10.1016/j.stem.2015.04.004

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
Cited by: 369
Author(s): Nicola K. Wilson, David G. Kent, Florian Buettner, Mona Shehata, Iain C. Macaulay, Fernando J. Calero-Nieto, Manuel Sánchez Castillo, Caroline A. Oedekoven, Evangelia Diamanti, Reiner Schulte, Chris P. Ponting, Thierry Voet, Carlos Caldas, John Stingl, Anthony Green, Fabian J. Theis, Berthold Göttgens
Software Mentions: 5
Published: about 11 years ago

10.1038/s41598-018-30657-6

Deep Learning and Radiomics predict complete response after neo-adjuvant chemoradiation for locally advanced rectal cancer
Cited by: 125
Author(s): Jean‐Emmanuel Bibault, P. Giraud, M. Housset, C. Durdux, Julien Taieb, Anne Berger, Romain Coriat, Stanislas Chaussade, B. Dousset, Bernard Nordlinger, Anita Burgun
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms22020678

JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions
Cited by: 15
Author(s): Tara Procida, Tobias Friedrich, Antonia Jack, Martina Peritore, Clemens Bönisch, H. Christian Eberl, Nadine Daus, Konstantin Kletenkov, Andrea Nist, Thorsten Stiewe, Tilman Borggrefe, Matthias Mann, Marek Bartkuhn, Sandra B. Hake
Software Mentions: 5
Published: over 5 years ago

10.1111/jcmm.16799

Comprehensive characterization of pathological stage‐related genes of papillary thyroid cancer along with survival prediction
Cited by: 1
Author(s): Lei Xu, Liang Feng, Haiyan Li, Menglong Li, Yongmei Xie, Zhihui Li, Yanzhi Guo
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13293-021-00368-1

Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies
Cited by: 16
Author(s): José F. Català-Senent, Marta R. Hidalgo, Marina Berenguer, Gopanandan Parthasarathy, Harmeet Malhi, Pablo Malmierca-Merlo, María de la Iglesia-Vayá, Francisco García‐García
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.102697

Identification of a nomogram based on long non-coding RNA to improve prognosis prediction of esophageal squamous cell carcinoma
Cited by: 45
Author(s): Wenli Li, Jun Li, Hetong Zhao
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008986

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-52177-7

Dominance relationships and coalitionary aggression against conspecifics in female carrion crows
Cited by: 11
Author(s): Benedikt Holtmann, Julia Buskas, Matthew Steele, Kristaps Solokovskis, Jochen B. W. Wolf
Software Mentions: 5
Published: over 6 years ago

10.1128/mBio.03042-19

Quantitative Framework for Model Evaluation in Microbiology Research Using <i>Pseudomonas aeruginosa</i> and Cystic Fibrosis Infection as a Test Case
Cited by: 83
Author(s): Daniel M. Cornforth, Frances L. Diggle, Jeffrey A. Melvin, Jennifer M. Bomberger, Marvin Whiteley
Software Mentions: 5
Published: over 6 years ago

10.3390/jcm10173888

A Machine Learning Predictive Model for Post-Ureteroscopy Urosepsis Needing Intensive Care Unit Admission: A Case–Control YAU Endourology Study from Nine European Centres
Cited by: 16
Author(s): Amelia Pietropaolo, Robert Geraghty, Rajan Veeratterapillay, Alistair Rogers, Panagiotis Kallidonis, Luca Villa, Luca Boeri, Emanuele Montanari, Gökhan Atış, Esteban Emiliani, Tarık Emre Şener, Feras Al Jaafari, John Fitzpatrick, Matthew B.K. Shaw, Chris Harding, Bhaskar K. Somani
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.51243

Global genome diversity of the Leishmania donovani complex
Cited by: 77
Author(s): Susanne U. Franssen, Caroline Durrant, Olivia Stark, Bettina A. Moser, Tim Downing, Hideo Imamura, Jean Claude Dujardin, Mandy Sanders, Isabel Maurício, Michael A. Miles, Lionel F. Schnur, Charles L. Jaffe, Abedelmajeed Nasereddin, Henk D. F. H. Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Zahangir Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A. Cotton
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-019-0622-9

