Renal Cell Carcinoma based on Tumor Suppressor Genomic Profiling
Cited by: 2
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.9682.1

CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara
Cited by: 5
Author(s): Jawoo Koo, Cindy M. Cox, Melanie Bacou, Carlo Azzarri, Zhe Guo, Ulrike Wood‐Sichra, Queenie Gong, Liangzhi You
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0216834

TCGA based integrated genomic analyses of ceRNA network and novel subtypes revealing potential biomarkers for the prognosis and target therapy of tongue squamous cell carcinoma
Cited by: 19
Author(s): Zaiye Li, Canhua Jiang, Yongxiang Yuan
Software Mentions: 4
Published: about 7 years ago

10.1002/ece3.5555

Collinearity in ecological niche modeling: Confusions and challenges
Cited by: 160
Author(s): Xiaohui Feng, Daniel Park, Ye Liang, Ranjit Pandey, Monica Papeş
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.63377

DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels
Cited by: 61
Author(s): James P Bohnslav, Nivanthika K Wimalasena, Kelsey J Clausing, Yu Dai, David A. Yarmolinsky, Tomás Cruz, Adam D Kashlan, M. Eugenia Chiappe, Lauren L. Orefice, Clifford J. Woolf, Christopher D. Harvey
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2017.02223

Modeling Effects of Temperature, Soil, Moisture, Nutrition and Variety As Determinants of Severity of Pythium Damping-Off and Root Disease in Subterranean Clover
Cited by: 17
Author(s): Ming Pei You, Kelly Rensing, Michael Renton, Martin J. Barbetti
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms21239070

A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification
Cited by: 45
Author(s): Nguyen Quoc Khanh Le, Duyen Thi, Truong Nguyen Khanh Hung, Luu Ho Thanh Lam, Chih-Min Lin, Ngan Thi Kim Nguyen
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/4582082

Identification of a Two-m6A RNA Methylation Regulator Risk Signature as an Independent Prognostic Biomarker in Papillary Renal Cell Carcinoma by Bioinformatic Analysis
Cited by: 5
Author(s): Fusheng Yang, Guojiang Zhao, Liyuan Ge, Yimeng Song, Kai Hong, Hongxian Zhang, Cheng Liu, Hong Peng, Lulin Ma
Software Mentions: 4
Published: over 5 years ago

10.1186/s13075-020-02195-y

Increased serum calpain activity is associated with HMGB1 levels in systemic sclerosis
Cited by: 9
Author(s): Ji-Na Zheng, Yang Li, Yue-Mei Yan, Yong Yu, Wenqi Shao, Qiang Wang
Software Mentions: 4
Published: about 6 years ago

10.1098/rspb.2012.1301

Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge
Cited by: 42
Author(s): Toni Lyn Morelli, Adam B. Smith, Christina R. Kastely, Ilaria Mastroserio, Craig Moritz, Steven R. Beissinger
Software Mentions: 4
Published: almost 14 years ago

10.1186/s13073-015-0196-5

Genomic prediction of celiac disease targeting HLA-positive individuals
Cited by: 24
Author(s): Gad Abraham, Alexia Rohmer, Jason A. Tye‐Din, Michael Inouye
Software Mentions: 4
Published: about 11 years ago

10.18632/aging.102579

Discovering master regulators in hepatocellular carcinoma: one novel MR, SEC14L2 inhibits cancer cells
Cited by: 14
Author(s): Zhihui Li, Yi Liu, Guoyan Tian, Jianyue Wu, Anqian Lu, Jin Chen, Beibei Xu, Junping Shi, Jin Yang
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2016.56

Species interactions in occurrence data for a community of tick-transmitted pathogens
Cited by: 37
Author(s): Agustı́n Estrada-Peña, José de la Fuente
Software Mentions: 4
Published: about 10 years ago

10.18632/aging.102459

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma
Cited by: 13
Author(s): Song Jing, Fangzhou Song, Kun Liu, Wanfeng Zhang, Ruihan Luo, Yongyao Tang
Software Mentions: 4
Published: over 6 years ago

10.1093/molbev/msab197

Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity
Cited by: 13
Author(s): Magda Lewandowska, Ton Sharoni, Yael Admoni, Reuven Aharoni, Yehu Moran
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0193925

From top to bottom: Do Lake Trout diversify along a depth gradient in Great Bear Lake, NT, Canada?
Cited by: 13
Author(s): Louise Chavarie, Kimberly L. Howland, Les N. Harris, Michael J. Hansen, William J. Harford, Colin P. Gallagher, Shauna M. Baillie, Brendan K. Malley, William M. Tonn, Andrew M. Muir, Charles C. Krueger
Software Mentions: 4
Published: over 8 years ago

10.1111/cns.13470

Bioinformatic analysis identifies key transcriptome signatures in temporal lobe epilepsy
Cited by: 22
Author(s): Qinglan Chen, Lu Xia, Shian Zhong, Qiang Wang, Jing Ding, Xin Wang
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.103254

Alterations in glycolytic/cholesterogenic gene expression in hepatocellular carcinoma
Cited by: 13
Author(s): Jianwen Jiang, Qiuxian Zheng, Weiwei Zhu, Xinhua Chen, Haifeng Lü, Deying Chen, Hua Zhang, Min Shao, Lin Zhou, Shusen Zheng
Software Mentions: 4
Published: about 6 years ago

10.1186/s13071-015-0974-3

Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210
Cited by: 58
Author(s): Benjamin Frank, Ana Marcu, Antônio Luis de Oliveira Almeida Petersen, Heike Weber, Christian Stigloher, Jeremy C. Mottram, Claus‐Jürgen Scholz, Uta Schurigt
Software Mentions: 4
Published: about 11 years ago