10.1371/journal.pone.0161018

A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity
Cited by: 30
Author(s): Keith Hunley, Kiela Gwin, Brendan Liberman
Software Mentions: 6
Published: almost 10 years ago

10.7554/eLife.55160

Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens
Cited by: 28
Author(s): Stephan Kamrad, María Rodríguez-López, Cristina Cotobal, Clara Correia‐Melo, Markus Ralser, Jürg Bähler
Software Mentions: 6
Published: about 6 years ago

10.1098/rspb.2018.2455

Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area
Cited by: 25
Author(s): Portia Joy Nillos Kleiven, Sigurd Heiberg Espeland, Esben Moland Olsen, Rene A. Abesamis, Even Moland, Alf Ring Kleiven
Software Mentions: 6
Published: over 7 years ago

10.1186/s13059-021-02280-8

iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
Cited by: 25
Author(s): Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang
Software Mentions: 6
Published: over 5 years ago

10.1002/ana.26009

The Effect of <scp> <i>SMN</i> </scp> Gene Dosage on <scp>ALS</scp> Risk and Disease Severity
Cited by: 9
Author(s): Matthieu Moisse, Ramona A J Zwamborn, Joke J.F.A. van Vugt, Rick A. A. van der Spek, Wouter van Rheenen, Brendan Kenna, Kristel van Eijk, Kevin P. Kenna, Philippe Corcia, Philippe Couratier, Patrick Vourc’h, Orla Hardiman, Russell L. McLaughlin, Marc Guillaume, Vivian E. Drory, Nicola Ticozzi, Vincenzo Silani, Mamede de Carvalho, Jesús Mora, Mónica Povedano, Michael Benatar, Markus Weber, A. Nazlı Başak, Xiao Chen, Michael A. Eberle, Ammar Al‐Chalabi, Christopher E. Shaw, Pamela J. Shaw, Karen Morrison, John E. Landers, Jonathan D. Glass, Wim Robberecht, Michael A. van Es, Leonard H. van den Berg, Jan H. Veldink, Philip Van Damme
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0243420

Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands
Cited by: 9
Author(s): Pamela Vega-Polo, María Mercedes Cobo, Andrea Argudo, Bernardo Gutiérrez, Jennifer K. Rowntree, María de Lourdes Torres
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2015.00277

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
Cited by: 44
Author(s): Ulisses Nunes da Rocha, Hinsby Cadillo‐Quiroz, Ulaş Karaöz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin P. Bowen, Ferrán García-Pichel, Aindrila Mukhopadhyay, Trent Northen, Eoin L. Brodie
Software Mentions: 6
Published: about 11 years ago

10.3389/fpls.2021.587482

Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice (Oryza sativa L.)
Cited by: 19
Author(s): K. Suman, C. N. Neeraja, P. Madhubabu, Santosha Rathod, Sonali Bej, Kashmiri Jadhav, Jitendra Kumar, U. Chaitanya, Sunil Pawar, Surekha H. Rani, L. V. Subbarao, S. R. Voleti
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-021-00844-8

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
Cited by: 21
Author(s): Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Argüero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower, Philip Quirke
Software Mentions: 6
Published: over 5 years ago

10.1186/s13062-018-0213-x

Predicting survival times for neuroblastoma patients using RNA-seq expression profiles
Cited by: 15
Author(s): Tyler Grimes, Alejandro R. Walker, Susmita Datta
Software Mentions: 6
Published: over 8 years ago

10.3389/fpls.2021.637860

Characterization of Groundnut (Arachis hypogaea L.) Test Locations Using Representative Testing Environments With Farmer-Preferred Traits
Cited by: 1
Author(s): Richard Oteng‐Frimpong, Yussif Baba Kassim, Doris K. Puozaa, Jerry Asalma Nboyine, Abdul-Rashid Issah, Masawudu Abdul Rasheed, Joseph Adjebeng‐Danquah, Francis Kusi
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-020-06831-4

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Cited by: 13
Author(s): Shubha Suresh, Teresa J. Crease, Melania E. Cristescu, Frédéric J. J. Chain
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pgen.1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Cited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: about 6 years ago

