pypi: py | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-24775-4

A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue
Cited by: 22
Author(s): Chih-Hung Chuang, Shean‐Jaw Chiou, Tian−Lu Cheng, Yeng‐Tseng Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-48200-6

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
Cited by: 27
Author(s): Carlos Eduardo Posada-Perlaza, Adán Andrés Ramírez Rojas, Paola Porras, Boahemaa Adu-Oppong, Ana María Botero-Coy, Félix Hernández, Juan Manuel Anzola, Lorena Díaz, Gautam Dantas, Alejandro Reyes, María Mercedes Zambrano
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-48155-8

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
Cited by: 11
Author(s): Carsten Krichel, Christina Möckel, Oliver Schillinger, Pitter F. Huesgen, Heinrich Sticht, Birgit Strodel, Oliver H. Weiergräber, Dieter Willbold, Philipp Neudecker
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-66791-3

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters
Cited by: 43
Author(s): Matteo Bergamaschi, Christian Maltecca, Constantino Schillebeeckx, Nathan P. McNulty, Charles V. Schwab, Caleb M Shull, Justin Fix, Francesco Tiezzi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-80769-1

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
Cited by: 41
Author(s): Germano Heinzelmann, Michael K. Gilson
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-90017-9

A python code for automatic construction of Fischer plots using proxy data
Cited by: 2
Author(s): Dayong Yang, Yongjian Huang, Zongyang Chen, Qinghua Huang, Yong’an Ren, Chengshan Wang
Software Mentions: 3
Published: over 3 years ago

10.3390/s18051312

Infrastructure for Integration of Legacy Electrical Equipment into a Smart-Grid Using Wireless Sensor Networks
Cited by: 21
Author(s): Paulo Régis C. de Araújo, Raimir Holanda Filho, Joel J. P. C. Rodrigues, João Paolo C. M. Oliveira, Stéphanie Alencar Braga
Software Mentions: 3
Published: over 6 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 11 years ago

10.1128/mBio.02376-18

Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments
Cited by: 38
Author(s): John Bird, Eric D. Tague, Laura Zinke, Jenna M. Schmidt, Andrew D. Steen, Brandi Kiel Reese, Ian P. G. Marshall, Gordon Webster, Andrew J. Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd
Software Mentions: 3
Published: over 5 years ago

10.1038/s41396-019-0468-y

Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert
Cited by: 50
Author(s): Gherman Uritskiy, Samantha Getsin, Adam Munn, Benito Gómez-Silva, Alfonso F. Dávila, B. Glass, James Taylor, Jocelyne DiRuggiero
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.33281

Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network
Cited by: 14
Author(s): Andrea Ferrario, Robert Merrison-Hort, Stephen R Soffe, Roman Borisyuk
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.27455

Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET
Cited by: 58
Author(s): Johannes M. Keegstra, Keita Kamino, François Anquez, Milena D. Lazova, Thierry Emonet, Thomas S. Shimizu
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.36278

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
Cited by: 77
Author(s): Christopher E. Laumer, Harald R. Gruber‐Vodicka, Michael G. Hadfield, Vicki B. Pearse, Ana Riesgo, John C. Marioni, Gonzalo Giribet
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.22086

Molecular architecture of the 90S small subunit pre-ribosome
Cited by: 116
Author(s): Qiaoyan Sun, Xing Zhu, Qiong Jia, Wenling An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng‐Qiu Dong, Keqiong Ye
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.60467

Qki regulates myelinogenesis through Srebp2-dependent cholesterol biosynthesis
Cited by: 9
Author(s): Xin Zhou, Sonyo Shin, Chenxi He, Qiang Zhang, Matthew N. Rasband, Jiangong Ren, Congxin Dai, Rocío I. Zorrilla-Veloz, Takashi Shingu, Liang Yuan, Yunfei Wang, Yiwen Chen, Fei Lan, Jian Hu
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22062861

