10.3390/ijms21207648

Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein–Inhibitor Complexes in Relevance to Developing Parkinson’s Therapeutics
Cited by: 8
Author(s): Natarajan Arul Murugan, Charuvaka Muvva, Chitra Jeyarajpandian, Jeyaraman Jeyakanthan, V. Subramanian
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0212949

The nasal and oropharyngeal microbiomes of healthy livestock workers
Cited by: 15
Author(s): Ashley E. Kates, Mark Dalman, James C. Torner, Tara C. Smith
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: about 10 years ago

10.1186/s13062-015-0071-8

Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-020-6520-5

Identification of eQTLs and sQTLs associated with meat quality in beef
Cited by: 16
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Raluca G. Mateescu
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5793-z

Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera
Cited by: 7
Author(s): Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang, Qingfa Wu
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0178532

Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism
Cited by: 21
Author(s): Brian Gudenas, Anand Srivastava, Liangjiang Wang
Software Mentions: 4
Published: about 9 years ago

10.3390/ph14060553

Equine Mesenchymal Stem/Stromal Cells Freeze-Dried Secretome (Lyosecretome) for the Treatment of Musculoskeletal Diseases: Production Process Validation and Batch Release Test for Clinical Use
Cited by: 8
Author(s): Michela Mocchi, Stefano Grolli, Silvia Dotti, Dario Di Silvestre, Riccardo Villa, Priscilla Berni, Virna Conti, Giulia Passignani, Francesca Brambilla, Maurizio Del Bue, Laura Catenacci, Milena Sorrenti, Lorena Segale, Elia Bari, Pierluigi Mauri, Maria Luisa Torre, Sara Perteghella
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.9326

Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea
Cited by: 2
Author(s): Yukino Mizutani, Tetsushi Mori, Taeko Miyazaki, Satoshi Fukuzaki, Reiji Tanaka
Software Mentions: 4
Published: about 6 years ago

10.3390/jof7090769

Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping
Cited by: 2
Author(s): Farzan Ghanegolmohammadi, Hiroki Okada, Yaxuan Liu, Kaori Itto-Nakama, Shinsuke Ohnuki, A. S. Savchenko, Erfei Bi, Satoshi Yoshida, Yoshikazu Ohya
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2020.569985

Diverse Macrophage Populations Contribute to the Inflammatory Microenvironment in Premalignant Lesions During Localized Invasion
Cited by: 16
Author(s): Ayman Ibrahim, Matthew Moss, Zane Gray, Michelle D. Rojo, Caitlin M. Burke, Kathryn L. Schwertfeger, Camila O. dos Santos, Heather L. Machado
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.7844

Effects of research disturbance on nest survival in a mixed colony of waterbirds
Cited by: 4
Author(s): Matthieu Guillemain, Hugo Carré, Lisa Gili
Software Mentions: 4
Published: almost 7 years ago

10.7150/thno.55645

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis
Cited by: 18
Author(s): Mei Wang, Yanwen Xu, Yuncong Zhang, Yuhan Chen, Gang Chang, Geng An, Xinyan Yang, Caihong Zheng, Jiexiang Zhao, Zhaoting Liu, Dazhuang Wang, Masahiro Kai, Rao S, Meng Dai, Dong Wang, Xiaoyang Zhao
Software Mentions: 4
Published: over 5 years ago

10.7150/thno.35573

Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA
Cited by: 54
Author(s): Ryan A. Hlady, Zhao Xiao, Xiaoyu Pan, Ju Dong Yang, Fowsiyo Ahmed, Samuel O. Antwi, Nasra H. Giama, Tushar Patel, Lewis R. Roberts, Chen Liu, Keith D. Robertson
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0175528

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown
Cited by: 61
Author(s): Shingo Miyauchi, David Navarro, Sacha Grisel, Didier Chevret, Jean‐Guy Berrin, Marie Noelle Rosso
Software Mentions: 4
Published: over 9 years ago