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology
Cited by: 62
Author(s): Christopher A. Gaulke, Maurício Laterça Martins, Virginia Watral, Ian R. Humphreys, Sean Spagnoli, Michael L. Kent, Thomas J. Sharpton
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0223745

Measuring the complexity of directed graphs: A polynomial-based approach
Cited by: 7
Author(s): Matthias Dehmer, Zengqiang Chen, Frank Emmert‐Streib, Shailesh Tripathi, Abbe Mowshowitz, Alexei Leviţchi, Lihua Feng, Yongtang Shi, Tao Jin
Software Mentions: 5
Published: over 6 years ago

10.1186/2043-9113-4-8

comoR: a software for disease comorbidity risk assessment
Cited by: 82
Author(s): Mohammad Ali Moni, Píetro Lió
Software Mentions: 5
Published: over 12 years ago

10.3389/fgene.2021.561254

Development and Validation of a Novel Metabolic-Related Signature Predicting Overall Survival for Pancreatic Cancer
Cited by: 5
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.67714

The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia
Cited by: 13
Author(s): Katalin Skrapits, Miklós Sárvári, Imre Farkas, Balázs Göcz, Szabolcs Takács, Éva Rumpler, Viktória Váczi, Csaba Vastagh, Gergely Rácz, András Matolcsy, Norbert Solymosi, Szilárd Póliska, Blanka Tóth, Ferenc Erdélyi, Gábor Szabó, Michael D. Culler, Cécile Allet, Ludovica Cotellessa, Vincent Prévot, Paolo Giacobini, Erik Hrabovszky
Software Mentions: 5
Published: about 5 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role of<i>doublesex</i>in sex differentiation and mimicry in<i>Papilio</i>swallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: almost 6 years ago

10.1128/mSystems.00344-21

Network Properties of Local Fungal Communities Reveal the Anthropogenic Disturbance Consequences of Farming Practices in Vineyard Soils
Cited by: 10
Author(s): Rüdiger Ortiz‐Álvarez, Héctor Ortega-Arranz, Vicente J. Ontiveros, Miguel de Celis, Charles N. J. Ravarani, Alberto Acedo, Ignacio Belda
Software Mentions: 5
Published: about 5 years ago

10.1016/j.molmet.2017.02.007

Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: about 9 years ago

10.1016/j.heliyon.2020.e04354

The coverage of environmental issues in FM radios in Nepal: the current status and challenges
Cited by: 1
Author(s): Prakash Kumar Paudel, Rabin Bastola, Pashe Tamang Lopchan
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0238764

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes
Cited by: 24
Author(s): Sahar Radwan, Darby Gilfillan, Bridget Eklund, Hend M. Radwan, Nagwan Galal El Menofy, Justin Lee, Marylee Kapuscinski, Zaid Abdo
Software Mentions: 5
Published: almost 6 years ago

10.3389/fninf.2014.00079

LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2
Cited by: 86
Author(s): Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Bóris Marin, Eugenio Piasini, R. Angus Silver
Software Mentions: 5
Published: almost 12 years ago

10.3390/nu13020432

Is Serum BDNF Altered in Acute, Short- and Long-Term Recovered Restrictive Type Anorexia Nervosa?
Cited by: 6
Author(s): Jonas L Steinhäuser, Joseph A. King, Friederike I. Tam, Maria Seidel, Ronald Biemann, Marie‐Louis Wronski, Daniel Geisler, Veit Roessner, Stefan Ehrlich
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0252862

Approaches to measure class importance in Knowledge Graphs
Cited by: 2
Author(s): Daniel Fernández-Álvarez, Johannes Frey, José Emilio Labra Gayo, Daniel Gayo-Avello, Sebastian Hellmann
Software Mentions: 5
Published: about 5 years ago