In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus
Cited by: 5
Author(s): Colleen Varaidzo Manyumwa, Özlem Tastan Bishop
Software Mentions: 3
Published: over 3 years ago

10.2196/19263

Efficiency of Computer-Aided Facial Phenotyping (DeepGestalt) in Individuals With and Without a Genetic Syndrome: Diagnostic Accuracy Study
Cited by: 19
Author(s): Jean Tori Pantel, Nurulhuda Hajjir, Magdalena Danyel, Jonas Elsner, Angela Teresa Abad-Perez, Peter C. Hansen, Stefan Mundlos, Malte Spielmann, Denise Horn, Claus‐Eric Ott, Martin A. Mensah
Software Mentions: 3
Published: about 4 years ago

10.1523/ENEURO.0305-18.2020

Circuit and Cellular Mechanisms Facilitate the Transformation from Dense to Sparse Coding in the Insect Olfactory System
Cited by: 16
Author(s): Rinaldo Betkiewicz, Benjamin Lindner, Martin Paul Nawrot
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.01485

Key Features Relevant to Select Antigens and TCR From the MHC-Mismatched Repertoire to Treat Cancer
Cited by: 8
Author(s): Stefan Audehm, Manuel Glaser, Matteo Pecoraro, Eva Bräunlein, Sabine Mall, Klar Richard, Manuel Effenberger, Julian J Albers, Henrique Bianchi, Janet Kerstin Peper, Nahid Yusufi, Dirk H. Busch, Stefan Stevanović, Matthias Mann, Iris Antes, Angela M. Krackhardt
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules26133882

Antiviral Activity of Metabolites from Peruvian Plants against SARS-CoV-2: An In Silico Approach
Cited by: 21
Author(s): Luis Daniel Goyzueta-Mamani, Haruna Luz Barazorda-Ccahuana, Karel Mena-Ulecia, Miguel Á. Chávez-Fumagalli
Software Mentions: 2
Published: over 3 years ago

10.3389/fmolb.2015.00056

A script to highlight hydrophobicity and charge on protein surfaces
Cited by: 83
Author(s): Dominique Hagemans, Ianthe A. E. M. van Belzen, Tania Morán Luengo, Stefan Rüdiger
Software Mentions: 2
Published: about 9 years ago

10.1038/srep29681

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing
Cited by: 162
Author(s): Jisoo Shin, Sooin Lee, Min‐Jeong Go, Sang Yup Lee, Sun Chang Kim, Chul‐Ho Lee, Byung-Kwan Cho
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj-cs.264

Implementation of adaptive integration method for free energy calculations in molecular systems
Cited by: 0
Author(s): Christopher A. Mirabzadeh, F. Marty Ytreberg
Software Mentions: 2
Published: over 4 years ago

10.3390/genes12050644

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
Cited by: 32
Author(s): Carlus Deneke, Holger Brendebach, Laura Uelze, Maria Blettner, Burkhard Malorny, Simon H. Tausch
Software Mentions: 2
Published: over 3 years ago

10.1186/s12711-016-0270-5

Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota
Cited by: 37
Author(s): Jinmei Ding, Lele Zhao, Lifeng Wang, Wenjing Zhao, Zhengxiao Zhai, Li Leng, Yuxiang Wang, Chuan He, Yan Zhang, Heping Zhang, Hui Li, He Meng
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-28630-4

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana
Cited by: 17
Author(s): Julie A. Koester, Chris T. Berthiaume, Naozumi Hiranuma, Micaela S. Parker, Vaughn Iverson, Rhonda Morales, Walter L. Ruzzo, E. Virginia Armbrust
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-31237-4

Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors
Cited by: 8
Author(s): Vivek S. Bharadwaj, Seonah Kim, Michael T. Guarnieri, Michael F. Crowley
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.05503

Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation
Cited by: 140
Author(s): Christopher E. Laumer, Andreas Hejnol, Gonzalo Giribet
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2019.02296

