Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: Biology

https://packages.ecosyste.ms/registries/pypi.org/packages/Biology

Biological Analysis
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Latest release: over 5 years ago
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Papers Mentioning Biology 311

10.1371/journal.pcbi.1007792
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago
10.1371/journal.pcbi.1005404
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 8 years ago
10.1371/journal.pcbi.1009136
Multidimensional analysis and detection of informative features in human brain white matter
Cited by: 14
Author(s): Adam Richie-Halford, Jason D. Yeatman, Noah Simon, Ariel Rokem
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pcbi.1007665
CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
Cited by: 8
Author(s): Thilde Terkelsen, Anders Krogh, Elena Papaleo
Software Mentions: 11
Published: almost 5 years ago
10.1371/journal.pcbi.1003929
dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: about 10 years ago
10.1371/journal.pcbi.1009380
Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Cited by: 11
Author(s): Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce
Software Mentions: 10
Published: over 3 years ago
10.1371/journal.pcbi.1008947
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Cited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: over 3 years ago
10.1371/journal.pcbi.1004873
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
Cited by: 1,141
Author(s): Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian
Software Mentions: 9
Published: over 8 years ago
10.1371/journal.pcbi.1009029
G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Cited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pcbi.1008720
Impact of between-tissue differences on pan-cancer predictions of drug sensitivity
Cited by: 4
Author(s): John P. Lloyd, Matthew B. Soellner, Sofía D. Merajver, Jun Z. Li
Software Mentions: 7
Published: almost 4 years ago
10.1371/journal.pcbi.1006158
Comment on "A comprehensive overview and evaluation of circular RNA detection tools"
Cited by: 14
Author(s): Chia-Ying Chen, Trees‐Juen Chuang
Software Mentions: 7
Published: over 5 years ago
10.1371/journal.pcbi.1008329
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Cited by: 6
Author(s): Aleksei Mironov, Stepan Denisov, Alexander Greß, Olga V. Kalinina, Dmitri D. Pervouchine
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pcbi.1004274
Genome Modeling System: A Knowledge Management Platform for Genomics
Cited by: 77
Author(s): Malachi Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam Coffman, Allison Regier, Benjamin J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, R.L. Long, Travis E. Abbott, Ian T. Ferguson, David Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam F. Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher Harris, Nicole Maher, Christopher A. Maher, Vincent Magrini, Benjamin Abbott, Ken Chen, Eric M. Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd Wylie, Shawn Leonard, W.E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason Walker, James M. Eldred, David E. Larson, David J. Dooling, Ding Li, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 6
Published: over 9 years ago
10.1371/journal.pone.0200390
Molecular marker sequences of cattle Cooperia species identify Cooperia spatulata as a morphotype of Cooperia punctata
Cited by: 18
Author(s): Sabrina Ramünke, Fernando de Almeida Borges, Elke von Son-de Fernex, Georg von Samson‐Himmelstjerna, Jürgen Krücken
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pcbi.1002970
Chaste: An Open Source C++ Library for Computational Physiology and Biology
Cited by: 366
Author(s): Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabéu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Néjib Zemzemi, David Gavaghan
Software Mentions: 6
Published: almost 12 years ago
10.1371/journal.pcbi.1008277
EventEpi—A natural language processing framework for event-based surveillance
Cited by: 11
Author(s): Auss Abbood, Alexander Ullrich, Rüdiger Busche, Stéphane Ghozzi
Software Mentions: 6
Published: about 4 years ago
10.1186/s13321-020-0408-x
Towards reproducible computational drug discovery
Cited by: 83
Author(s): Nalini Schaduangrat, Samuel Lampa, Saw Simeon, M. Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
Software Mentions: 6
Published: almost 5 years ago
10.1186/s13071-020-04265-1
Molecular analysis of polymorphic species of the genus Marshallagia (Nematoda: Ostertagiinae)
Cited by: 9
Author(s): Abdurakhim Kuchboev, Khanifakhon Sobirova, R. Karimova, Oybek Amirov, Georg von Samson‐Himmelstjerna, Jürgen Krücken
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pcbi.1005564
sourceR: Classification and source attribution of infectious agents among heterogeneous populations