10.1038/s41392-020-00263-y

Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals
Cited by: 127
Author(s): Fan Zhang, Rui Gan, Ziqi Zhen, Xiaoli Hu, Xiang Li, Fengxia Zhou, Ying Liu, Chuangeng Chen, Shuangyu Xie, Bailing Zhang, Xiaoke Wu, Zhiwei Huang
Software Mentions: 6
Published: almost 6 years ago

10.3390/ani9050271

Equitable Chick Survival in Three Species of the Non-Migratory Shorebird Despite Species-Specific Sexual Dimorphism of the Young
Cited by: 3
Author(s): Daniel Lees, Tom Schmidt, Grainne S. Maguire, Peter Dann, Michael A. Weston
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0192023

Spatiotemporal patterns of the macrofaunal community structure in the East China Sea, off the coast of Zhejiang, China, and the impact of the Kuroshio Branch Current
Cited by: 5
Author(s): Yong Xu, Fei Yu, Xinzheng Li, Lin Ma, Dong Dong, Qi Kou, Jixing Sui, Zhibin Gan, Lin Gong, Mei Yang, Yue-Yun Wang, Yue Sun, Jinbao Wang, Hongfa Wang
Software Mentions: 6
Published: over 8 years ago

10.1186/s12859-020-3434-9

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Cited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: over 6 years ago

10.1016/j.tube.2019.101859

Distinct serum biosignatures are associated with different tuberculosis treatment outcomes
Cited by: 22
Author(s): Katharina Ronacher, Novel N. Chegou, Léanie Kleynhans, Joel Fleury Djoba Siawaya, Nelita du Plessis, André G. Loxton, Elizna Maasdorp, Gerard Tromp, Martin Kidd, Kim Stanley, Magdalena Kriel, Ângela Menezes, Andrea Gutschmidt, Gian D. van der Spuy, Robin M. Warren, Reynaldo Dietze, Alphonse Okwera, Bonnie Thiel, John T. Belisle, Jacqueline M. Cliff, W. Henry Boom, John L. Johnson, Paul D. van Helden, Hazel M. Dockrell, Gerhard Walzl
Software Mentions: 6
Published: almost 7 years ago

10.3390/microorganisms8020175

Biostimulating Gut Microbiome with Bilberry Anthocyanin Combo to Enhance Anti-PD-L1 Efficiency against Murine Colon Cancer
Cited by: 35
Author(s): Xuerun Liu, Luoyang Wang, Nan Jing, Guoqiang Jiang, Zheng Liu
Software Mentions: 6
Published: over 6 years ago

10.1038/s41597-019-0172-9

Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria
Cited by: 20
Author(s): Avril Jean Elisabeth von Hoyningen-Huene, Dominik Schneider, Dario Fussmann, Andreas Reimer, Gernot Arp, Rolf Daniel
Software Mentions: 6
Published: almost 7 years ago

10.15252/embj.2019101695

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma
Cited by: 61
Author(s): María D. Giraldez, Ryan M Spengler, Alton Etheridge, Annika Jane Goicochea, Missy Tuck, Sung Won Choi, David J. Galas, Muneesh Tewari
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0186488

Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing
Cited by: 17
Author(s): Niloofar Vaghefi, Julie R. Kikkert, Melvin D. Bolton, Linda E. Hanson, Gary A. Secor, Scot Nelson, Sarah J. Pethybridge
Software Mentions: 6
Published: over 8 years ago

10.1128/mSystems.00269-18

Calour: an Interactive, Microbe-Centric Analysis Tool
Cited by: 24
Author(s): Zhenjiang Zech Xu, Amir Almasi‐Hashiani, Jon G. Sanders, Quanyin Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Software Mentions: 6
Published: over 7 years ago

10.3390/v12080891

Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity
Cited by: 17
Author(s): Ivana Šimić, Tomaž Mark Zorec, Ivana Lojkić, Nina Krešić, Mario Poljak, Florence Cliquet, Evelyne Picard-Meyer, Marine Wasniewski, Vida Zrnčić, Anđela Čukušić, Tomislav Bedeković
Software Mentions: 6
Published: almost 6 years ago