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments
Cited by: 12
Author(s): Stefanie Böhnke, Katharina Saß, Giorgio Gonnella, Alexander Diehl, Charlotte Kleint, Wolfgang Bach, Rebecca Zitoun, Andrea Koschinsky, Daniela Indenbirken, Sylvia G. Sander, Stefan Kurtz, Mirjam Perner
Software Mentions: 2
Published: about 5 years ago

10.3390/molecules26040777

A Multi-Objective Approach for Drug Repurposing in Preeclampsia
Cited by: 3
Author(s): Eduardo Tejera, Yunierkis Pérez-Castillo, Andrea Chamorro, Alejandro Cabrera-Andrade, Marı́a Eugenia Sánchez
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.7040

Composition and dynamics of the bacterial communities present in the post-slaughter environment of farmed Atlantic salmon (Salmo salarL.) and correlations to gelatin degrading activity
Cited by: 2
Author(s): Ása Jacobsen, Svein‐Ole Mikalsen, Hóraldur Joensen, Jonhard Eysturskarð
Software Mentions: 2
Published: over 5 years ago

10.1107/S2059798319010519

Methods for merging data sets in electron cryo-microscopy
Cited by: 29
Author(s): Max E. Wilkinson, Aman Kumar, Ana Casañal
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-020-02014-2

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Cited by: 74
Author(s): Vanessa R. Marcelino, Philip Thomas Lanken Conradsen Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell, Edward C. Holmes
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-61435-y

Phonatory and articulatory representations of speech production in cortical and subcortical fMRI responses
Cited by: 17
Author(s): João Correia, Cesar Caballero‐Gaudes, Sara Guediche, Manuel Carreiras
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.6984

CAM: an alignment-free method to recover phylogenies using codon aversion motifs
Cited by: 8
Author(s): Justin Miller, Lauren M. McKinnon, Michael F. Whiting, Perry G. Ridge
Software Mentions: 2
Published: over 5 years ago

10.1002/mbo3.135

Symbiotic prokaryotic communities from different populations of the giant barrel sponge, Xestospongia muta
Cited by: 43
Author(s): Cara L. Fiore, Jessica K. Jarett, Michael P. Lesser
Software Mentions: 2
Published: about 11 years ago

10.1111/1751-7915.12380

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities
Cited by: 19
Author(s): Kate O’Brien, Michael S. Chimenti, Morgan B. Farnell, Tom Tabler, Thomas B. Bair, Joey Lynn Bray, Matthew W. Nonnenmann
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.11552

Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
Cited by: 6
Author(s): Mohini Yadav, Manabu Igarashi, Norifumi Yamamoto
Software Mentions: 2
Published: over 3 years ago

10.1186/s12866-019-1425-7

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice
Cited by: 31
Author(s): Pedro J. Torres, Danalea V. Skarra, Brian Ho, Lillian Sau, Arya R. Anvar, Scott T. Kelley, Varykina G. Thackray
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0080847

Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis
Cited by: 88
Author(s): Patrícia Martins, Daniel F. R. Cleary, Ana C. C. Pires, Ana María Rodrigues, Victor Quintino, Ricardo Calado, Newton C. M. Gomes
Software Mentions: 2
Published: about 11 years ago

10.3390/ijms21197102

Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction
Cited by: 10
Author(s): Fabian Mayr, Gabriele Möller, Ulrike Garscha, Jana Fischer, Patricia Rodríguez Castaño, Silvia G. Inderbinen, Veronika Temml, Birgit Waltenberger, Stefan Schwaiger, Rolf W. Hartmann, Christian Gege, Stefan Martens, Alex Odermatt, Amit V. Pandey, Oliver Werz, Jerzy Adamski, Hermann Stuppner, Daniela Schuster
Software Mentions: 2
Published: about 4 years ago