10.1002/2211-5463.13134

Identification of hub lncRNAs in head and neck cancer based on weighted gene co‐expression network analysis and experiments
Cited by: 13
Author(s): Longquan Shao
Software Mentions: 5
Published: about 5 years ago

10.3389/fpls.2018.01256

Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms
Cited by: 14
Author(s): Kai Battenberg, Daniel Potter, Christine A. Tabuloc, Joanna C. Chiu, Alison M. Berry
Software Mentions: 5
Published: almost 8 years ago

10.3390/v11030299

Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses
Cited by: 19
Author(s): Marli Vlok, Adrian Gibbs, Curtis A. Suttle
Software Mentions: 5
Published: over 7 years ago

10.1186/s12866-021-02099-0

The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice
Cited by: 41
Author(s): Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, W.H. Wilson Tang, Lee S, Seong‐Tshool Hong, Seungkoo Lee
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2017.00655

Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Cited by: 66
Author(s): Guillermo Marcial, Amanda Ford, Michael J. Haller, Salvador A. Gezan, Natalie A. Harrison, David Cai, Julie Meyer, Daniel J. Perry, Mark A. Atkinson, Clive Wasserfall, Timothy J. Garrett, Claudio F. González, Todd M. Brusko, Wendy J. Dahl, Graciela L. Lorca
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0227860

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)
Cited by: 4
Author(s): Andy R. Nilsen, Suliana Teasdale, P. L. Guy, Tina C. Summerfield, David A. Orlovich
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-95486-6

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin
Cited by: 10
Author(s): Tika B. Adhikari, Norman Muzhinji, Dennis Halterman, Frank J. Louws
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12967-021-02705-9

Eight-lncRNA signature of cervical cancer were identified by integrating DNA methylation, copy number variation and transcriptome data
Cited by: 23
Author(s): Qihang Zhong, Minzhen Lu, Wei Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao, Jing Hang
Software Mentions: 5
Published: over 5 years ago

10.1111/acel.13320

BiT age: A transcriptome‐based aging clock near the theoretical limit of accuracy
Cited by: 45
Author(s): David Meyer, Björn Schumacher
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2019.01497

Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment
Cited by: 27
Author(s): Rongfang Shen, Ping Li, Bing Li, Botao Zhang, Feng Li, Shujun Cheng
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms21093229

A PIANO (Proper, Insufficient, Aberrant, and NO Reprogramming) Response to the Yamanaka Factors in the Initial Stages of Human iPSC Reprogramming
Cited by: 6
Author(s): Kejin Hu
Software Mentions: 5
Published: about 6 years ago

10.1264/jsme2.ME20153

Inoculation of &lt;i&gt;Mimosa Pudica&lt;/i&gt; with &lt;i&gt;Paraburkholderia phymatum&lt;/i&gt; Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: over 12 years ago

10.18632/aging.203021

Development of a prognostic model for hepatocellular carcinoma using genes involved in aerobic respiration
Cited by: 1
Author(s): Jiawei Rao, Xukun Wu, Xiaozhuan Zhou, Ronghai Deng, Yu Ma
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms9071457

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants
Cited by: 7
Author(s): Julia Hassa, Johanna Klang, Dirk Benndorf, Marcel Pohl, Benedikt Hülsemann, Torsten Mächtig, Mathias Effenberger, Alfred Pühler, Andreas Schlüter, Susanne Theuerl
Software Mentions: 5
Published: about 5 years ago

10.1186/s40644-020-00297-z

A CT-based radiomics nomogram for differentiation of focal nodular hyperplasia from hepatocellular carcinoma in the non-cirrhotic liver
Cited by: 41
Author(s): Pei Nie, Guangli Yang, Jian Guo, Jingjing Chen, Xiaoli Li, Qianqian Ji, Jie Wu, Jingjing Cui, Wenjian Xu
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.37072

Changes in the genetic requirements for microbial interactions with increasing community complexity
Cited by: 60
Author(s): Manon Morin, Emily C Pierce, Rachel J Dutton
Software Mentions: 5
Published: almost 8 years ago

