10.1126/sciadv.abg9923

Structure of the mycobacterial ESX-5 type VII secretion system pore complex
Cited by: 38
Author(s): Katherine S. H. Beckham, Christina Ritter, Grzegorz Chojnowski, Daniel S. Ziemianowicz, Edukondalu Mullapudi, Mandy Rettel, Mikhail M. Savitski, Simon A. Mortensen, Jan Kosiński, Matthias Wilmanns
Software Mentions: 4
Published: about 5 years ago

10.1107/S2052252520000895

The predictive power of data-processing statistics
Cited by: 6
Author(s): M. Vollmar, James M. Parkhurst, Dominic Jaques, Arnaud Baslé, Garib N. Murshudov, David Waterman, Gwyndaf Evans
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ymeth.2017.09.010

Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data
Cited by: 30
Author(s): Dominic Waithe, Falk Schneider, Jakub Chojnacki, Mathias P. Clausen, Dilip Shrestha, Jorge Bernardino de la Serna, Christian Eggeling
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0021931

Real-Time PyMOL Visualization for Rosetta and PyRosetta
Cited by: 51
Author(s): Evan H. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray
Software Mentions: 4
Published: almost 15 years ago

10.1002/ece3.7146

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data
Cited by: 22
Author(s): Kristoffer Sahlin, Marisa Lim, Stefan Prost
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1002952

Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling
Cited by: 31
Author(s): David W. White, Melissa A. Kinney, Todd C. McDevitt, Melissa L. Kemp
Software Mentions: 4
Published: over 13 years ago

10.1084/jem.20190730

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid
Cited by: 47
Author(s): Guillermo L. Lehmann, Christin Hanke-Gogokhia, Yang Hu, Rohan Bareja, Zelda Salfati, Michael Ginsberg, Daniel J. Nolan, Santiago P. Méndez-Huergo, Tomás Dalotto-Moreno, Alexandre Wojcinski, Francisca Ochoa, Siyuan Zeng, Juan P. Cerliani, Lampros Panagis, Patrick J. Zager, Robert F. Mullins, Shuntaro Ogura, Gerard A. Lutty, Jakyung Bang, Jonathan H. Zippin, Carmelo Romano, Gabriel A. Rabinovich, Olivier Elemento, Alexandra L. Joyner, Shahin Rafii, Enrique Rodríguez-Boulan, Ignacio Benedicto
Software Mentions: 4
Published: over 6 years ago

10.3389/fnana.2020.585793

Neuronize v2: Bridging the Gap Between Existing Proprietary Tools to Optimize Neuroscientific Workflows
Cited by: 4
Author(s): Iván Velasco, Pablo Toharia, Ruth Benavides-Piccione, Isabel Fernaud-Espinosa, Juan P. Brito, Susana Mata, Javier DeFelipe, Luis Pastor, Sofía Bayona
Software Mentions: 4
Published: almost 6 years ago

10.3390/molecules26071996

Deciphering the Interactions of Bioactive Compounds in Selected Traditional Medicinal Plants against Alzheimer’s Diseases via Pharmacophore Modeling, Auto-QSAR, and Molecular Docking Approaches
Cited by: 25
Author(s): Oluwafemi Adeleke Ojo, Adebola Busola Ojo, Charles E. Okolie, Mary-Ann Chinyere Nwakama, Matthew Iyobhebhe, Ikponmwosa Owen Evbuomwan, Charles Obiora Nwonuma, Rotdelmwa Filibus Maimako, Abayomi Emmanuel Adegboyega, Odunayo Anthonia Taiwo, Khalaf F. Alsharif, Gaber El‐Saber Batiha
Software Mentions: 4
Published: over 5 years ago

10.1111/1751-7915.12751

The dynamics of the bacterial communities developed in maize silage
Cited by: 66
Author(s): Javad Gharechahi, Zohreh Akhavan Kharazian, Sajjad Sarikhan, Gholamreza Salehi Jouzani, Mahnaz Aghdasi, Ghasem Hosseini Salekdeh
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-020-74775-6

A digital reconstruction of the 1630–1631 large plague outbreak in Venice
Cited by: 6
Author(s): Gianrocco Lazzari, Giovanni Colavizza, Fabio Bortoluzzi, Davide Drago, Andrea Erboso, Francesca Zugno, Frédé́ric Kaplan, Marcel Salathé
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1009774