10.1016/j.gpb.2019.11.008

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Cited by: 48
Author(s): Tiansheng Zhu, Yi Zhu, Yue Xuan, Huanhuan Gao, Xue Cai, Sander R. Piersma, Thang V. Pham, Tim Schelfhorst, Richard R Goeij De Haas, Irene V. Bijnsdorp, Rui Sun, Yue Liang, Guan Ruan, Qiushi Zhang, Mo Hu, Yue Zhou, Winan J. van Houdt, Tessa Y.S. Le Large, Jacqueline Cloos, Anna Wojtuszkiewicz, Danijela Koppers-Lalić, Franziska Böttger, Chantal Scheepbouwer, Ruud H. Brakenhoff, Geert J.L.H. van Leenders, Jan N.M. IJzermans, John W.M. Martens, Renske D.M. Steenbergen, Nicole C.T. van Grieken, Sathiyamoorthy Selvarajan, Sangeeta Mantoo, Sze S. Lee, Serene Yeow, Syed Muhammad Fahmy Alkaff, Nan Xiang, Yaoting Sun, Xiao Yi, Sheng Dai, Wei Liu, Li Tian, Zhicheng Wu, Xiao Liang, Man Wang, Yingkuan Shao, Xi Zheng, Kailun Xu, Qin Yang, Yifan Meng, Cong Lu, Jiang Zhu, Jianming Zheng, Bo Wang, Sai Lou, Yibei Dai, Chao Xu, Chunjing Yu, Hua‐Zhong Ying, Tony Kiat-Hon Lim, Jianmin Wu, Xiaofei Gao, Zhongzhi Luan, Xiaodong Teng, Peng Wu, Shiang Huang, Zhihua Tao, N. Gopalakrishna Iyer, Shuigeng Zhou, Wenguang Shao, Henry H N Lam, Ding Ma, Jiafu Ji, Oi Lian Kon, Shu Zheng, Ruedi Aebersold, Connie R. Jiménez, Tiannan Guo
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21218373

How Many Messenger RNAs Can Be Translated by the START Mechanism?
Cited by: 1
Author(s): Laurence Despons, Franck Martin
Software Mentions: 2
Published: about 4 years ago

10.1186/s12866-017-1042-2

Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle
Cited by: 37
Author(s): Mohamed Zeineldin, James Lowe, Elsbeth D. Grimmer, María R C de Godoy, Mohamed M. Ghanem, Yassein M. Abd El-Raof, Brian Aldridge
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms22041643

Biochemical and Computational Studies of the Interaction between a Glucosamine Derivative, NAPA, and the IKKα Kinase
Cited by: 3
Author(s): Mariangela Lopreiato, Samuele Di Cristofano, Rossana Cocchiola, Alessia Mariano, Libera Guerrizio, Roberto Scandurra, Luciana Mosca, Domenico Raimondo, Anna Scotto d’Abusco
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12866-017-1098-z

Comparison of rumen bacterial communities in dairy herds of different production
Cited by: 50
Author(s): Nagaraju Indugu, Bonnie Vecchiarelli, Linda D. Baker, James D. Ferguson, Jairam Vanamala, Dipti Pitta
Software Mentions: 2
Published: about 7 years ago

10.3390/s20020547

Benchmarking Deep Trackers on Aerial Videos
Cited by: 9
Author(s): Abu Md Niamul Taufique, Breton Minnehan, Andreas Savakis
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/gix003

drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes
Cited by: 16
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-019-2726-4

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources
Cited by: 0
Author(s): D. Perez-Gil, Francisco J. López, Joaquín Dopazo, Pablo Marín-García, Augusto Rendon, Ignacio Medina
Software Mentions: 2
Published: over 5 years ago

10.3390/s21165310

Residential Water Meters as Edge Computing Nodes: Disaggregating End Uses and Creating Actionable Information at the Edge
Cited by: 3
Author(s): Nour A. Attallah, Jeffery S. Horsburgh, Arle S. Beckwith, Robb J. Tracy
Software Mentions: 2
Published: over 3 years ago