10.1098/rspb.2021.0200

Macroevolution of dimensionless life-history metrics in tetrapods
Cited by: 2
Author(s): Cecina Babich Morrow, S. K. Morgan Ernest, Andrew J. Kerkhoff
Software Mentions: 6
Published: about 5 years ago

10.1186/s40246-021-00323-6

An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients
Cited by: 2
Author(s): Suyan Tian, Chi Wang
Software Mentions: 6
Published: about 5 years ago

10.1523/ENEURO.0315-18.2018

What, If Anything, Is Rodent Prefrontal Cortex?
Cited by: 271
Author(s): Mark Laubach, Linda M. Amarante, Tom Swanson, Samantha R. White
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pcbi.1008978

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
Cited by: 9
Author(s): Xinjun Li, Fan Feng, Hongxi Pu, Wai Yan Leung, Jie Liu
Software Mentions: 6
Published: about 5 years ago

10.1080/19490976.2021.1874815

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer
Cited by: 33
Author(s): Kellyanne Duncan, Kelly Carey-Ewend, Shipra Vaishnava
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0219807

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm
Cited by: 12
Author(s): Korin Eckstrom, John W. Barlow
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pntd.0007609

A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing
Cited by: 37
Author(s): Joel Barratt, Meredith Lane, Emir Talundzic, Travis Richins, Gemma Robertson, Fabio Formenti, Bobbi S. Pritt, Guilherme G. Verocai, Robson da Paixão de Souza, Neci Mato Soares, Rebecca J. Traub, Dora Buonfrate, Richard S. Bradbury
Software Mentions: 6
Published: almost 7 years ago

10.1093/gbe/evaa143

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis
Cited by: 5
Author(s): David C. Plachetzki, M. Sabrina Pankey, Matthew D. MacManes, Michael P. Lesser, Charles W. Walker
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.devcel.2018.06.028

Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development
Cited by: 36
Author(s): Magdalena K. Sznurkowska, Édouard Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher J. Hindley, Jennifer Nichols, Berthold Göttgens, Meritxell Huch, Anna Philpott, Benjamin D. Simons
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13059-018-1522-1

Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations
Cited by: 66
Author(s): Kristiina Tambets, Bayazit Yunusbayev, Georgi Hudjashov, Anne-Mai Ilumäe, Siiri Rootsi, Terhi Honkola, Outi Vesakoski, Quentin D. Atkinson, Pontus Skoglund, Alena Kushniarevich, Sergey Litvinov, Maere Reidla, Ene Metspalu, Lehti Saag, Timo Rantanen, Monika Karmin, Jüri Parik, Sergey I. Zhadanov, Marina Gubina, Л. Д. Дамба, Marina Bermisheva, Tuuli Reisberg, Khadizhat Dibirova, Irina Evseeva, Mari Nelis, Jānis Kloviņš, Andres Metspalu, Tõnu Esko, Oleg Balanovsky, Elena Balanovska, Elza Khusnutdinova, Ludmila P. Osipova, М. И. Воевода, Richard Villems, Toomas Kivisild, Mait Metspalu
Software Mentions: 6
Published: almost 8 years ago

10.3389/fimmu.2021.634741

Activation of the DDR Pathway Leads to the Down-Regulation of the TGFβ Pathway and a Better Response to ICIs in Patients With Metastatic Urothelial Carcinoma
Cited by: 18
Author(s): Chaozheng Zhou, Anqi Lin, Manming Cao, Weimin Ding, Weiming Mou, Ningyi Guo, Zhenyu Chen, Jian Zhang, Peng Luo
Software Mentions: 6
Published: about 5 years ago

10.3390/v13010085

Mixed Effects of Habitat Degradation and Resources on Hantaviruses in Sympatric Wild Rodent Reservoirs within a Neotropical Forest
Cited by: 4
Author(s): Jeremy V. Camp, Briana Spruill-Harrell, Robert Dale Owen, Carles Solà-Riera, Evan P. Williams, Gillian Eastwood, Aubrey M. Sawyer, Colleen B. Jonsson
Software Mentions: 6
Published: over 5 years ago