A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation
Cited by: 4
Author(s): Payel Ganguly, Landiso Madonsela, Jesse T. Chao, Christopher Loewen, Timothy P. O’Connor, Esther M. Verheyen, Douglas W. Allan
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12915-020-00911-3

CloneSifter: enrichment of rare clones from heterogeneous cell populations
Cited by: 11
Author(s): David Feldman, FuNien Tsai, Anthony J. Garrity, Ryan O’Rourke, Lisa Brenan, Patricia Ho, Elizabeth M. Gonzalez, Silvana Konermann, Cory M. Johannessen, Rameen Beroukhim, Pratiti Bandopadhayay, Paul C. Blainey
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0009595

The Viscoelastic Properties of Passive Eye Muscle in Primates. III: Force Elicited by Natural Elongations
Cited by: 19
Author(s): Christian Quaia, Howard S. Ying, Lance M. Optican
Software Mentions: 4
Published: over 16 years ago

10.1371/journal.pgen.1009221

Short-range template switching in great ape genomes explored using pair hidden Markov models
Cited by: 10
Author(s): Conor R Walker, Aylwyn Scally, Nicola De Maio, Nick Goldman
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.50901

A genetic, genomic, and computational resource for exploring neural circuit function
Cited by: 151
Author(s): Fred P. Davis, Aljoscha Nern, Serge Picard, Michael B. Reiser, Gerald M. Rubin, Sean R. Eddy, Gilbert L. Henry
Software Mentions: 4
Published: over 6 years ago

10.1126/sciimmunol.abe1670

MAIT cell activation and dynamics associated with COVID-19 disease severity
Cited by: 138
Author(s): Tiphaine Parrot, Jean‐Baptiste Gorin, Andrea Ponzetta, Kimia T. Maleki, Tobias Kammann, Johanna Emgård, André Perez‐Potti, Takuya Sekine, Olga Rivera‐Ballesteros, Sara Gredmark‐Russ, Olav Rooyackers, Elin Folkesson, Lars Eriksson, Anna Norrby‐Teglund, Hans‐Gustaf Ljunggren, Niklas K. Björkström, Soo Aleman, Marcus Buggert, Jonas Klingström, Kristoffer Strålin, Johan K. Sandberg
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-12730-8

Doping colloidal bcc crystals — interstitial solids and meta-stable clusters
Cited by: 8
Author(s): Ruben Higler, Joris Sprakel
Software Mentions: 4
Published: almost 9 years ago

10.1093/gigascience/giab046

NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data
Cited by: 4
Author(s): Michael D. Linderman, Crystal Paudyal, Musab Shakeel, William L. Kelley, Ali Kashif Bashir, Bruce D. Gelb
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-021-02852-7

High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility
Cited by: 8
Author(s): Benqi Wang, Zunaira Farooq, Lei Chu, Jie Liu, Huadong Wang, Jian Guo, Jinxing Tu, Chaozhi Ma, Cheng Dai, Jia Wen, Jinxiong Shen, Tingdong Fu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0203839

Using wearable sensors to classify subject-specific running biomechanical gait patterns based on changes in environmental weather conditions
Cited by: 40
Author(s): Nizam Uddin Ahamed, Dylan Kobsar, Lauren C. Benson, Christian A. Clermont, Russell Kohrs, Sean T. Osis, Reed Ferber
Software Mentions: 4
Published: almost 8 years ago

10.3389/fonc.2021.620154

Bioinformatics-Based Identification of HDAC Inhibitors as Potential Drugs to Target EGFR Wild-Type Non-Small-Cell Lung Cancer
Cited by: 0
Author(s): Yizhe Wang, Chunlei Zheng, Wenqing Lü, Duo Wang, Cheng Yang, Yang Chen, Kezuo Hou, Jianfei Qi, Yunpeng Liu, Xiaofang Che, Xuejun Hu
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.44889