Cited by: 17
Author(s): Poppy Miller, Jonathan Marshall, Nigel P. French, Chris Jewell
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0252759
Antimicrobial activity of methanolic extracts of Vernonia cinerea against Xanthomonas oryzae and identification of their compounds using in silico techniques
Cited by: 6
Author(s): Tushar Joshi, Satish Chandra Pandey, Priyanka Maiti, Manish Kumar Tripathi, Ashutosh Paliwal, Mahesha Nand, Priyanka Sharma, Mukesh Samant, Veena Pande, Subhash Chandra
Software Mentions: 5
Published: over 3 years ago
10.1186/s12936-020-03512-1
Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study
Cited by: 5
Author(s): Rita Afriyie Boateng, Özlem Tastan Bishop, Thommas M. Musyoka
Software Mentions: 5
Published: about 4 years ago
10.1186/s13062-015-0088-z
The human disease network in terms of dysfunctional regulatory mechanisms
Cited by: 22
Author(s): Jing Yang, Sujuan Wu, Wentao Dai, Yixue Li, Yuanyuan Li
Software Mentions: 5
Published: about 9 years ago
10.1371/journal.pcbi.1009138
Behavioral correlates of cortical semantic representations modeled by word vectors
Cited by: 6
Author(s): Shogo Nishida, Antione Blanc, Naoya Maeda, Masataka Kado, Shinji Nishimoto
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pcbi.1007636
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
Cited by: 23
Author(s): Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pcbi.1009108
Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis
Cited by: 5
Author(s): Necati Esener, Alexandre Maciel-Guerra, Katharina Giebel, Daniel Lea, Martin J. Green, Andrew J. Bradley, Tania Dottorini
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pcbi.1007481
Bayesian inference of neuronal assemblies
Cited by: 18
Author(s): Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pcbi.1009256
Computational identification and experimental characterization of preferred downstream positions in human core promoters
Cited by: 2
Author(s): René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bücher, Tamar Juven‐Gershon
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pcbi.1008457
Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain
Cited by: 4
Author(s): Sreejan Kumar, Cameron T. Ellis, Thomas O’Connell, Marvin M. Chun, Nicholas B. Turk‐Browne
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pcbi.1008893
Computation of the electroencephalogram (EEG) from network models of point neurons
Cited by: 19
Author(s): Pablo Martínez‐Cañada, Torbjørn V. Ness, Gaute T. Einevoll, Tommaso Fellin, Stefano Panzeri
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pcbi.1008856
Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment
Cited by: 26
Author(s): Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz, Alexis Joly
Software Mentions: 5
Published: over 3 years ago
10.1186/1471-2105-10-S10-S5
KA-SB: from data integration to large scale reasoning
Cited by: 3
Author(s): María del Mar Roldán‐García, Ismael Navas‐Delgado, Amine Kerzazi, Othmane Chniber, Joaquin J. Molina-Castro, José F. Aldana‐Montes
Software Mentions: 5
Published: about 15 years ago
10.1371/journal.pcbi.1008310
Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
Cited by: 12
Author(s): Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1009014
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Cited by: 8
Author(s): Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1008955
Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder
Cited by: 12
Author(s): Mads Lund Pedersen, Maria Ironside, Ken‐ichi Amemori, Callie L. McGrath, Min Su Kang, Ann M. Graybiel, Diego A. Pizzagalli, Michael J. Frank
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1009298
Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
Cited by: 8
Author(s): Natalie Schaworonkow, Bradley Voytek
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0227724
Gut-derived Flavonifractor species variants are differentially enriched during in vitro incubation with quercetin
Cited by: 6
Author(s): Gina Paola Rodriguez-Castaño, Federico E. Rey, Alejandro Caro‐Quintero, Alejandro Acosta-González
Software Mentions: 4
Published: about 4 years ago
10.1016/j.cels.2019.11.006
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning
Cited by: 44
Author(s): Gregory L. Medlock, Jason A. Papin
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pcbi.1008580
A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation
Cited by: 23
Author(s): Diego Vidaurre
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1008830
Using Hawkes Processes to model imported and local malaria cases in near-elimination settings
Cited by: 9
Author(s): H. Juliette T. Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin M. Cohen, Daniel J. Weiss, Swapnil Mishra, Samir Bhatt
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1008278
Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation
Cited by: 6
Author(s): Edward M. Hill, Stavros Petrou, Henry Forster, Simon de Lusignan, Ivelina Yonova, Matthew James Keeling
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pcbi.1008870
Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death
Cited by: 10
Author(s): Irina Veith, Arianna Mencattini, Valentin Picant, Marco Serra, Marine Leclerc, Maria Colomba Comes, Fathia Mami‐Chouaib, Jacques Camonis, Stéphanie Descroix, Hamasseh Shirvani, Fatima Mechta‐Grigoriou, Gérard Zalcman, Maria Carla Parrini, Eugenio Martinelli
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1009040
A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila
Cited by: 0
Author(s): Claudio D. T. Barros, Maira Arruda Cardoso, Paulo Mascarello Bisch, Helena Araujo, Francisco J. P. Lopes
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1007988
Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases
Cited by: 7
Author(s): Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pcbi.1008476
Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage
Cited by: 7
Author(s): Samuel Ingram, Nicholas Henthorn, John-William Warmenhoven, N.F. Kirkby, Ranald I Mackay, Karen J Kirkby, Michael J Merchant
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pcbi.1009370
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders
Cited by: 4
Author(s): Jaie Woodard, Wei Zheng, Zifeng Yang
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1007271
Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks
Cited by: 3
Author(s): Carly Adams, D. K. Young, Paul A. Gastañaduy, Prabasaj Paul, Zach Marsh, Aron J. Hall, Benjamin A. Lopman
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pcbi.1008284
Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants
Cited by: 5
Author(s): Adil Alsiyabi, Ariadna González-Solís, Edgar B. Cahoon, Rajib Saha
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1007924
A validation framework for neuroimaging software: The case of population receptive fields
Cited by: 28
Author(s): Garikoitz Lerma-Usabiaga, Noah C. Benson, Jonathan Winawer, Brian A. Wandell
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pcbi.1003750
A Real-Time All-Atom Structural Search Engine for Proteins
Cited by: 10
Author(s): Gabriel González, Brett T. Hannigan, William F. DeGrado
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pcbi.1008689
Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography
Cited by: 27
Author(s): Viktor Sip, Meysam Hashemi, Anirudh Nihalani Vattikonda, Michael Woodman, Huifang Wang, Julia Scholly, Samuel Médina Villalon, Maxime Guye, Fabricē Bartolomei, Viktor K. Jirsa
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1003829
eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
Cited by: 26
Author(s): Michał Bryliński
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pcbi.1008919
Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum
Cited by: 5
Author(s): Lorenzo Betti, Gianmarco De Francisci Morales, Laetitia Gauvin, Kyriaki Kalimeri, Yelena Mejova, Daniela Paolotti, Michele Starnini
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pcbi.1008786
Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children
Cited by: 9
Author(s): Laurens F. M. Verscheijden, Carlijn H. C. Litjens, Jan B. Koenderink, Ron H.J. Mathijssen, Marcel M. Verbeek, Saskia N. de Wildt, Frans G. M. Rüssel
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pcbi.1007249
Predicting Meridian in Chinese traditional medicine using machine learning approaches
Cited by: 33
Author(s): Yinyin Wang, Mohieddin Jafari, Yun Tang, Jing Tang
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pcbi.1008003
Biological network growth in complex environments: A computational framework
Cited by: 6
Author(s): Torsten Johann Paul, Philip Kollmannsberger
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pcbi.1008489
A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro
Cited by: 40
Author(s): Haiping Zhang, Yang Yang, Junxin Li, Min Wang, Konda Mani Saravanan, Jinli Wei, Jiawei Ng, Tofazzal Hossain, Maoxuan Liu, Huiling Zhang, Xiaohu Ren, Yi Pan, Yin Peng, Yi Shi, Xiaochun Wan, Yingxia Liu, Yanjie Wei
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pcbi.1008287
An analysis of tissue-specific alternative splicing at the protein level
Cited by: 49
Author(s): José Manuel Rodriguez, Fernando Campo del Pozo, Tomàs Di Domenico, Jesús Vázquez, Michael L. Tress
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pcbi.1008852
Personalized computational model quantifies heterogeneity in postprandial responses to oral glucose challenge
Cited by: 9
Author(s): Balázs Erdős, Bart van Sloun, Michiel E. Adriaens, Shauna D. O’Donovan, Dominique Langin, Arne Astrup, Ellen E. Blaak, Ilja C. W. Arts, Natal A. W. van Riel
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1007455