10.1093/database/baaa096

The IMEx coronavirus interactome: an evolving map of <i>Coronaviridae</i>–host molecular interactions
Cited by: 31
Author(s): Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, Negin Rahimzadeh, Sylvie Ricard‐Blum, Łukasz Salwiński, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra Orchard, Igor Jurišica, Henning Hermjakob, Pablo Porras
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2229-12-106

Genome-wide analysis of the MYB transcription factor superfamily in soybean
Cited by: 320
Author(s): Hongwu Du, Sisi Yang, Zhe Liang, Bo-Run Feng, Lei Liu, Yubi Huang, Yixiong Tang
Software Mentions: 5
Published: about 14 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: almost 10 years ago

10.1038/s41598-021-92448-w

Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia
Cited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: about 5 years ago

10.1128/mBio.01457-20

Kaposi’s Sarcoma-Associated Herpesvirus Drives a Super-Enhancer-Mediated Survival Gene Expression Program in Primary Effusion Lymphoma
Cited by: 13
Author(s): Mark Manzano, Thomas Guenther, Honglyoul Ju, John Nicholas, Elizabeth T. Bartom, Adam Grundhoff, Eva Gottwein
Software Mentions: 5
Published: almost 6 years ago

10.1164/rccm.202003-0510OC

Whole-Blood RNA Profiles Associated with Pulmonary Arterial Hypertension and Clinical Outcome
Cited by: 36
Author(s): Christopher J. Rhodes, Pablo Otero-Núñez, John Wharton, Emilia M. Swietlik, Sokratis Kariotis, Lars Harbaum, Mark J. Dunning, Jason M. Elinoff, Niamh Errington, A. A. Roger Thompson, James Iremonger, J. Gerry Coghlan, Paul A. Corris, Luke Howard, David G. Kiely, Colin Church, Joanna Pepke‐Zaba, Mark Toshner, Stephen J. Wort, Ankit A. Desai, Marc Humbert, William C. Nichols, Laura Southgate, David‐Alexandre Trégouët, Richard Trembath, Inga Prokopenko, Stefan Gräf, Nicholas W. Morrell, Dennis Wang, Allan Lawrie, Martin R. Wilkins
Software Mentions: 5
Published: almost 6 years ago

10.18632/aging.103861

Development of a susceptibility gene based novel predictive model for the diagnosis of ulcerative colitis using random forest and artificial neural network
Cited by: 20
Author(s): Hanyang Li, Lijie Lai, Jun Shen
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0206844

Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotency
Cited by: 1
Author(s): Chao Wu, Jiao Yang, Minhong Shen, Ci Pan, Cheng Guo, Danmei Jia, Jing Zhu, Long Zhang, Min Zheng, Junling Jia
Software Mentions: 5
Published: over 7 years ago

10.1186/s12866-020-02076-z

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota
Cited by: 5
Author(s): Catharina Vendl, Tiffanie M. Nelson, Belinda C. Ferrari, Torsten Thomas, Tracey L. Rogers
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.6880

Structural implications of traditional agricultural landscapes on the functional diversity of birds near the Korean Demilitarized Zone
Cited by: 8
Author(s): Jae Hyun Kim, Shinyeong Park, Seung Ho Kim, Kyungsik Kang, Bruce Waldman, Myung Hwa Lee, Minhye Yu, Hyunyoung Yang, Hyun Yong Chung, Eun Ju Lee
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.ppat.1009769

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections
Cited by: 11
Author(s): Kai Fang, Jie Zhou, Lin Chen, Yuxuan Li, Ai-Ling Yang, Xing-Fan Dong, Hanbo Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: almost 6 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0181173

Predicting all-cause risk of 30-day hospital readmission using artificial neural networks
Cited by: 104
Author(s): Mehdi Jamei, Aleksandr Nisnevich, Everett Wetchler, Sylvia Sudat, Eric Liu
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-018-28720-3

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus
Cited by: 9
Author(s): Inga Reich, Umer Zeeshan Ijaz, Michael J. Gormally, Cindy J. Smith
Software Mentions: 5
Published: almost 8 years ago