Identification of compounds that rescue otic and myelination defects in the zebrafish adgrg6 (gpr126) mutant
Cited by: 19
Author(s): Elvira Diamantopoulou, Sarah Baxendale, Antonio de la Vega de León, Anzar Asad, Celia J. Holdsworth, Leïla Abbas, Valerie J. Gillet, Giselle R. Wiggin, Tanya T. Whitfield
Software Mentions: 4
Published: about 7 years ago

10.3390/s120607109

Personal Pervasive Environments: Practice and Experience
Cited by: 5
Author(s): Francisco Ballesteros, Gorka Guardiola, Enrique Soriano
Software Mentions: 4
Published: about 14 years ago

10.4049/jimmunol.1900940

<i>Malat1</i> Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells
Cited by: 45
Author(s): James P. Hewitson, Katie A West, Kylie R. James, Gulab Fatima Rani, Nidhi Sharma Dey, Audrey Romano, Najmeeyah Brown, Sarah A. Teichmann, Paul M. Kaye, Dimitrios Lagos
Software Mentions: 4
Published: about 6 years ago

10.18632/aging.203454

METTL21B is a prognostic biomarker and potential therapeutic target in low-grade gliomas
Cited by: 5
Author(s): Xin Shu, Xinquan Li, Xiaochen Xiang, Qiang Wang, Qingming Wu
Software Mentions: 4
Published: almost 5 years ago

10.7150/jca.59933

Hallmark microRNA signature in liquid biopsy identifies hepatocellular carcinoma and differentiates it from liver metastasis
Cited by: 6
Author(s): Vernon G. Wong, Ming-In Wong, Chi-Tat Lam, Maria Li Lung, Ka-On Lam, Victor Lee
Software Mentions: 4
Published: over 5 years ago

10.1186/s12909-021-02609-8

Evaluation of an international medical E-learning course with natural language processing and machine learning
Cited by: 8
Author(s): Aditya Borakati
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0081760

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
Cited by: 205
Author(s): Shea N. Gardner, Barry G. Hall
Software Mentions: 4
Published: over 12 years ago

10.7554/eLife.42535

An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
Cited by: 77
Author(s): Sergio A. Muñoz-Gómez, Sebastian Hess, Gertraud Burger, B. Franz Lang, Edward Susko, Claudio H. Slamovits, Andrew J. Roger
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.38888

Structural principles of SNARE complex recognition by the AAA+ protein NSF
Cited by: 68
Author(s): K. Ian White, Minglei Zhao, Ucheor B. Choi, Richard A. Pfuetzner, Axel T. Brunger
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-46686-8

High-throughput stability screening for detergent-solubilized membrane proteins
Cited by: 69
Author(s): Vadim Kotov, Kim Bartels, Katharina Veith, Inokentijs Josts, Udaya Kumar Tiruttani Subhramanyam, Christian Günther, Jörg Labahn, Thomas C. Marlovits, Isabel Moraes, Henning Tidow, Christian Löw, María García-Alai
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-47857-3

Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria
Cited by: 37
Author(s): Harrison Edwards, Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Kamlesh D. Patel, Michael Bartsch
Software Mentions: 4
Published: almost 7 years ago

10.1002/cam4.4108

Expression of 5‐methylcytosine regulators is highly associated with the clinical phenotypes of prostate cancer and <i>DNMTs</i> expression predicts biochemical recurrence
Cited by: 3
Author(s): Lin Wang, Guoping Ren, Biaoyang Lin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0224143

Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data
Cited by: 14
Author(s): J. Abecassis, Anne-Sophie Hamy, Cécile Laurent, Benjamin Sadacca, Hélène Bonsang-Kitzis, Fabien Reyal, Jean-Philippe Vert
Software Mentions: 4
Published: over 6 years ago

10.7150/thno.55676

A panel of selected serum protein biomarkers for the detection of aggressive prostate cancer
Cited by: 12
Author(s): Jin Song, Shiyong Ma, Lori J. Sokoll, Rodrigo Vargas Eguez, Naseruddin Höti, Hui Zhang, Phaedre Mohr, Renu Dua, Dattatraya Patil, Kristen Douglas May, Sierra Williams, Rebecca S. Arnold, Martin G. Sanda, Daniel W. Chan, Zhen Zhang
Software Mentions: 4
Published: over 5 years ago