10.18632/aging.202474

Clinical and genomic characteristics of metabolic syndrome in colorectal cancer
Cited by: 2
Author(s): Yanyan Li, Jungang Zhao, Xiaoli Wu, Yini Zhang, Jia Yin, Weiyang Cai
Software Mentions: 6
Published: over 5 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0090801

Biclustering Methods: Biological Relevance and Application in Gene Expression Analysis
Cited by: 77
Author(s): Ali Oghabian, Sami Kilpinen, Sampsa Hautaniemi, Elena Czeizler
Software Mentions: 6
Published: over 12 years ago

10.7717/peerj.8192

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Cited by: 21
Author(s): Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Süner
Software Mentions: 6
Published: over 6 years ago

10.1186/s13059-015-0815-x

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1
Cited by: 48
Author(s): Florian Duclot, Mohamed Kabbaj
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-019-44302-3

Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: about 7 years ago

10.3389/fimmu.2021.632667

PD-1 Blockade Modulates Functional Activities of Exhausted-Like T Cell in Patients With Cutaneous Leishmaniasis
Cited by: 16
Author(s): Renan Garcia de Moura, Luciana Polaco Covre, Carlos Henrique Fantecelle, Vitor Alejandro Torres Gajardo, Carla Baroni Cunha, Lorenzzo Lyrio Stringari, Ashton T. Belew, Camila Batista Daniel, Sandra Ventorin von Zeidler, Carlos E. Tadokoro, Herbert Leonel de Matos Guedes, Raphael Lubiana Zanotti, David M. Mosser, Aloísio Falqueto, Arne N. Akbar, Daniel Cláudio Oliveira Gomes
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0236574

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya
Cited by: 11
Author(s): Edward Nderitu Karanja, Andreas Fließbach, Noah Adamtey, Anne Kelly Kambura, Martha W. Musyoka, Komi K. M. Fiaboe, Romano Mwirichia
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pmed.1002730

Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study
Cited by: 505
Author(s): Jakob Nikolas Kather, Johannes Krisam, Pornpimol Charoentong, Tom Luedde, Esther Herpel, Cleo Aron Weis, Timo Gaiser, Alexander Marx, Nektarios A. Valous, Dyke Ferber, Lina Jansen, Constantino Carlos Reyes-Aldasoro, Inka Zörnig, Dirk Jäger, Hermann Brenner, Jenny Chang‐Claude, Michael Hoffmeister, Niels Halama
Software Mentions: 6
Published: over 7 years ago

10.1016/j.xcrm.2021.100267

Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma
Cited by: 2
Author(s): Hui Wen Lue, Daniel S. Derrick, Soumya Rao, Ahna Van Gaest, Larry C. Cheng, Jennifer Podolak, Samantha Lawson, Changhui Xue, Devin Garg, Ralph E. White, Christopher W. Ryan, Justin M. Drake, Anna Ritz, Laura M. Heiser, George V. Thomas
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2021.640190

Pre-existing Immunity to Japanese Encephalitis Virus Alters CD4 T Cell Responses to Zika Virus Inactivated Vaccine
Cited by: 7
Author(s): Noemia S. Lima, Damee Moon, Samuel Darko, Rafael A. De La Barrera, Leyi Lin, Michael Koren, Richard G. Jarman, Kenneth H. Eckels, Stephen J. Thomas, Nelson L. Michael, Kayvon Modjarrad, Daniel C. Douek, Lydie Trautmann
Software Mentions: 6
Published: over 5 years ago

10.1186/s13071-021-04717-2

Transcriptomic profiling of three-dimensional cholangiocyte spheroids long term exposed to repetitive Clonorchis sinensis excretory-secretory products
Cited by: 4
Author(s): Jung Woong Kim, Junyeong Yi, Jin‐Hong Park, Ji Hoon Jeong, Jin-Ho Kim, Jihee Won, Seok Chung, Tong Soo Kim, Jhang Ho Pak
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1005351