10.1186/s12885-017-3948-3

CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension
Cited by: 22
Author(s): Ricardo Celestino, Torfinn Nome, Ana Pestana, Andreas Hoff, A. Pedro Gonçalves, Luı́sa Pereira, Bruno Cavadas, Catarina Eloy, Trine Bjøro, Manuel Sobrinho-Simões, Rolf Inge Skotheim, Paula Soares
Software Mentions: 2
Published: almost 7 years ago

10.1021/acs.jpca.0c10845

Optimal Solution to the Torsional Coefficient Fitting Problem in Force Field Parametrization
Cited by: 4
Author(s): Adrian Kania, Krzysztof Sarapata, Michał Gucwa, Anna Wójcik-Augustyn
Software Mentions: 2
Published: over 3 years ago

10.1186/s12911-018-0595-9

A pattern learning-based method for temporal expression extraction and normalization from multi-lingual heterogeneous clinical texts
Cited by: 12
Author(s): Tianyong Hao, Xiaoju Pan, Zhiying Gu, Yingying Qu, Heng Weng
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1090

Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism
Cited by: 54
Author(s): Henrik Stranneheim, Martin Engvall, K Naess, Nicole Lesko, Pontus Larsson, Mats Dahlberg, Robin Andeer, Anna Wredenberg, Christoph Freyer, Michela Barbaro, Helene Bruhn, Tesfail Emahazion, Måns Magnusson, Rolf Wibom, Rolf Zetterström, Valtteri Wirta, Ulrika von Döbeln, Anna Wedell
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-11-408

Small RNAs, DNA methylation and transposable elements in wheat
Cited by: 86
Author(s): Dario Cantu, Leonardo Sebastián Vanzetti, Adam Sumner, Martin Dubcovsky, Marta Matvienko, Assaf Distelfeld, Richard W. Michelmore, Jorge Dubcovsky
Software Mentions: 2
Published: over 14 years ago

10.3390/ijms22136859

Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera
Cited by: 1
Author(s): Chun-Hsiung Wang, Donghua Chen, Shih-Hsin Huang, Yimin A. Wu, Yiyun Chen, Y. Hwu, David Bushnell, Roger D. Kornberg, Wen Ho Chang
Software Mentions: 2
Published: over 3 years ago

10.3934/microbiol.2018.2.240

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure
Cited by: 2
Author(s): Inês Barros, Hugo J.C. Froufe, George Marnellos, Conceição Egas, Jennifer A. Delaney, Michele Clamp, Ricardo Serrão Santos, Raúl Bettencourt
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-017-3541-9

An approach of identifying differential nucleosome regions in multiple samples
Cited by: 8
Author(s): Lingjie Liu, Jingjing Xie, Xiao Sun, Kun Luo, Zhaohui S. Qin, Hongde Liu
Software Mentions: 2
Published: almost 8 years ago

10.1038/hortres.2017.29

An eFP browser for visualizing strawberry fruit and flower transcriptomes
Cited by: 53
Author(s): Charles Hawkins, Julie Caruana, Jiaming Li, Chris Zawora, Omar Darwish, Jun Wu, Nadim W. Alkharouf, Zhongchi Liu
Software Mentions: 2
Published: over 7 years ago

10.1186/s12858-015-0048-3

Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets
Cited by: 10
Author(s): Terrence S. Neumann, Elise A. Span, Kelsey S. Kalous, Robert D. Bongard, Adam Gastonguay, Michael Lepley, Raman G. Kutty, Jaladhi Nayak, Chris Bohl, Rachel G. Lange, Majher I. Sarker, Marat R. Talipov, Rajendra Rathore, Ramani Ramchandran, Daniel S. Sem
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-016-2883-z

Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade
Cited by: 49
Author(s): Jasna Kovač, Robert W. Miller, Laura M. Carroll, David J. Kent, Jiahui Jian, Sarah M. Beno, Martin Wiedmann
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-3271-4