10.1080/17453674.2020.1837422

Association between fixation type and revision risk in total knee arthroplasty patients aged 65 years and older: a cohort study of 265,877 patients from the Nordic Arthroplasty Register Association 2000–2016
Cited by: 6
Author(s): Tero Irmola, Ville Ponkilainen, Keijo Mäkelä, Otto Robertsson, Annette W‐Dahl, Ove Furnes, Anne Marie Fenstad, Alma B Pedersen, Henrik Morville Schrøder, Antti Eskelinen, Mika Niemeläinen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.3000333

Challenges and recommendations to improve the installability and archival stability of omics computational tools
Cited by: 53
Author(s): Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, Jaqueline J. Brito, Russell Littman, Benjamin Statz, Angela Ka Mei Lam, Gargi Dayama, Laura Grieneisen, Lana S. Martin, Jonathan Flint, Eleazar Eskin, Ran Blekhman
Software Mentions: 4
Published: about 7 years ago

10.1111/tpj.14312

μ<scp>CT</scp> trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives
Cited by: 19
Author(s): Nathan Hughes, Hugo R. Oliveira, Nick Fradgley, Fiona Corke, James Cockram, John H. Doonan, Cândida Nibau
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.3340

Effects of knee sleeves on coordination of lower-limb segments in healthy adults during level walking and one-leg hopping
Cited by: 3
Author(s): Chang-Yong Ko, Yun Hee Chang, Bora Jeong, Sungjae Kang, Jeicheong Ryu, Gyoosuk Kim
Software Mentions: 4
Published: about 9 years ago

10.3390/s21134546

Diagnostic of Operation Conditions and Sensor Faults Using Machine Learning in Sucker-Rod Pumping Wells
Cited by: 6
Author(s): João Nascimento, André Laurindo Maitelli, C. W. S. P. Maitelli, Anderson Luiz de Oliveira Cavalcanti
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-8-232

TMM@: a web application for the analysis of transmembrane helix mobility
Cited by: 2
Author(s): Lars Skjærven, Inge Jonassen, Nathalie Reuter
Software Mentions: 4
Published: about 19 years ago

10.1128/mSystems.00211-19

Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning
Cited by: 16
Author(s): Finlay Maguire, Muhammad Attiq Rehman, Catherine D. Carrillo, Moussa S. Diarra, Robert G. Beiko
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12872-021-02147-7

Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy
Cited by: 2
Author(s): Jing Xu, Xiangdong Liu, Qiang Dai
Software Mentions: 4
Published: about 5 years ago

10.1002/1878-0261.12895

Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy
Cited by: 15
Author(s): Xiangyong Li, Chi Zhou, Ke Chen, Bingding Huang, Qi Liu, Yue Hao
Software Mentions: 4
Published: over 5 years ago

10.1186/1751-0473-8-20

MIA - A free and open source software for gray scale medical image analysis
Cited by: 35
Author(s): Gert Wollny, Peter Kellman, María J. Ledesma-Carbayo, Matthew M. Skinner, Jean‐Jacques Hublin, Thomas Hierl
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0233336

Artificial intelligence may offer insight into factors determining individual TSH level
Cited by: 7
Author(s): Prasanna Santhanam, Tanmay Nath, Faiz Khan Mohammad, Rexford S. Ahima
Software Mentions: 4
Published: about 6 years ago

10.1016/j.stem.2020.06.020

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
Cited by: 251
Author(s): Jinwook Choi, Jong-Eun Park, Georgia Tsagkogeorga, Motoko Yanagita, Bon‐Kyoung Koo, Namshik Han, Joo Hyeon Lee
Software Mentions: 4
Published: almost 6 years ago

10.1089/bio.2017.0014

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking
Cited by: 19
Author(s): Hocine Bendou, Lunga Sizani, Tim Reid, Carmen Swanepoel, Toluwaleke Ademuyiwa, Roxana Merino-Martinez, Heimo Meuller, Akin Abayomi, Alan Christoffels
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-6-132

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
Cited by: 457
Author(s): Bjoern Peters, Alessandro Sette
Software Mentions: 4
Published: about 21 years ago