A computational study on the role of glutamate and NMDA receptors on cortical spreading depression using a multidomain electrodiffusion model
Cited by: 18
Author(s): Austin Tuttle, Jorge J. Riera, Yoichiro Mori
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pcbi.1008198
A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology
Cited by: 85
Author(s): Ziqiang Wei, Bei Jung Lin, Tsai Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1008573
Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons
Cited by: 12
Author(s): Aniello Lombardi, Paul Jedlicka, Heiko J. Luhmann, Werner Kilb
Software Mentions: 3
Published: almost 4 years ago
10.3389/fonc.2020.580276
Transcriptome Based System Biology Exploration Reveals Homogeneous Tumorigenicity of Alimentary Tract Malignancy
Cited by: 2
Author(s): You Lu, Jingqi Shi, Zixin Zhang, Jiayi Zhou, Haikun Zhou, Yuancai Feng, Zhenhua Lu, Shuya Yang, Xi-Yang Zhang, Yang Liu, Zichao Li, Yuanjie Sun, Lianhe Zheng, Duyin Jiang, Kun Yang
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1003441
VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
Cited by: 265
Author(s): Jean Daunizeau, Vincent Adam, Lionel Rigoux
Software Mentions: 3
Published: almost 11 years ago
10.1186/1471-2105-10-S10-S11
BioGateway: a semantic systems biology tool for the life sciences
Cited by: 61
Author(s): Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
Software Mentions: 3
Published: about 15 years ago
10.1371/journal.pcbi.1002708
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří­ Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: about 12 years ago
10.1016/j.dib.2021.107114
RNA-seq and miRNA-seq data from pharmacological inhibition of the G9a/GLP histone methyltransferase complex with UNC0642 in SAMP8 mice
Cited by: 1
Author(s): Shrikant Pawar, Aina Bellver-Sanchis, Christian Griñán-Ferré
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1008939
How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
Cited by: 22
Author(s): Fan Jin, Frauke Gräter
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1007970
Real time structural search of the Protein Data Bank
Cited by: 36
Author(s): Dmytro Guzenko, S.K. Burley, José M. Duarte
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1003842
IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
Cited by: 25
Author(s): N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pcbi.1008773
Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex
Cited by: 15
Author(s): Annika Hagemann, Jens Wilting, Bita Samimizad, Florian Mormann, Viola Priesemann
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pcbi.1009085
Analyzing cancer gene expression data through the lens of normal tissue-specificity
Cited by: 8
Author(s): H. Robert Frost
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1007983
Task-evoked activity quenches neural correlations and variability across cortical areas
Cited by: 52
Author(s): Takuya Ito, Scott L. Brincat, Markus Siegel, Ravi D. Mill, Biyu J. He, Earl K. Miller, Horacio G. Rotstein, Michael W. Cole
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2105-13-201
SDAR: a practical tool for graphical analysis of two-dimensional data
Cited by: 23
Author(s): Saroja Weeratunga, Nien-Jen Hu, Anne Simon, Andreas Hofmann
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pcbi.1009261
Interspike interval correlations in neuron models with adaptation and correlated noise
Cited by: 4
Author(s): Lukas Ramlow, Benjamin Lindner
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1008927
Embedding optimization reveals long-lasting history dependence in neural spiking activity
Cited by: 6
Author(s): Lucas Rudelt, D Marx, Michael Wibral, Viola Priesemann
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1007822
Biophysically grounded mean-field models of neural populations under electrical stimulation
Cited by: 36
Author(s): Caglar Cakan, Klaus Obermayer
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1007425
Computational design and interpretation of single-RNA translation experiments
Cited by: 12
Author(s): Luis U. Aguilera, William Raymond, Zachary Fox, Michael P. May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, Brian Munsky
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pcbi.1007937
Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity
Cited by: 13
Author(s): Stefano Masoli, Alessandra Ottaviani, Stefano Casali, Egidio D’Angelo
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pcbi.1003720
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
Cited by: 53
Author(s): Jacob D. Durrant, Rommie E. Amaro
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pcbi.1007659
Achieving stable dynamics in neural circuits
Cited by: 14
Author(s): Leo Kozachkov, Mikael Lundqvist, Jean‐Jacques E. Slotine, Earl K. Miller
Software Mentions: 3
Published: over 4 years ago
10.1186/s12885-018-4594-0
Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples
Cited by: 13
Author(s): George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin, Jennifer M. Kachergus, Brian M. Necela, E. Aubrey Thompson
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pcbi.1008192
Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance
Cited by: 17
Author(s): Cody Baker, Vicky Zhu, Robert Rosenbaum
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1007996
A mathematical model for persistent post-CSD vasoconstriction
Cited by: 3
Author(s): Shixin Xu, Junbiao Chang, C. C. Chow, K. C. Brennan, Huaxiong Huang
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pcbi.1008395
Bacteria use structural imperfect mimicry to hijack the host interactome
Cited by: 5
Author(s): Natalia Sánchez de Groot, M. C. Torrent
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pcbi.1008359
A first-takes-all model of centriole copy number control based on cartwheel elongation
Cited by: 1
Author(s): Marco António Dias Louro, Mónica Bettencourt-Dias, Jorge Carneiro
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1008646
PEtab—Interoperable specification of parameter estimation problems in systems biology
Cited by: 50
Author(s): Leonard Schmiester, Yannik Schälte, Frank Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang G. Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
Software Mentions: 3
Published: almost 4 years ago
10.1186/1471-2105-8-168
BioPP: a tool for web-publication of biological networks
Cited by: 14
Author(s): Ganesh A. Viswanathan, German Nudelman, Sangita Patil, Stuart C. Sealfon
Software Mentions: 2
Published: over 17 years ago
10.1186/1745-6150-8-24
Interaction-based evolution: how natural selection and nonrandom mutation work together
Cited by: 29
Author(s): Adi Livnat
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pcbi.1008691
Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation
Cited by: 1
Author(s): Jiayin Hong, Julius Palme, Bo Hua, Michael Springer
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1008847
Avoiding the bullies: The resilience of cooperation among unequals
Cited by: 1
Author(s): Michael Foley, Rory Smead, Patrick Forber, Christoph Riedl
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2180-12-S1-S5
Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches
Cited by: 37
Author(s): Carmen M. González-Domenech, Eugeni Belda, Rafael Patiño-Navarrete, Andrés Moya, Juli Peretó, Amparo Latorre
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pcbi.1008075
Electrical coupling controls dimensionality and chaotic firing of inferior olive neurons
Cited by: 14
Author(s): Huu Hoang, Eric J. Lang, Yoshito Hirata, Isao T. Tokuda, Kazuyuki Aihara, Keisuke Toyama, Mitsuo Kawato, Nicolas Schweighofer
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pcbi.1008057
Temperature-robust activity patterns arise from coordinated axonal Sodium channel properties
Cited by: 7
Author(s): Margaret DeMaegd, Wolfgang Stein
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pcbi.1007954
Winter is coming: Pathogen emergence in seasonal environments
Cited by: 9
Author(s): Philippe Carmona, Sylvain Gandon
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pcbi.1009202
Dendritic normalisation improves learning in sparsely connected artificial neural networks
Cited by: 6
Author(s): Alex D. Bird, Paul Jedlicka, Hermann Cuntz
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1008958
Balanced networks under spike-time dependent plasticity
Cited by: 10
Author(s): Alan Eric Akil, Robert Rosenbaum, Krešimir Josić
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-15-1060
Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
Cited by: 64
Author(s): Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca E O'Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D. Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin
Software Mentions: 2
Published: about 10 years ago
10.1093/bib/bby024
Community-driven roadmap for integrated disease maps
Cited by: 44
Author(s): Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Uḡur Doḡrusöz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis, David Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pcbi.1007693
Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry
Cited by: 15
Author(s): Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P. Trzeciakowski, Andreea Trache, Yi Jiang
Software Mentions: 2
Published: over 4 years ago
10.1016/j.biopsych.2019.04.034
Novel Insight Into the Etiology of Autism Spectrum Disorder Gained by Integrating Expression Data With Genome-wide Association Statistics
Cited by: 59
Author(s): Oliver Pain, Andrew Pocklington, Peter Holmans, Nicholas John Bray, Heath O’Brien, Lynsey S. Hall, Antonio F. Pardiñas, Michael O’Donovan, Richard Anney
Software Mentions: 2
Published: over 5 years ago