10.1042/BSR20204301

Construction of a five-gene prognostic model based on immune-related genes for the prediction of survival in pancreatic cancer
Cited by: 12
Author(s): Bo Liu, Tingting Fu, Ping He, Changsheng Du, Ke Xu
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-021-04161-0

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments
Cited by: 4
Author(s): Aimeric Bruno, Jean‐Marc Aury, Stéfan Engelen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2019.01347

Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating Sows
Cited by: 11
Author(s): Jiajie Sun, Haojie Zhang, Bao-Yu Hu, Yueqin Xie, Dongyang Wang, Jinzhi Zhang, Ting Chen, Junyi Luo, Songbo Wang, Qinyan Jiang, Qianyun Xi, Zujing Chen, Yongliang Zhang
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.118.200540

Regulation of Root Angle and Gravitropism
Cited by: 19
Author(s): Ted Toal, Mily Ron, Donald J Gibson, Kaisa Kajala, Bessie L. Splitt, Logan Johnson, Nathan D. Miller, Radka Slovak, Allison Gaudinier, Rohan Patel, Miguel de Lucas, Nicholas J. Provart, Edgar P. Spalding, Wolfgang Busch, Daniel J. Kliebenstein, Siobhán M. Brady
Software Mentions: 5
Published: over 7 years ago

10.1007/s00442-019-04499-6

Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis
Cited by: 20
Author(s): Thomas M. Lilley, Jenni M. Prokkola, Anna Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomáš Bartonička, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 5
Published: almost 7 years ago

10.1098/rstb.2014.0240

Assigning and visualizing germline genes in antibody repertoires
Cited by: 19
Author(s): Simon D. W. Frost, Ben Murrell, Alamgir Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0239480

Horizontal and vertical movements of starry smooth-hound Mustelus asterias in the northeast Atlantic
Cited by: 4
Author(s): Christopher A. Griffiths, Serena Wright, Joana F. Silva, Jim R. Ellis, David Righton, Sophy R. McCully Phillips
Software Mentions: 5
Published: over 5 years ago

10.1534/g3.118.200852

Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant <i>Ferula assafoetida</i>
Cited by: 21
Author(s): Hajar Amini, Mohammad Reza Naghavi, Tong Shen, Yanhong Wang, Jaber Nasiri, Ikhlas A. Khan, Oliver Fiehn, Philipp Zerbe, Julin Maloof
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2021.646124

Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient
Cited by: 25
Author(s): Qifeng Tian, Ying Jiang, Yanan Tang, Yu Wu, Zhiyao Tang, Feng Liu
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmolb.2020.566491

Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma
Cited by: 15
Author(s): Muqi Li, Minni Liang, Tian Lan, Xiwen Wu, Wenlin Xie, Tielong Wang, Z Chen, Shunli Shen, Baogang Peng
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-018-2252-9

npInv: accurate detection and genotyping of inversions using long read sub-alignment
Cited by: 26
Author(s): Haojing Shao, Devika Ganesamoorthy, Tânia Duarte, Minh Duc Cao, Clive Hoggart, Lachlan Coin
Software Mentions: 5
Published: almost 8 years ago

10.3390/genes12060876

High SGO2 Expression Predicts Poor Overall Survival: A Potential Therapeutic Target for Hepatocellular Carcinoma
Cited by: 3
Author(s): Min Deng, Shaohua Li, Jie Mei, Wenping Lin, Jingwen Zou, Wei Wei, Rong Guo
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-019-49956-7

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing
Cited by: 14
Author(s): Emma Elizabeth Ilett, Mette Jørgensen, Marc Noguera‐Julian, Gedske Daugaard, Daniel D. Murray, Marie Helleberg, Roger Paredes, Jens D Lundgren, Henrik Sengeløv, Cameron Ross MacPherson
Software Mentions: 5
Published: almost 7 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-019-53623-2

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome
Cited by: 41
Author(s): Shijie Deng, Heidi M.-L. Wipf, Grady Pierroz, Theodore K. Raab, Rajnish Khanna, Devin Coleman‐Derr
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.1900