10.1001/jamanetworkopen.2020.12887

Association of Timely Outpatient Mental Health Services for Youths After Psychiatric Hospitalization With Risk of Death by Suicide
Cited by: 52
Author(s): Cynthia A. Fontanella, Lynn A. Warner, Danielle L. Steelesmith, Guy Brock, Jeffrey A. Bridge, John V. Campo
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41419-020-03232-z

Molecular subtype-specific responses of colon cancer cells to the SMAC mimetic Birinapant
Cited by: 12
Author(s): Michael Fichtner, Emir Bozkurt, Manuela Salvucci, Christopher McCann, Katherine McAllister, Luise Halang, Heiko Düßmann, Sinéad Kinsella, Nyree Crawford, Tamas Sessler, Daniel B. Longley, Jochen H M Prehn
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-021-03015-w

Multi-parametric MRI phenotype with trustworthy machine learning for differentiating CNS demyelinating diseases
Cited by: 4
Author(s): Jing Huang, Bowen Xin, Xiuying Wang, Zhigang Qi, Hui Dong, Kuncheng Li, Yun Zhou, Jie Lu
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1006077

New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images
Cited by: 1
Author(s): Ilya Patrushev, Christina James-Zorn, Aldo Ciau-Uitz, Roger Patient, Michael J. Gilchrist
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.str.2011.03.023

Insights into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13
Cited by: 79
Author(s): Mohammad W. Bahar, Stephen C. Graham, David I. Stuart, Jonathan M. Grimes
Software Mentions: 4
Published: about 15 years ago

10.1136/esmoopen-2020-001040

Prediction of relapse-free survival according to adjuvant chemotherapy and regulator of chromosome condensation 2 (RCC2) expression in colorectal cancer
Cited by: 4
Author(s): Christian H. Bergsland, Jarle Bruun, Marianne G. Guren, Aud Svindland, Merete Bjørnslett, Jørgen Smeby, Merete Hektoen, Matthias Kolberg, Enric Domingo, Teijo Pellinen, Ian Tomlinson, David Kerr, David N. Church, Arild Nesbakken, Anita Sveen, Ragnhild A. Lothe
Software Mentions: 4
Published: over 6 years ago

10.1038/srep36493

Big genomics and clinical data analytics strategies for precision cancer prognosis
Cited by: 18
Author(s): Ghim Siong Ow, Vladimir A. Kuznetsov
Software Mentions: 4
Published: over 9 years ago

10.3389/fpsyg.2018.02322

Using Card Sorting to Explore the Mental Representation of Energy Transition Pathways Among Laypeople
Cited by: 6
Author(s): Rouven Doran, Gisela Böhm, Daniel Hanss
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1009557

Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes
Cited by: 51
Author(s): S Wang, Huimin Li, Mei Song, Ziyu Tao, Tao Wu, Zaoke He, Xiangyu Zhao, Kai Wu, Xue Song Liu
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.54082

Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity
Cited by: 10
Author(s): Tarun Kumar, Leo Blondel, Cassandra G. Extavour
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.10558

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
Cited by: 1
Author(s): Hanna Kranas, Irina Tuszyńska, Bartek Wilczyński
Software Mentions: 4
Published: over 5 years ago

10.1042/BSR20203812

An autophagy-related prognostic signature associated with immune microenvironment features of uveal melanoma
Cited by: 8
Author(s): Zhuotao Zheng, Lingyue Zhang, Zewei Tu, Yan Deng, Xingtian Yin
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0118330

Primates Decline Rapidly in Unprotected Forests: Evidence from a Monitoring Program with Data Constraints
Cited by: 34
Author(s): Francesco Rovero, Arafat S. Mtui, Amani Kitegile, Philipo Jacob, Alessandro Araldi, Simone Tenan
Software Mentions: 4
Published: over 11 years ago

10.1186/s12918-016-0315-y

A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes
Cited by: 8
Author(s): Sujuan Wu, Junyi Li, Mushui Cao, Jing Yang, Yixue Li, Yuanyuan Li
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0224695

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology
Cited by: 13
Author(s): Lisa Sakamoto, Hiromi Kajiya‐Kanegae, Koji Noshita, Hideki Takanashi, Mariko Kobayashi, Toru Kudo, Kentarô Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi, Hiroyoshi Iwata
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202153