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection
Cited by: 25
Author(s): Ajay Kumar Mishra, G Duraisamy, J. Matoušek, Sebastjan Radišek, Branka Javornik, Jernej Jakše
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2016.00316

Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata
Cited by: 35
Author(s): Christophe Vieira, Aschwin H. Engelen, Linda Guentas, Tânia Aires, Fanny Houlbrèque, Julie Gaubert, Ester A. Serrão, Olivier De Clerck, Claude Payri
Software Mentions: 2
Published: over 8 years ago

10.3389/fnhum.2021.638052

Deep-Learning-Based Multivariate Pattern Analysis (dMVPA): A Tutorial and a Toolbox
Cited by: 5
Author(s): Karl Kuntzelman, Jacob Williams, Phui Cheng Lim, Ashok Samal, Prahalada Rao, Matthew Johnson
Software Mentions: 2
Published: over 3 years ago

10.1107/S2052252520013238

Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography
Cited by: 1
Author(s): Isabelle Martiel, Chia‐Ying Huang, P. Villanueva-Pérez, Ezequiel Panepucci, Shibom Basu, Martin Caffrey, Bill Pedrini, Oliver Bunk, Marco Stampanoni, Meitian Wang
Software Mentions: 2
Published: about 4 years ago

10.2218/ijdc.v12i2.581

Navigating Unmountable Media with the Digital Forensics XML File System
Cited by: 0
Author(s): Alexander J. Nelson, Alexandra Chassanoff, Alexandra Holloway
Software Mentions: 2
Published: almost 55 years ago

10.1371/journal.pgen.1007199

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
Cited by: 19
Author(s): Rohan Maddamsetti, Richard E. Lenski
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijerph16081375

Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment
Cited by: 25
Author(s): Hamza Mbareche, Marc Veillette, Jonathan Pilote, Valérie Létourneau, Caroline Duchaine
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1002397

AutoClickChem: Click Chemistry in Silico
Cited by: 38
Author(s): Jacob D. Durrant, J. Andrew McCammon
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1007710

Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein
Cited by: 22
Author(s): Lenka Stejskal, William D. Lees, David S. Moss, Machaela Palor, Richard J. Bingham, Adrian J. Shepherd, Joe Grove
Software Mentions: 2
Published: over 4 years ago

10.1117/1.JBO.25.11.112903

Deep learning in photoacoustic tomography: current approaches and future directions
Cited by: 75
Author(s): Andreas Hauptmann, Ben Cox
Software Mentions: 2
Published: about 4 years ago

10.1186/s12863-016-0455-5

Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources
Cited by: 13
Author(s): Ana S. B. Rodrigues, Sara E. Silva, Francisco Pina‐Martins, João Loureiro, Mariana Castro, Karim Gharbi, Kevin P. Johnson, Christopher H. Dietrich, Paulo A. V. Borges, J. A. Quartau, Chris D. Jiggins, Octávio S. Paulo, Sofia G. Seabra
Software Mentions: 2
Published: about 8 years ago

10.1186/1752-153X-6-144

Python algorithms in particle tracking microrheology
Cited by: 8
Author(s): Timo Maier, Tamás Haraszti
Software Mentions: 2
Published: almost 12 years ago

10.3390/cells8070767

Ensemble of Deep Recurrent Neural Networks for Identifying Enhancers via Dinucleotide Physicochemical Properties
Cited by: 27
Author(s): Kok Keng Tan, Nguyen Quoc Khanh Le, Hui‐Yuan Yeh, Matthew Chin Heng Chua
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2019.01310

Probing the Druggablility on the Interface of the Protein–Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer
Cited by: 5
Author(s): Liting Shen, Yuan Yuan, Yanzhi Guo, Menglong Li, Chuan Li, Xuemei Pu
Software Mentions: 2
Published: about 5 years ago