A comparison of species composition and community assemblage of secondary forests between the birch and pine-oak belts in the mid-altitude zone of the Qinling Mountains, China
Cited by: 13
Author(s): Zongzheng Chai, Dexiang Wang
Software Mentions: 5
Published: about 10 years ago

10.3389/fcell.2020.592348

Limited Mitochondrial Activity Coupled With Strong Expression of CD34, CD90 and EPCR Determines the Functional Fitness of ex vivo Expanded Human Hematopoietic Stem Cells
Cited by: 7
Author(s): Luena Papa, Mansour Djedaini, Tiphaine Martin, Mahtab Zangui, Kristin G. Beaumont, Robert Sebra, Ramon Parsons, Christoph Schaniel, Ronald Hoffman
Software Mentions: 5
Published: over 5 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: over 9 years ago

10.1038/s41388-021-02005-y

Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma
Cited by: 19
Author(s): Chuanpeng Dong, Annamaria Cesarano, Giuseppe Bombaci, Jill L. Reiter, Christina Y. Yu, Yue Wang, Zhaoyang Jiang, Mohammad Abu Zaid, Kun Huang, Xiongbin Lu, Brian A Walker, Fabiana Perna, Yunlong Liu
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.63745

Perinatal granulopoiesis and risk of pediatric asthma
Cited by: 2
Author(s): Benjamin A. Turturice, Juliana Theorell, Mary Dawn Koenig, Lisa Tussing‐Humphreys, Diane R. Gold, Augusto A. Litonjua, Emily Oken, Sheryl L. Rifas–Shiman, David L. Perkins, Patricia W. Finn
Software Mentions: 5
Published: over 5 years ago

10.1128/mBio.03551-20

The Termite Fungal Cultivar <i>Termitomyces</i> Combines Diverse Enzymes and Oxidative Reactions for Plant Biomass Conversion
Cited by: 13
Author(s): Felix Schalk, Cene Gostinčar, Nina B. Kreuzenbeck, Benjamin H. Conlon, Elisabeth Sommerwerk, Patrick Rabe, Immo Burkhardt, Thomas Krüger, Olaf Kniemeyer, Axel A. Brakhage, Nina Gunde‐Cimerman, Z. Wilhelm de Beer, Jeroen S. Dickschat, Michael Poulsen, Christine Beemelmanns
Software Mentions: 5
Published: about 5 years ago

10.1155/2021/8880585

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: about 5 years ago

10.3390/diagnostics11071245

Mandibular Third Molar Surgery: Intraosseous Localization of the Inferior Alveolar Nerve Using 3D Double-Echo Steady-State MRI (3D-DESS)
Cited by: 10
Author(s): Adib Al‐Haj Husain, Bernd Stadlinger, Sebastian Winklhofer, Marcel Müller, Marco Piccirelli, Silvio Valdec
Software Mentions: 5
Published: almost 5 years ago

10.18632/aging.103977

Identification of immune landscape signatures associated with clinical and prognostic features of hepatocellular carcinoma
Cited by: 2
Author(s): Hongmei Yan, Yu-Chuan Chen, Kai Wang, Yu Lu, Xixin Huang, Qianyu Li, Yuwen Xie, Jiayu Lin, Yueyun He, Xinyu Yi, Yanzhi Wang, Longhua Chen, Yi Ding, Yiyi Li
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.7755

Legacy of pre‐eruption vegetation affects ground‐dwelling arthropod communities after different types of volcanic disturbance
Cited by: 2
Author(s): Kyohei Iida, Daisuke Hayasaka, Yuka Suzuki, Tatsuo Uchida, Takuo Sawahata, Koya Hashimoto
Software Mentions: 5
Published: about 5 years ago