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
Cited by: 3
Author(s): Stephanie Evans, Kieran Alden, Lourdes Cucurull‐Sanchez, Christopher Larminie, Mark Coles, Marika C. Kullberg, Jon Timmis
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pcbi.1007625

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Cited by: 14
Author(s): Jordan A. Berg, Jonathan R Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
Software Mentions: 6
Published: over 6 years ago

10.3389/fpls.2021.615277

Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects
Cited by: 12
Author(s): Isaiah Catalino M. Pabuayon, Ai Kitazumi, Kevin R. Cushman, Rakesh Kumar Singh, Glenn B. Gregorio, Balpreet K. Dhatt, Masoud Zabet-Moghaddam, Harkamal Walia, Benildo G. de los Reyes
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.ppat.1007634

The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response
Cited by: 49
Author(s): Leon Louis Seifert, Clara Si, Debjani Saha, Mohammad Sadic, Maren de Vries, Sarah Ballentine, Aaron Briley, Guojun Wang, Ana M. Valero-Jimenez, Adil Mohamed, Uwe Schaefer, Hong M. Moulton, Adolfo Garcı́a-Sastre, Shashank Tripathi, Brad R. Rosenberg, Meike Dittmann
Software Mentions: 6
Published: over 6 years ago

10.1242/bio.058222

RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first–second trimester transition
Cited by: 15
Author(s): Malwina Prater, Russell S. Hamilton, Hong Wa Yung, Andrew Sharkey, Paul Robson, N. Erlyani Abd Hamid, Eric Jauniaux, D. Stephen Charnock-Jones, Graham J. Burton, Tereza Cindrová‐Davies
Software Mentions: 6
Published: about 5 years ago

10.3390/metabo11050269

Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)
Cited by: 4
Author(s): Nay Min Min Thaw Saw, Pipob Suwanchaikasem, Rogelio Zuniga-Montanez, Guanglei Qiu, Ezequiel M. Marzinelli, Stefan Wuertz, Rohan B.H. Williams
Software Mentions: 6
Published: about 5 years ago

10.1001/jamanetworkopen.2021.7737

Predictors of 30-Day Mortality Among Dutch Patients Undergoing Colorectal Cancer Surgery, 2011-2016
Cited by: 31
Author(s): Tom van den Bosch, A. K. Warps, Michael P.M. de Neree tot Babberich, C Stamm, Bart F. Geerts, Louis Vermeulen, Michel W.J.M. Wouters, Jan Willem T. Dekker, Rob A.E.M. Tollenaar, Pieter J. Tanis, Daniël M. Miedema, Dutch ColoRectal Audit
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0148203

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)
Cited by: 67
Author(s): Simon Uribe‐Convers, Matthew L. Settles, David C. Tank
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.ppat.1008408

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
Cited by: 16
Author(s): Dylan de Vries, Vasiliki Matzaraki, Olivier B. Bakker, Harm Brugge, Harm-Jan Westra, Mihai G. Netea, Lude Franke, Vinod Kumar, Monique G. P. van der Wijst
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-021-90538-3

Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma
Cited by: 6
Author(s): Junwei Du, Guoquan Li, Yang-sen Li, Xinguang Qiu
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13059-017-1374-0

Epigenetic supersimilarity of monozygotic twin pairs
Cited by: 76
Author(s): Timothy E. Van Baak, Cristian Coarfa, Pierre Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Gong, Zdenko Herceg, Paolo Víneis, Gianluca Severi, John L. Hopper, Melissa C. Southey, Graham G. Giles, Roger L. Milne, Robert A. Waterland
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.ppat.1008645

The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence
Cited by: 23
Author(s): Laure Nicolas Annick Ries, Lakhansing Pardeshi, Zhiqiang Dong, Kaeling Tan, Jacob L. Steenwyk, Ana Cristina Colabardini, Jaire Alves Ferreira Filho, Patrícia Alves de Castro, Lilian Pereira Silva, Nycolas Willian Preite, Fausto Almeida, Leandro José de Assis, Renato Augusto Corrêa dos Santos, Paul Bowyer, Michael Bromley, Rebecca A. Owens, Seán Doyle, Marilene Demasi, Diego Hernández, Luís Eduardo Soares Netto, Mônica Tallarico Pupo, Antonis Rokas, Flávio Vieira Loures, Koon Ho Wong, Gustavo H. Goldman
Software Mentions: 6
Published: almost 6 years ago