10.1111/1755-0998.13012

Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring
Cited by: 40
Author(s): Filipa M. S. Martins, Mafalda Galhardo, Ana Filipa Filipe, Amílcar Teixeira, Paulo D. P. Pinheiro, Joana Paupério, Paulo C. Alves, Pedro Beja
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.8541

Rhizosphere bacterial and fungal communities during the growth of <i>Angelica sinensis</i> seedlings cultivated in an Alpine uncultivated meadow soil
Cited by: 12
Author(s): An Zhigang, Fengjing Guo, Yuan Chen, Gang Bai, Zhengjun Chen
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0236347

Understanding the spatial dimension of natural language by measuring the spatial semantic similarity of words through a scalable geospatial context window
Cited by: 4
Author(s): Bozhi Wang, Teng Fei, Yuhao Kang, Meng Li, Qingyun Du, Meng Han, Ning Dong
Software Mentions: 4
Published: about 6 years ago

10.3390/biology10070665

FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists
Cited by: 22
Author(s): Foteini Thanati, Evangelos Karatzas, Fotis A. Baltoumas, Dimitrios J. Stravopodis, Aristides G. Eliopoulos, Georgios A. Pavlopoulos
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0247534

Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics
Cited by: 9
Author(s): Jessica A. Day, Christian Diener, Anne E. Otwell, Kourtney E. Tams, Brad M. Bebout, Angela M. Detweiler, Michael Lee, Madeline T. Scott, Wilson Ta, Monica Ha, Shienna A. Carreon, Kenny Tong, Abdirizak A. Ali, Sean M. Gibbons, Nitin S. Baliga
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0218899

Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 4
Published: about 7 years ago

10.1111/jcmm.15271

Systematic prediction of key genes for ovarian cancer by co‐expression network analysis
Cited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0201690

Strap associates with Csde1 and affects expression of select Csde1-bound transcripts
Cited by: 5
Author(s): Kat Moore, Nurcan Yağcı, Floris van Alphen, Alexander B. Meijer, Peter A.C. ’t Hoen, Marieke von Lindern
Software Mentions: 4
Published: almost 8 years ago

10.3390/nu11061425

Mixed Spices at Culinary Doses Have Prebiotic Effects in Healthy Adults: A Pilot Study
Cited by: 24
Author(s): Qing-Yi Lu, Anna Rasmussen, Jieping Yang, Ru-Po Lee, Jianjun Huang, Paul Shao, Catherine L. Carpenter, Irene Gilbuena, Gail Thames, Susanne M. Henning, David Heber, Zhaoping Li
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0223397

Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells
Cited by: 10
Author(s): Qingtai Su, Aurélie Bouteau, Jacob Cardenas, Uthra Balaji, Yuanyaun Wang, Cynthia Smitherman, Jin Gu, Botond Z. Igyártó
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0245243

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study
Cited by: 13
Author(s): Suhana Chattopadhyay, Justin D. Arnold, Leena Malayil, Lauren E. Hittle, Emmanuel F. Mongodin, Kalyani Marathe, Veronica Gómez-Lobo, Amy R. Sapkota
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.14779

Four transcription profile–based models identify novel prognostic signatures in oesophageal cancer
Cited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.57260

Construction of a ceRNA Network and a Prognostic lncRNA Signature associated with Vascular Invasion in Hepatocellular Carcinoma based on Weighted Gene Co-Expression Network Analysis
Cited by: 10
Author(s): Haisu Tao, Li Jiang, Junjie Liu, Tong Yuan, Erlei Zhang, Huifang Liang, Zhiyong Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/nu12041063

Specific Dietary Components and Gut Microbiota Composition are Associated with Obesity in Children and Adolescents with Prader–Willi Syndrome
Cited by: 16
Author(s): Sonika Garcia-Ribera, Montse Amat-Bou, Eric Climent, M. Villangómez Llobet, Empar Chenoll, Raquel Corripio, Lourdes Ibáñez, Marta Ramón-Krauel, Carles Lerín
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0211705