10.1093/dnares/dsy035

Landscape of gene transposition–duplication within the Brassicaceae family
Cited by: 19
Author(s): Dong Ha Oh, Maheshi Dassanayake
Software Mentions: 2
Published: about 6 years ago

10.3390/v9080226

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing
Cited by: 9
Author(s): Alison M. Morse, Kaitlyn R. Calabro, Justin M. Fear, David C. Bloom, Lauren McIntyre
Software Mentions: 2
Published: over 7 years ago

10.1002/jcc.26198

<scp>MkVsites</scp>: A tool for creating <scp>GROMACS</scp> virtual sites parameters to increase performance in all‐atom molecular dynamics simulations
Cited by: 14
Author(s): Per Larsson, Rosita Kneiszl, Erik Marklund
Software Mentions: 2
Published: over 4 years ago

10.3390/biom11040573

Molecular Simulation-Based Investigation of Highly Potent Natural Products to Abrogate Formation of the nsp10–nsp16 Complex of SARS-CoV-2
Cited by: 12
Author(s): Anwar Mohammad, Eman Alshawaf, Sulaiman K. Marafie, Mohamed Abu‐Farha, Fahd Al-Mulla, Jehad Abubaker
Software Mentions: 2
Published: over 3 years ago

10.1002/ece3.4960

Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics
Cited by: 41
Author(s): Manuel Curto, Silvia Winter, Anna Seiter, Lukas Schmid, Klaus Scheicher, Leon M. F. Barthel, Jürgen Plass, Harald Meimberg
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1006080

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning
Cited by: 17
Author(s): Elisabeth Silberhorn, Uwe Schwartz, Patrick Löffler, Samuel Schmitz, Anne Symelka, Tania F. de Koning-Ward, Rainer Merkl, Gernot Längst
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0112373

The Same Microbiota and a Potentially Discriminant Metabolome in the Saliva of Omnivore, Ovo-Lacto-Vegetarian and Vegan Individuals
Cited by: 110
Author(s): Francesca De Filippis, Lucia Vannini, Antonietta La Storia, Luca Laghi, Paola Piombino, Giuseppina Stellato, Diana Isabella Serrazanetti, Giorgia Gozzi, Silvia Turroni, Ilario Ferrocino, Camilla Lazzi, Raffaella Di Cagno, Marco Gobbetti
Software Mentions: 2
Published: about 10 years ago

10.3390/e21070630

Stationary-State Statistics of a Binary Neural Network Model with Quenched Disorder
Cited by: 2
Author(s): Diego Fasoli, Stefano Panzeri
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1006670

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles
Cited by: 55
Author(s): Eva-Maria Niehaus, Hee-Kyoung Kim, Martin Münsterkötter, Slavica Janevska, Birgit Arndt, Svetlana A. Kalinina, Petra M. Houterman, Il-Pyung Ahn, I. Alberti, Stefano Tonti, Da-Woon Kim, Christian M. K. Sieber, Hans‐Ulrich Humpf, Sung-Hwan Yun, Ulrich Güldener, Bettina Tudzynski
Software Mentions: 2
Published: about 7 years ago

10.18632/oncotarget.12430

Automated analysis of acute myeloid leukemia minimal residual disease using a support vector machine
Cited by: 21
Author(s): Wanmao Ni, Beili Hu, Cuiping Zheng, Tong Yin, Lei Wang, Qing Li, Xiangmin Tong, Yong Han
Software Mentions: 2
Published: about 8 years ago

10.1186/s13072-020-00377-1

Chromatin accessibility maps provide evidence of multilineage gene priming in hematopoietic stem cells
Cited by: 18
Author(s): Eric W. Martin, Jana Krietsch, Roman E. Reggiardo, Rebekah Sousae, Daniel H. Kim, Erik Forsberg
Software Mentions: 2
Published: almost 4 years ago