10.3390/microorganisms8101554

HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts
Cited by: 6
Author(s): Soukaina Timouma, Jean-Marc Schwartz, Daniela Delneri
Software Mentions: 6
Published: over 5 years ago

10.3390/v12070695

Ross River Virus Provokes Differentially Expressed MicroRNA and RNA Interference Responses in Aedes aegypti Mosquitoes
Cited by: 10
Author(s): J. B. Sinclair, Sassan Asgari
Software Mentions: 6
Published: about 6 years ago

10.1186/s12859-016-1204-5

LMAP: Lightweight Multigene Analyses in PAML
Cited by: 12
Author(s): Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 6
Published: almost 10 years ago

10.1371/journal.ppat.1009304

Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Cited by: 39
Author(s): Anna Both, Jia-Bin Huang, Minyue Qi, Christian Lausmann, Samira Weißelberg, Henning Büttner, Susanne Lezius, Antonio Virgilio Failla, Coralie Martin, Marc Stegger, Thorsten Gehrke, Sharmin Baig, Mustafa Citak, Malik Alawi, Martin Aepfelbacher, Holger Rohde
Software Mentions: 6
Published: over 5 years ago

10.1186/s12862-018-1244-8

Microhabitat change drives diversification in pholcid spiders
Cited by: 34
Author(s): Jonas Eberle, Dimitar Dimitrov, Alejandro Valdez‐Mondragón, Bernhard A. Huber
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41598-019-39866-z

Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions
Cited by: 10
Author(s): Adrian I. Campos-González, Julio A. Freyre-González
Software Mentions: 6
Published: over 7 years ago

10.1186/s12862-019-1548-3

Phylogenetic signals in pest abundance and distribution range of spider mites
Cited by: 1
Author(s): Peng‐Yu Jin, Jing‐Tao Sun, Ary A. Hoffmann, Yanfei Guo, Jin‐Cheng Zhou, Yu‐Xi Zhu, Lei Chen, Xiao‐Yue Hong
Software Mentions: 6
Published: over 6 years ago

10.7717/peerj.3411

Taxonomic richness and abundance of cryptic peracarid crustaceans in the Puerto Morelos Reef National Park, Mexico
Cited by: 9
Author(s): Luz Verónica Monroy-Velázquez, Rosa E. Rodríguez-Martínez, Fernando Álvarez
Software Mentions: 6
Published: about 9 years ago

10.7717/peerj.10556

A risk score model with five long non-coding RNAs for predicting prognosis in gastric cancer: an integrated analysis combining TCGA and GEO datasets
Cited by: 11
Author(s): Yiguo Wu, Jieqiong Deng, Shuhui Lai, Yujuan You, Jing Wu
Software Mentions: 6
Published: over 5 years ago

10.1002/1878-0261.12385

Genome‐wide identification of a novel mi <scp>RNA</scp> ‐based signature to predict recurrence in patients with gastric cancer
Cited by: 26
Author(s): Yongmei Yang, Ailin Qu, Rui Zhao, Mengmeng Hua, Xin Zhang, Zhaogang Dong, Guixi Zheng, Hongwei Pan, Hongchun Wang, Xiaoyun Yang, Yi Zhang
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.ppat.1008754

JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0174035

Exploratory graph analysis: A new approach for estimating the number of dimensions in psychological research
Cited by: 342
Author(s): Hudson Golino, Sacha Epskamp
Software Mentions: 6
Published: about 9 years ago

10.1172/jci.insight.143654

A longitudinal and transancestral analysis of DNA methylation patterns and disease activity in lupus patients
Cited by: 34
Author(s): Patrick Coit, Lourdes Ortíz-Fernández, Edith A. Lewis, W. Joseph McCune, Kathleen Maksimowicz-McKinnon, Amr H. Sawalha
Software Mentions: 6
Published: over 5 years ago