Little cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper
Cited by: 11
Author(s): Suhana Chattopadhyay, Eoghan M. Smyth, Prachi Kulkarni, Kelsey R. Babik, Molly C. Reid, Lauren E. Hittle, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 4
Published: over 7 years ago

10.3389/fvets.2017.00244

Drivers of Live Cattle Price in the Livestock Trading System of Central Cameroon
Cited by: 3
Author(s): Paolo Carlo Motta, Ian Handel, Gustaf Rydevik, Saidou M. Hamman, Victor Ngu Ngwa, Vincent N. Tanya, K. L. Morgan, Barend M. deC. Bronsvoort, Thibaud Porphyre
Software Mentions: 4
Published: over 8 years ago

10.3390/nu11051135

Safety of Hyaluronan 35 in Healthy Human Subjects: A Pilot Study
Cited by: 8
Author(s): Annette Bellar, Sean P. Kessler, Dana R. Obery, Naseer Sangwan, Nicole Welch, Laura E. Nagy, Srinivasan Dasarathy, Carol de la Motte
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-86504-8

Identification and external validation of a prognostic signature associated with DNA repair genes in gastric cancer
Cited by: 5
Author(s): Shimin Chen, Wenbo Liu, Haojun Yu
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3394

SIX4 promotes metastasis via activation of the PI3K-AKT pathway in colorectal cancer
Cited by: 26
Author(s): Guodong Li, Fang Hu, Xuelai Luo, Jian Hu, Yongzeng Feng
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0180751

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs
Cited by: 14
Author(s): Lizhi Cao, Robert Lafyatis, Linda C. Burkly
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-020-02022-2

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Cited by: 28
Author(s): Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Li Pan, Bao‐Fa Sun, Ying Yang, Ning Zhang, Yongliang Zhao, Hailin Wang, Feng Liu, Qiangfeng Cliff Zhang, Yun‐Gui Yang
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.8133

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Cited by: 19
Author(s): Lauren V. Carruthers, Moses Arinaitwe, Moses Adriko, Christina L. Faust, Edridah M. Tukahebwa, Lindsay J. Hall, Lisa Ranford-Cartwright, Poppy H. L. Lamberton
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232189

Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity
Cited by: 10
Author(s): Iva Cvitaš, Simone Oberhänsli, Tosso Leeb, Martina Dettwiler, Eliane J. Müller, Rémy Bruggman, Eliane Marti
Software Mentions: 4
Published: about 6 years ago

10.3390/nu13062069

Timing of Tributyrin Supplementation Differentially Modulates Gastrointestinal Inflammation and Gut Microbial Recolonization Following Murine Ileocecal Resection
Cited by: 1
Author(s): Valentin Mocanu, Heekuk Park, Jerry Dang, Naomi Hotte, Aducio Thiesen, Michael Laffin, Haili Wang, Daniel W. Birch, Karen Madsen
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.6377

Disentangling the effect of host-genotype and environment on the microbiome of the coral <i>Acropora tenuis</i>
Cited by: 50
Author(s): Bettina Glasl, Caitlin E. Smith, David G. Bourne, Nicole S. Webster
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0136765

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq
Cited by: 35
Author(s): Guoqiang Yi, Jiahui Yuan, Huijuan Bi, Wei Yan, Ning Yang, Lujiang Qu
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0240885

Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats
Cited by: 2
Author(s): J. L. Webb, Amanda Bries, Brooke Vogel, Claudia Carrillo, Lily Harvison, Timothy A. Day, Michael J. Kimber, Rudy J. Valentine, Matthew J. Rowling, Stephanie Clark, Elizabeth McNeill, Kevin L. Schalinske
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22147266

Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Cited by: 12
Author(s): Weitao Li, Li Huang, Nian Liu, Manish K. Pandey, Yuning Chen, Cheng Ling, Jianbin Guo, Bin Yu, Huaiyong Luo, Xiaojing Zhou, Dongxin Huai, Weigang Chen, Liying Yan, Xin Wang, Yong Lei, Rajeev K. Varshney, Boshou Liao, Huifang Jiang
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers13184518

The Tumor Microenvironment-Dependent Transcription Factors AHR and HIF-1α Are Dispensable for Leukemogenesis in the Eµ-TCL1 Mouse Model of Chronic Lymphocytic Leukemia
Cited by: 3
Author(s): Susanne Gonder, Anne Largeot, Ernesto Gargiulo, Sandrine Pierson, Iria Fernandez Botana, Giulia Pagano, Jérôme Paggetti, Etienne Moussay
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-018-2512-8

A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data
Cited by: 9
Author(s): A. M. C. Chan, Amy L. Williams, Jean‐Luc Jannink
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers13102306

Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas
Cited by: 3
Author(s): Thaise Nayane Ribeiro Carneiro, Larissa Valdemarin Bim, Vanessa Candiotti Buzatto, Vanessa Galdeno, Paula Fontes Asprino, Eunjung Alice Lee, Pedro A. F. Galante, Janete M. Cerutti
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1003130

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

10.3390/ijms22116101

Loss of Nnt Increases Expression of Oxidative Phosphorylation Complexes in C57BL/6J Hearts
Cited by: 4
Author(s): Jack Williams, Charlotte Hall, Eirini Meimaridou, Louise A. Metherell
Software Mentions: 4
Published: about 5 years ago

10.12688/wellcomeopenres.15590.1

Evolutionary analysis of the most polymorphic gene family in falciparum malaria
Cited by: 56
Author(s): Thomas D. Otto, Sammy A. Assefa, Ulrike Böhme, Mandy Sanders, Dominic Kwiatkowski, Matthew Berriman, Chris Newbold
Software Mentions: 4
Published: over 6 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-84173-1

Predictive values, uncertainty, and interpretation of serology tests for the novel coronavirus
Cited by: 19
Author(s): Naomi C. Brownstein, Yian Ann Chen
Software Mentions: 4
Published: over 5 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 14 years ago

10.3390/v12111285

Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus
Cited by: 15
Author(s): Giovanni Franzo, Michele Drigo, Matteo Legnardi, L. Grassi, Daniela Pasotto, Maria Luisa Menandro, Mattia Cecchinato, Claudia Maria Tucciarone
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.61531

HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration
Cited by: 6
Author(s): Alicia Tapias, David Rodríguez Lázaro, Bo-Kun Yin, Seyed Mohammad Mahdi Rasa, Anna Krepelova, Erika Kelmer Sacramento, Paulius Grigaravičius, Philipp Koch, Joanna Kirkpatrick, Alessandro Ori, Francesco Neri, Zhaoqi Wang
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms9081673

Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types
Cited by: 2
Author(s): Andrea K. Borsodi, Márton Mucsi, Gergely Krett, Attila Szabó, Tamás Felföldi, Tibor Szili‐Kovács
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.cell.2018.07.001

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
Cited by: 110
Author(s): Jan Attig, Antonella Federico, Clare Gooding, Anob M. Chakrabarti, Aarti Singh, Nejc Haberman, Julian A. Zagalak, Warren Emmett, Christopher W. Smith, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12887-019-1564-x

Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Cited by: 22
Author(s): Najeeha Talat Iqbal, Sana Syed, Kamran Sadiq, Marium Khan, Junaid Iqbal, Z. Jennie, Fayaz Umrani, Sheraz Ahmed, Elizabeth A. Maier, Lee A. Denson, Yael Haberman, Monica McNeal, Kenneth D.R. Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A. Moskaluk, Ta‐Chiang Liu, Ömer H. Yılmaz, Donald E. Brown, Michael J. Barratt, Vanderlene L. Kung, Jeffrey I. Gordon, Sean R. Moore, Syed Asad Ali
Software Mentions: 4
Published: about 7 years ago