10.3389/fphar.2021.626735

Molecular Dynamics Studies of Therapeutic Liquid Mixtures and Their Binding to Mycobacteria
Cited by: 4
Author(s): Hugo P. Monteiro, Filipa Santos, Alexandre Paiva, Ana Rita C. Duarte, Ricardo B. Ferreira
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.32110

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Cited by: 88
Author(s): Samuel T. Coradetti, Dominic Pinel, Gina M. Geiselman, Masakazu Ito, Stephen J. Mondo, Morgann C. Reilly, Yafang Cheng, Štefan Bauer, Igor V. Grigoriev, John M. Gladden, Blake A. Simmons, Rachel B. Brem, Adam P. Arkin, Jeffrey M. Skerker
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.613078

Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens
Cited by: 2
Author(s): Xiayi Liu, Zhou Wu, Junying Li, Haigang Bao, Changxin Wu
Software Mentions: 2
Published: almost 4 years ago

10.1073/pnas.2024287118

A modular computational framework for medical digital twins
Cited by: 28
Author(s): Joseph Masison, Jonathan D. Beezley, Yefeng Mei, Henrique Al Ribeiro, Ádám Knapp, Luis Sordo Vieira, Bandita Adhikari, Yogesh Scindia, Michael Grauer, Brian Helba, W. J. Schroeder, Borna Mehrad, Reinhard Laubenbacher
Software Mentions: 2
Published: over 3 years ago

10.1186/s12862-017-0924-0

Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC
Cited by: 13
Author(s): Maciej Chyleński, Anna Juras, E Ehler, Helena Malmström, Janusz Piontek, Mattias Jakobsson, Arkadiusz Marciniak, Mirosława Dabert
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2020.584981

The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data
Cited by: 5
Author(s): Ran Meng, Liying Luo, Jiyuan Zhang, Dai-Gui Zhang, Ze‐Long Nie, Ying Meng
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.723479

Multivariate Analysis in Microbiome Description: Correlation of Human Gut Protein Degraders, Metabolites, and Predicted Metabolic Functions
Cited by: 7
Author(s): Stefano Raimondi, Rosalba Calvini, Francesco Candeliere, Alan Leonardi, Alessandro Ulrici, Maddalena Rossi, Alberto Amaretti
Software Mentions: 2
Published: about 3 years ago

10.3390/biom11071040

Systematic Structure-Based Search for Ochratoxin-Degrading Enzymes in Proteomes from Filamentous Fungi
Cited by: 9
Author(s): Ana Lúcia Leitão, Francisco J. Enguita
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0119465

Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
Cited by: 67
Author(s): Patrícia S. Costa, Mariana P. Reis, Marcelo P. Ávila, Laura Hora Rios Leite, Flávio Marcos Gomes Araújo, Anna C. M. Salim, Guilherme Oliveira, Francisco A. R. Barbosa, Edmar Chartone-Souza, Andréa M. A. Nascimento
Software Mentions: 2
Published: over 9 years ago

10.1038/sdata.2016.100

3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons
Cited by: 32
Author(s): Adrian Wanner, Christel Genoud, Rainer W. Friedrich
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2020.01343

First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna
Cited by: 14
Author(s): María Florencia Perez, Daniel Kurth, Marı́a Eugenia Farı́as, Mariana Soria, Genis Castillo-Villamizar, Anja Poehlein, Rolf Daniel, Julián Rafael Dib
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0101227

Fluorescence2D: Software for Accelerated Acquisition and Analysis of Two-Dimensional Fluorescence Spectra
Cited by: 3
Author(s): Evgenii L. Kovrigin
Software Mentions: 2
Published: over 10 years ago

10.3389/fcell.2020.591487

Identifying Antioxidant Proteins by Using Amino Acid Composition and Protein-Protein Interactions
Cited by: 40
Author(s): Yixiao Zhai, Yu Chen, Zhaogang Teng, Yuming Zhao
Software Mentions: 2
Published: about 4 years ago

Projects: pypi: py

Papers Mentioning py 403