Upregulation of KIF20A promotes tumor proliferation and invasion in renal clear cell carcinoma and is associated with adverse clinical outcome
Cited by: 30
Author(s): Xiaohan Ren, Xinglin Chen, Yisheng Ji, Liang-In Lin, Yunxin Li, Chao Qin, Kai Fang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5779-x

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function
Cited by: 39
Author(s): Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka, John A. Capra
Software Mentions: 4
Published: about 7 years ago

10.1128/AEM.02278-20

Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: a Case Study
Cited by: 5
Author(s): Jonathan Sogin, Gabriela López-Velasco, Burcu Yordem, Cari Lingle, John David, Mario Çobo, Randy W. Worobo
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102275

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice
Cited by: 52
Author(s): Huimin Li, Xinhui Wang, Xinyue Lu, Hongxin Zhu, Sheng Li, Shiwei Duan, Xinzhi Zhao, Fuquan Zhang, Gil Alterovitz, Fudi Wang, Qiang Li, Xiao-Li Tian, Mingqing Xu
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-51245-2

Environmental factors and river network position allow prediction of benthic community assemblies: A model of nematode metacommunities
Cited by: 10
Author(s): Birgit Gansfort, Walter Traunspurger
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: about 8 years ago

10.3390/microorganisms8111631

Rapid Changes in Microbial Community Structures along a Meandering River
Cited by: 11
Author(s): Perrine Cruaud, Adrien Vigneron, Caetano C. Dorea, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms8070987

Analysis of Tick Surface Decontamination Methods
Cited by: 13
Author(s): Angeline Hoffmann, Volker Fingerle, Matthias Noll
Software Mentions: 4
Published: about 6 years ago

10.1007/s00204-021-03127-8

Fluorescent tagging of endogenous Heme oxygenase-1 in human induced pluripotent stem cells for high content imaging of oxidative stress in various differentiated lineages
Cited by: 11
Author(s): Kirsten E. Snijders, András Fehér, Zsuzsanna Táncos, István Bock, Annamária Téglási, Linda van den Berk, Marije Niemeijer, Peter Bouwman, Sylvia E. Le Dévédec, Martijn J. Moné, Rob Van Rossom, Manoj Kumar, Anja Wilmes, Paul Jennings, Cathérine Verfaillie, Julianna Kobolák, Bas ter Braak, András Dinnyés, Bob van de Water
Software Mentions: 4
Published: almost 5 years ago

10.12688/wellcomeopenres.16320.2

Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data
Cited by: 2
Author(s): Carolyne Ndila, Vysaul Nyirongo, Alexander Macharia, Anna E. Jeffreys, Kate Rowlands, Christina Hubbart, George B.J. Busby, Gavin Band, Rosalind M. Harding, Kirk A. Rockett, Thomas N. Williams
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0235089

Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation
Cited by: 26
Author(s): Waltram Ravelombola, Jun Qin, Ainong Shi, Liana Nice, Yong Bao, Aaron J. Lorenz, J. H. Orf, Nevin D. Young, Senyu Chen
Software Mentions: 4
Published: about 6 years ago

10.1002/ece3.3847

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

10.1186/s12870-018-1611-z

Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens
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Author(s): Igor Fesenko, Regina Azarkina, Ilya Kirov, Andrei Kniazev, Anna Filippova, Ekaterina N. Grafskaia, В. Н. Лазарев, Victor G. Zgoda, Ivan Butenko, Olga Bukato, Irina Lyapina, Dmitry Nazarenko, S. N. Elansky, Anna Mamaeva, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0232436

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

10.1371/journal.pone.0237741

A step towards Balkan Capsicum annuum L. core collection: Phenotypic and biochemical characterization of 180 accessions for agronomic, fruit quality, and virus resistance traits
Cited by: 17
Author(s): Amol N. Nankar, Velichka Todorova, Ivanka Tringovska, Gancho Pasev, Vesela Radeva-Ivanova, Valentina Ivanova, D. Kostova
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0241374

The dark ventral patch: A bimodal flexible trait related to male competition in red deer
Cited by: 5
Author(s): Juan Carranza, Eva de la Peña, Concha Mateos Martín, Javier Pérez‐González, Susana Alarcos, Jerónimo Torres-Porras, Juliana Valencia, Cristina B. Sánchez-Prieto, Leticia Castillo
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2018.11.032

Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming
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Author(s): Andreia Gomes, Ilia Kurochkin, Betty Chang, Michael G. Daniel, Kenneth Law, Namita Satija, Alexander Lachmann, Zichen Wang, Lino Ferreira, Avi Ma’ayan, Benjamin Chen, Dmitri Papatsenko, Ihor R. Lemischka, Kateri Moore, Carlos Filipe Pereira
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-019-0306-9

Mechanistic insights into the evolution of DUF26-containing proteins in land plants
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Software Mentions: 4
Published: over 7 years ago

10.1093/g3journal/jkab085

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

10.1371/journal.pone.0239609

Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selection
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Author(s): Kiran Baral, Bruce Coulman, Bill Biligetu, Yong‐Bi Fu
Software Mentions: 4
Published: almost 6 years ago

10.3390/cells8101117

Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles
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Author(s): Stefaan Verhulst, Tania Roskams, Pau Sancho–Bru, Leo A. van Grunsven
Software Mentions: 4
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10.1186/s12859-020-03601-7

AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids
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Author(s): Alexander Coulton, Keith J. Edwards
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0157343

Exploring the Structure of Spatial Representations
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Author(s): Tobias Madl, Stan Franklin, Ke Chen, Robert Trappl, Daniela Montaldi
Software Mentions: 4
Published: about 10 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
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Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0255977

A machine learning approach to predict extreme inactivity in COPD patients using non-activity-related clinical data
Cited by: 1
Author(s): B. Aguilaniu, David J. Hess, É. Kelkel, Amandine Briault, Marie Destors, Jacques Boutros, Pei Zhi Li, Anestis Antoniadis
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2105-7-335

AMDA: an R package for the automated microarray data analysis
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Author(s): Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi‐Castagnoli
Software Mentions: 4
Published: about 20 years ago

10.3389/fphar.2019.00005

Exposure of Infants to Isoniazid via Breast Milk After Maternal Drug Intake of Recommended Doses Is Clinically Insignificant Irrespective of Metaboliser Status. A Physiologically-Based Pharmacokinetic (PBPK) Modelling Approach to Estimate Drug Exposure of Infants via Breast-Feeding
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Author(s): Estella Dora Germaine Garessus, Hans Mielke, Ursula Gundert‐Remy
Software Mentions: 4
Published: over 7 years ago

10.1084/jem.20150907

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
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Author(s): Alejandro V. Villarino, Giuseppe Sciumè, Fred P. Davis, S. Iwata, Beatrice Zitti, Gertraud W. Robinson, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: almost 9 years ago

10.1155/2020/2137319

Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Dengyong Xu, Yuzi Xu, Yiming Lv, Fei Wu, Yunlong Liu, Ming Zhu, Dake Chen, Bingjun Bai
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-018-2150-1

Identification of residue pairing in interacting β-strands from a predicted residue contact map
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Author(s): Wenzhi Mao, Tong Wang, Wenxuan Zhang, H. Gong
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pntd.0008212

Potential geographic distribution of the tiger mosquito Aedes albopictus (Skuse, 1894) (Diptera: Culicidae) in current and future conditions for Colombia
Cited by: 12
Author(s): Emmanuel Echeverry-Cárdenas, Carolina López-Castañeda, Juan D. Carvajal-Castro, Oscar Alexander Aguirre-Obando
Software Mentions: 4
Published: about 5 years ago

10.3389/fcell.2021.631982

Integrated Protein–Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma
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Author(s): Li Tian, Tong Chen, Jiaju Lü, Jing Yan, Yuting Zhang, Peifang Qin, Sentai Ding, Yali Zhou
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00484-19

Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia
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Author(s): Feargal J. Ryan, Damian Paul Drew, Chloe A. Douglas, Lex E. X. Leong, Max Moldovan, Miriam A. Lynn, Naomi Fink, Anastasia Sribnaia, Irmeli A. Penttila, Andrew J McPhee, Carmel T Collins, Maria Makrides, Robert Gibson, Geraint B. Rogers, David J. Lynn
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12862-019-1523-z

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages
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Software Mentions: 4
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10.1186/s13321-021-00535-x

Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
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Software Mentions: 4
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