10.1016/j.cell.2018.11.044

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation
Cited by: 115
Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B. Meyer, Ricardo J. Miragaia, Graham Dy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa, Sarah A. Teichmann
Software Mentions: 4
Published: over 7 years ago

10.3390/s19092047

Design and Implementation of Cloud Analytics-Assisted Smart Power Meters Considering Advanced Artificial Intelligence as Edge Analytics in Demand-Side Management for Smart Homes
Cited by: 105
Author(s): Yung-Yao Chen, Yu‐Hsiu Lin, Chia-Ching Kung, Ming-Feng Chung, I-Hsuan Yen
Software Mentions: 4
Published: about 7 years ago

10.1080/19336918.2021.1903684

A role for GLUT3 in glioblastoma cell invasion that is not recapitulated by GLUT1
Cited by: 16
Author(s): Catherine Libby, Sajina Gc, Gloria A. Benavides, Jennifer L. Fisher, Sarah Williford, Sixue Zhang, Anh Tran, Emily R. Gordon, Amber Jones, Kaysaw Tuy, William Flavahan, Juan Gordillo, Ashlee Long, Sara J. Cooper, Brittany N. Lasseigne, Corinne E. Augelli‐Szafran, Victor Darley‐Usmar, Anita B. Hjelmeland
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.652601

Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
Cited by: 8
Author(s): Xiong Guo, Xiaolong Liang, Yujun Wang, Anqi Cheng, Chuan Qin, Han Zhang, Ziwei Wang
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.53459

The histone modification reader ZCWPW1 links histone methylation to PRDM9-induced double-strand break repair
Cited by: 28
Author(s): Tao Huang, Shenli Yuan, Lei Gao, Mengjing Li, Xiaochen Yu, Jianhong Zhan, Yingying Yin, Chao Liu, Chuanxin Zhang, Gang Lü, Wei Li, Jiang Liu, Zi‐Jiang Chen, Hongbin Liu
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: about 7 years ago

10.3390/cancers12061431

Characterization of a Myeloid Activation Signature That Correlates with Survival in Melanoma Patients
Cited by: 1
Author(s): Mirela Kremenovic, Nives Rombini, Alfred A. Chan, Thomas Gruber, Lukas Bäriswyl, Delphine J. Lee, Mirjam Schenk
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.8583

A comparative study of machine learning algorithms for predicting acute kidney injury after liver cancer resection
Cited by: 19
Author(s): Lei Lei, Ying Wang, Qingyun Xue, Jianhua Tong, Chengmao Zhou, Jianjun Yang
Software Mentions: 4
Published: over 6 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: about 6 years ago

10.1038/s41419-020-03020-9

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death
Cited by: 51
Author(s): Ling Huang, Daniel B. McClatchy, Pamela Maher, Zhibin Liang, Jolene K. Diedrich, David Soriano-Castell, Joshua Goldberg, Maxim N. Shokhirev, John R. Yates, David Schubert, António Currais
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-82866-1

The protective role of daidzein in intestinal health of turbot (Scophthalmus maximus L.) fed soybean meal-based diets
Cited by: 14
Author(s): Guijuan Yu, Yang Liu, Weihao Ou, Jihong Dai, Qinghui Ai, Wenbing Zhang, Kangsen Mai, Yan-Jiao Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-82362-6

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Cited by: 11
Author(s): Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary Simon, Seppe Kuehn, Kelly S. Swanson, Tzu Wen L. Cross, Kristin M. Hedman, Stanley H. Ambrose, Ripan S. Malhi
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.43738

Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice
Cited by: 66
Author(s): Mina Kojima, Dirk G. de Rooij, David C. Page
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0230254

Forecasting severe grape downy mildew attacks using machine learning
Cited by: 26
Author(s): Mathilde Chen, François Brun, M. Raynal, David Makowski
Software Mentions: 4
Published: over 6 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: almost 5 years ago