10.1186/1471-2105-8-328

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest
Cited by: 169
Author(s): Ramón Dı́az-Uriarte
Software Mentions: 6
Published: almost 19 years ago

10.1534/g3.114.016196

A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, <i>Aedes aegypti</i>
Cited by: 53
Author(s): Benjamin R. Evans, Andrea Gloria‐Soria, Lin Hou, Carolyn S. McBride, Mariangela Bonizzoni, Hongyu Zhao, Jeffrey R. Powell
Software Mentions: 6
Published: about 11 years ago

10.1098/rsos.191480

Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress
Cited by: 2
Author(s): Signe Dille Løvmo, Angelico Madaro, Paul Whatmore, Tora Bardal, Mari‐Ann Östensen, Simen Rød Sandve, Rolf Erik Olsen
Software Mentions: 6
Published: over 6 years ago

10.1080/17453674.2019.1624339

Reduced periprosthetic fracture rate when changing from a tapered polished stem to an anatomical stem for cemented hip arthroplasty: an observational prospective cohort study with a follow-up of 2 years
Cited by: 17
Author(s): Jabbar Mohammed, Sebastian Mukka, Carl-Johan Hedbeck, Ghazi Chammout, Max Gordon, Olof Sköldenberg
Software Mentions: 6
Published: about 7 years ago

10.3390/microorganisms8040567

Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities
Cited by: 11
Author(s): Stephanie Elferink, Uwe John, Stefan Neuhaus, Sylke Wohlrab
Software Mentions: 6
Published: about 6 years ago

10.3389/fninf.2013.00044

An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook
Cited by: 19
Author(s): Jean-Luc Stevens, Marco Elver, James A. Bednar
Software Mentions: 6
Published: over 13 years ago

10.1371/journal.pcbi.1007509

Clustering-independent analysis of genomic data using spectral simplicial theory
Cited by: 19
Author(s): Kiya W. Govek, Venkata S. Yamajala, Pablo G. Cámara
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0237881

Identification of key odorants in honeysuckle by headspace-solid phase microextraction and solvent-assisted flavour evaporation with gas chromatography-mass spectrometry and gas chromatograph-olfactometry in combination with chemometrics
Cited by: 6
Author(s): Keran Su, Xin Zhang, Shao-Quan Liu, LiHui Jia, Benjamin Lassabliere, Kim Huey Ee, Aileen Pua, Rui Min Vivian Goh, Jingcan Sun, Bin Yu, XiaoXue Hu
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-019-48118-z

Mapping behaviorally relevant light pollution levels to improve urban habitat planning
Cited by: 16
Author(s): Aaron E. Schirmer, Caleb Gallemore, Ting Liu, Seth B. Magle, Elisabeth DiNello, Humerah Ahmed, Thomas Gilday
Software Mentions: 6
Published: almost 7 years ago

10.3390/v10120685

The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data
Cited by: 15
Author(s): Matthew A. Knox, Kristene Gedye, David T. S. Hayman
Software Mentions: 6
Published: over 7 years ago

10.1186/1471-2105-14-158

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Cited by: 33
Author(s): Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian L. Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Megan Pirrung, Brian C. O’Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark W. Westneat, Michael E. Alfaro, Aaron Steele, G. Gulli Jordan
Software Mentions: 6
Published: about 13 years ago

10.1038/s41598-020-79736-7

BIRC5 is a prognostic biomarker associated with tumor immune cell infiltration
Cited by: 37
Author(s): Lijun Xu, Wenpeng Yu, Han Xiao, Lin Kang
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2019.00823

Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages
Cited by: 19
Author(s): Lucas F. Maciel, David A. Morales-Vicente, Gilbert O. Silveira, Raphael O. Ribeiro, Giovanna G. O. Olberg, David S. Pires, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: almost 7 years ago

10.1186/s40168-021-01136-4

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes
Cited by: 24
Author(s): Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, S. Druyan, Roni Shapira, O. Krifucks, Yan Zhu, Xinyuan Zhou, Jian‐Qiang Su, Eddie Cytryn
Software Mentions: 6
Published: almost 5 years ago