10.1016/j.isci.2021.103048

Post-weaning A1/A2 β-casein milk intake modulates depressive-like behavior, brain μ-opioid receptors, and the metabolome of rats
Cited by: 5
Author(s): Aya Osman, Simone Zuffa, Gemma Walton, Elizabeth Fagbodun, Panos Zanos, Polymnia Georgiou, Ian Kitchen, Jonathan R. Swann, Alexis Bailey
Software Mentions: 5
Published: almost 5 years ago

10.3389/fgene.2019.00770

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk
Cited by: 65
Author(s): Sebastian Rauschert, Phillip E. Melton, Graham C. Burdge, Jeffrey M. Craig, Keith M. Godfrey, Joanna D. Holbrook, Karen A. Lillycrop, Trevor A. Mori, Lawrence J. Beilin, Wendy H. Oddy, Craig E. Pennell, Rae‐Chi Huang
Software Mentions: 5
Published: almost 7 years ago

10.1128/AEM.02992-18

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation
Cited by: 33
Author(s): Liang Liang Liu, Xinqi Huang, Jun Zhao, Jinbo Zhang, Zucong Cai
Software Mentions: 5
Published: over 7 years ago

10.18632/oncotarget.14091

The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma
Cited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: over 9 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-021-93297-3

Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2021.647861

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed
Cited by: 4
Author(s): Alyssa A. Carrell, Grace E. Schwartz, Melissa Cregger, Caitlin M. Gionfriddo, Dwayne A. Elias, Regina L. Wilpiszeski, Dawn M. Klingeman, Ann M. Wymore, Katherine A. Muller, Scott C. Brooks
Software Mentions: 5
Published: over 5 years ago

10.1111/mpp.13003

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode <i>Hirschmanniella oryzae</i> , increase host susceptibility by manipulating secondary metabolite content of rice
Cited by: 8
Author(s): Lander Bauters, Tina Kyndt, Tim De Meyer, Kris Morreel, Wout Boerjan, Hannes Lefevere, Godelieve Gheysen
Software Mentions: 5
Published: over 5 years ago

10.1186/s40793-021-00377-y

Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion
Cited by: 45
Author(s): Weidong Chen, Donghui Wen
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2021.620945

Individualized Prediction of Colorectal Cancer Metastasis Using a Radiogenomics Approach
Cited by: 2
Author(s): Qin Liu, Jie Li, Lin Xu, Jiasi Wang, Zong Yuan Zeng, Jiangping Fu, Xuan Huang, Yanpeng Chu, Jing Wang, Hongyu Zhang, Fanxin Zeng
Software Mentions: 5
Published: about 5 years ago

10.1186/s12920-020-00740-x

Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension
Cited by: 15
Author(s): Jing Luo, Haiyan Li, Zhenwei Liu, Chenlu Li, Ruochen Wang, Jinxia Fang, Saisai Lu, Jing Guo, Xiongzhao Zhu, Xiaobing Wang
Software Mentions: 5
Published: about 6 years ago

10.3390/nu12082308

Plasma Metabolites Related to Peripheral and Hepatic Insulin Sensitivity Are Not Directly Linked to Gut Microbiota Composition
Cited by: 6
Author(s): Annefleur M. Koopen, Nicolien C. de Clercq, Moritz V. Warmbrunn, Hilde Herrema, Mark Davids, Pieter F. de Groot, Ruud S. Kootte, Kristien E. Bouter, Max Nieuwdorp, Albert K. Groen, Andrei Prodan
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-020-6558-4

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)
Cited by: 10
Author(s): Fugui Zhang, Xin Xiao, Kun Xu, Xi Cheng, Ting Xie, Jihong Hu, Xiaoming Wu
Software Mentions: 5
Published: over 6 years ago

10.1186/1756-0500-5-596

MetabR: an R script for linear model analysis of quantitative metabolomic data
Cited by: 30
Author(s): Ben Ernest, Jessica Gooding, Shawn R. Campagna, Arnold M. Saxton, Brynn H. Voy
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0022176

Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Cited by: 9
Author(s): Jitao David Zhang, Cindy Körner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Şahin, Stefan Wiemann, Ulrich Tschulena
Software Mentions: 5
Published: almost 15 years ago