10.1089/hum.2020.213

Genetic Rescue of X-Linked Retinoschisis Mouse (<i>Rs1</i>^−/y) Retina Induces Quiescence of the Retinal Microglial Inflammatory State Following AAV8-<i>RS1</i> Gene Transfer and Identifies Gene Networks Underlying Retinal Recovery
Cited by: 16
Author(s): Camasamudram Vijayasarathy, Yong Zeng, Matthew Brooks, Robert N Fariss, Paul A. Sieving
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0120014

Poor Transferability of Species Distribution Models for a Pelagic Predator, the Grey Petrel, Indicates Contrasting Habitat Preferences across Ocean Basins
Cited by: 80
Author(s): Leigh G. Torres, Philip Sutton, David R. Thompson, Karine Delord, Henri Weimerskirch, Paul M. Sagar, Erica Sommer, Ben J. Dilley, Peter G. Ryan, Richard A. Phillips
Software Mentions: 4
Published: over 11 years ago

10.3390/ijms19010245

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review
Cited by: 106
Author(s): Arun Sudhagar, Gokhlesh Kumar, Mansour El-Matbouli
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-60623-0

First evidence of production of the lantibiotic nisin P
Cited by: 29
Author(s): Enriqueta García-Gutiérrez, Paula M. O’Connor, Gerhard Saalbach, Calum J. Walsh, James W. Hegarty, Caitriona M. Guinane, Melinda J. Mayer, Arjan Narbad, Paul D. Cotter
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0117917

Spatial Niche Partitioning in Sub-Tropical Solitary Ungulates: Four-Horned Antelope and Barking Deer in Nepal
Cited by: 20
Author(s): Krishna Prasad Pokharel, Tobias Ludwig, Ilse Storch
Software Mentions: 4
Published: over 11 years ago

10.1038/s41438-021-00531-0

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Cited by: 28
Author(s): Chen Hong-guo, Xiangling Zeng, Jie Yang, Xuan Cai, Yumin Shi, Rencheng Zheng, Zhenqi Wang, Junyi Liu, Xiao Su Yi, Siwei Xiao, Qiang Fu, Jingjing Zou, Caiyun Wang
Software Mentions: 4
Published: about 5 years ago

10.1038/s41419-020-2585-y

Loss of Spry1 reduces growth of BRAFV600-mutant cutaneous melanoma and improves response to targeted therapy
Cited by: 13
Author(s): Barbara Montico, Francesca Colizzi, Giorgio Giurato, Aurora Rizzo, Annamaria Salvati, Lorena Baboci, Dania Benedetti, Eliana Pivetta, Alessia Covre, Michele Dal Bo, Alessandro Weisz, Agostino Steffan, Michele Maio, Luca Sigalotti, Elisabetta Fratta
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0185793

The importance of vegetation density for tourists’ wildlife viewing experience and satisfaction in African savannah ecosystems
Cited by: 13
Author(s): Ugo Arbieu, Claudia Grünewald, Matthias Schleuning, Katrin Böhning‐Gaese
Software Mentions: 4
Published: almost 9 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: over 7 years ago

10.1155/2013/873595

A Gradient Boosting Algorithm for Survival Analysis via Direct Optimization of Concordance Index
Cited by: 57
Author(s): Yifei Chen, Zhenyu Jia, Dan Mercola, Xiaohui Xie
Software Mentions: 4
Published: over 13 years ago

10.7554/eLife.27861

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
Cited by: 124
Author(s): Neel Shah, Ping Wang, John Wongvipat, Wouter R. Karthaus, Wassim Abida, Joshua Armenia, Shira Rockowitz, Yotam Drier, B Bernstein, Henry W. Long, Matthew L. Freedman, Vivek Arora, Deyou Zheng, Charles L. Sawyers
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-021-98126-1

Distance-based clustering challenges for unbiased benchmarking studies
Cited by: 9
Author(s): Michael C. Thrun
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.60681

SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Cited by: 6
Author(s): Charlotte P Choi, Rebecca J Tay, Margaret R. Starostik, Suhua Feng, James J. Moresco, Brooke E. E. Montgomery, Emily Xu, Maya A Hammonds, Michael C. Schatz, Taiowa A. Montgomery, John R. Yates, Steven E. Jacobsen, John K. Kim
Software Mentions: 4
Published: over 5 years ago

10.3389/frai.2021.625573

Artificial Intelligence for Prognostic Scores in Oncology: a Benchmarking Study
Cited by: 2
Author(s): Hugo Loureiro, Tim Becker, Anna Bauer-Mehren, Narges Ahmidi, Janick Weberpals
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-56227-y

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing
Cited by: 13
Author(s): Luke Braidwood, Sebastian Müller, David C. Baulcombe
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btt294

SVGenes: a library for rendering genomic features in scalable vector graphic format
Cited by: 2
Author(s): Graham J. Etherington, Dan MacLean
Software Mentions: 4
Published: about 13 years ago

10.1016/j.stem.2020.08.004

Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development
Cited by: 43
Author(s): Edie I. Crosse, Sabrina Gordon-Keylock, Stanislav Rybtsov, Anahí Binagui-Casas, Hannah Felchle, Nneka C. Nnadi, Kristina Kirschner, Tamir Chandra, Sara Tamagno, David J. Webb, Fiona Rossi, Richard A. Anderson, Alexander Medvinsky
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.119.400413

The Genome Sequence of the Eastern Woodchuck (<i>Marmota monax</i>) – A Preclinical Animal Model for Chronic Hepatitis B
Cited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms7100441

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale
Cited by: 17
Author(s): Sonia S. Valencia-Agami, Daniel Cerqueda‐García, S. Putzeys, María Magdalena Uribe-Flores, Ulises García-Cruz, Daniel Pech, Jorge A. Herrera-Silveira, M. Leopoldina Aguirre-Macedo, José Q. García-Maldonado
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-54983-5

Plasma metabolomics in tuberculosis patients with and without concurrent type 2 diabetes at diagnosis and during antibiotic treatment
Cited by: 36
Author(s): Frank Vrieling, Bachti Alisjahbana, Edhyana Sahiratmadja, Reinout van Crevel, Amy C. Harms, Thomas Hankemeier, Tom H. M. Ottenhoff, Simone A. Joosten
Software Mentions: 4
Published: over 6 years ago

10.1016/j.cels.2020.05.003

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons
Cited by: 24
Author(s): Daria Bunina, Nade Abazova, Nichole Diaz, Kyung‐Min Noh, Jeroen Krijgsveld, Judith B. Zaugg
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.16220

Trisomy 21 consistently activates the interferon response
Cited by: 205
Author(s): Kelly D. Sullivan, Hannah C. Lewis, Amanda A. Hill, Ahwan Pandey, Leisa Jackson, Joseph M Cabral, Keith P Smith, L. Alexander Liggett, Eliana B. Gómez, Matthew D. Galbraith, James DeGregori, Joaquín M. Espinosa
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.29132

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
Cited by: 122
Author(s): David R. Hill, Sha Huang, Melinda S. Nagy, Veda K. Yadagiri, Courtney Fields, Dishari Mukherjee, Brooke Bons, Priya H. Dedhia, Alana M. Chin, Yu Hwai Tsai, Shrikar Thodla, Thomas M. Schmidt, Seth T. Walk, Vincent B. Young, Jason R. Spence
Software Mentions: 4
Published: over 8 years ago

10.3390/microorganisms8111729

A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes
Cited by: 7
Author(s): Kshitij Tandon, Bayanmunkh Baatar, Pei‐Wen Chiang, Dashdondog Narangarvuu, Bolormaa Oyuntsetseg, Sen‐Lin Tang
Software Mentions: 4
Published: over 5 years ago