10.3390/ijms22168482

Multicellular Human Cardiac Organoids Transcriptomically Model Distinct Tissue-Level Features of Adult Myocardium
Cited by: 17
Author(s): Charles M. Kerr, Dylan Richards, Donald R. Menick, Kristine Y. DeLeon‐Pennell, Ying Mei
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12915-021-01147-5

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model
Cited by: 13
Author(s): Hisayo Ono, Yasuhito Arai, Eisaku Furukawa, Daichi Narushima, Tetsuya Matsuura, Hiromi Nakamura, Daisuke Shiokawa, Masaya Nagai, Toshio Imai, Koshi Mimori, Koji Okamoto, Yoshitaka Hippo, Tatsuhiro Shibata, Mamoru Kato
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0240010

Framing COVID-19: How we conceptualize and discuss the pandemic on Twitter
Cited by: 135
Author(s): Philipp Wicke, Marianna Bolognesi
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13023-019-1020-x

The mutational and phenotypic spectrum of TUBA1A-associated tubulinopathy
Cited by: 46
Author(s): Moritz Hebebrand, Ulrike Hüffmeier, Regina Trollmann, Ute Hehr, Steffen Uebe, Arif B. Ekici, Cornelia Kraus, Mandy Krumbiegel, André Reis, Christian T. Thiel, Bernt Popp
Software Mentions: 6
Published: over 7 years ago

10.1242/bio.047316

Assessing the role of historical temperature regime and algal symbionts on the heat tolerance of coral juveniles
Cited by: 30
Author(s): Kate M. Quigley, Carly J. Randall, Madeleine J. H. van Oppen, Line K. Bay
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2017.00744

Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring
Cited by: 36
Author(s): Melanie Schären, Kerstin Kiri, Susanne Riede, Mark C. Gardener, Ulrich Meyer, Jürgen Hummel, Tim Urich, Gerhard Breves, Sven Dänicke
Software Mentions: 6
Published: about 9 years ago

10.1186/s12896-019-0540-8

Enhancement of using combined packing materials on the removal of mixed sulfur compounds in a biotrickling filter and analysis of microbial communities
Cited by: 12
Author(s): Xiang Tu, Meiying Xu, Jianjun Li, Enze Li, Rongfang Feng, Gang Zhao, Shaobin Huang, Jun Guo
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0186025

Using worldwide edaphic data to model plant species niches: An assessment at a continental extent
Cited by: 67
Author(s): Santiago José Elías Velazco, Franklin Galvão, Fabricio Villalobos, Paulo de Marco Júnior
Software Mentions: 6
Published: over 8 years ago

10.1186/s12885-015-1993-3

TGFβ isoforms and receptors mRNA expression in breast tumours: prognostic value and clinical implications
Cited by: 23
Author(s): Chenfeng Chen, Kong‐Nan Zhao, Paul P. Masci, Sunil R. Lakhani, Annika Antonsson, Peter T. Simpson, Luis Vitetta
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.ppat.1009539

Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis
Cited by: 8
Author(s): Jae Hak Son, Brian L. Weiss, Daniela Schneider, Kiswend-Sida Mikhailou Dera, Fabian Gstöttenmayer, Robert Opiro, Richard Echodu, Norah P. Saarman, Geoffrey M. Attardo, Maria G Onyango, Adly M. M. Abd-Alla, Serap Aksoy
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-020-70198-5

Computational flow cytometry of planktonic populations for the evaluation of microbiological-control programs in district cooling plants
Cited by: 0
Author(s): James McElhinney, Aurélie Mawart, Ruba Alkaabi, H. S. S. Abdelsamad, Afnan Mansour, Ayesha Hasan
Software Mentions: 6
Published: almost 6 years ago

10.1186/1471-2105-13-115

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools
Cited by: 60
Author(s): Sean O’Callaghan, David P. De Souza, Andrew P. Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia Tull, Ute Roessner, Antony Bacic, Malcolm J. McConville, Vladimir A Likić
Software Mentions: 6
Published: about 14 years ago