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: scipy

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

Fundamental algorithms for scientific computing in Python
93 versions
Latest release: about 1 year ago
10,709 dependent packages
64,812,363 downloads last month

Papers Mentioning scipy 1,071

10.1038/s41396-020-00814-9
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 4 years ago
10.3389/fninf.2019.00057
Comparing Open-Source Toolboxes for Processing and Analysis of Spike and Local Field Potentials Data
Cited by: 14
Author(s): Valentina A. Unakafova, Alexander Gail
Software Mentions: 23
Published: over 5 years ago
10.1371/journal.pgen.1009065
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago
10.1186/s13059-020-02100-5
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Cited by: 56
Author(s): Nikolaus Fortelny, Christoph Bock
Software Mentions: 20
Published: over 4 years ago
10.1016/j.cub.2020.12.047
A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior
Cited by: 32
Author(s): Tetsuya Nojima, Annika Rings, Annette D. Allen, Nils Otto, Thomas A. Verschut, Jean‐Christophe Billeter, Megan C Neville, Stephen F. Goodwin
Software Mentions: 19
Published: over 3 years ago
10.1186/s40168-019-0702-x
Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago
10.3390/cancers13102419
Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images
Cited by: 16
Author(s): Georg Steinbuß, Mark Kriegsmann, Christiane Zgorzelski, Alexander Brobeil, Benjamin Goeppert, Sascha Dietrich, Gunhild Mechtersheimer, Katharina Kriegsmann
Software Mentions: 18
Published: over 3 years ago
10.3390/ijms22105385
Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma
Cited by: 15
Author(s): Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida
Software Mentions: 18
Published: over 3 years ago
10.3389/fninf.2018.00068
Code Generation in Computational Neuroscience: A Review of Tools and Techniques
Cited by: 27
Author(s): Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz-Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael L. Hines, Michael Hopkins, Pramod Kumbhar, David Lester, Bóris Marin, Abigail Morrison, Eric Müller, Thomas Nowotny, Alexander Peyser, Dimitri Plotnikov, Paul Richmond, Andrew Rowley, Bernhard Rumpe, Marcel Stimberg, Alan B. Stokes, Adam Tomkins, Guido Trensch, Michael Woodman, Jochen Martin Eppler
Software Mentions: 16
Published: about 6 years ago
10.1371/journal.pone.0230416
The citation advantage of linking publications to research data
Cited by: 131
Author(s): Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray
Software Mentions: 16
Published: over 4 years ago
10.7554/eLife.55913
An image-based data-driven analysis of cellular architecture in a developing tissue
Cited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: over 4 years ago
10.3389/fnins.2014.00067
Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF
Cited by: 11
Author(s): Vincent Thomas, Solveig Badillo, Laurent Risser, Lotfi Chaâri, Christine Bakhous, Florence Forbes, Philippe Ciuciu
Software Mentions: 14
Published: over 10 years ago
10.1186/s13742-016-0147-0
2015 Brainhack Proceedings
Cited by: 6
Author(s): R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel J. Clark, Krzysztof J. Gorgolewski, Daniel J. Clark, Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades, Sébastien Déry, Weiran Deng, Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ružić, Nick Ketz, Andrew E. Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez‐Castillo, Caroline Froehlich, Gil Dekel, Daniel S. Margulies, Ben D. Fulcher, Tristan Glatard, Reza Adalat, Natacha Beck, R. Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans, Yaroslav Halchenko, Matteo Visconti di Oleggio Castello, Raúl Hernández-Pérez, Edgar Abarca Morales, Laura V. Cuaya, Kaori Ito, Sook‐Lei Liew, Hans J. Johnson, Erik Kan, Julia Anglin, Michael R. Borich, Neda Jahanshad, Paul Thompson, Marcel Falkiewicz, Julia M. Huntenburg, David O’Connor, Michael P. Milham, Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre R. Franco, Augusto Buchweitz, Felipe Meneguzzi, Rickson C. Mesquita, Luis C. T. Herrera, Daniela Dentico, Vanessa Sochat, Julio E. Villalon‐Reina, Eleftherios Garyfallidis
Software Mentions: 14
Published: about 8 years ago
10.1186/s13059-021-02264-8
GeneWalk identifies relevant gene functions for a biological context using network representation learning
Cited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: almost 4 years ago
10.1039/d0sc05337f
A data-driven perspective on the colours of metal–organic frameworks
Cited by: 14
Author(s): Kevin Maik Jablonka, Seyed Mohamad Moosavi, Mehrdad Asgari, Christopher P. Ireland, Luc Patiny, Berend Smit
Software Mentions: 14
Published: almost 4 years ago
10.15252/msb.20209498
Developmental function and state transitions of a gene expression oscillator in <i>Caenorhabditis elegans</i>
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago
10.12688/f1000research.15140.2
Recommendations for the packaging and containerizing of bioinformatics software
Cited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago
10.1186/s12859-021-04057-z
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Cited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: over 3 years ago
10.1186/s13321-020-00455-2
spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: about 4 years ago
10.1186/s13073-021-00904-z
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility
Cited by: 33
Author(s): Liuyang Wang, Thomas J Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R Ko, Geoffrey S. Ginsburg, Mark DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser, Dennis C. Ko
Software Mentions: 13
Published: over 3 years ago
10.3390/jcm10051089
Prediction of Neurologically Intact Survival in Cardiac Arrest Patients without Pre-Hospital Return of Spontaneous Circulation: Machine Learning Approach
Cited by: 4
Author(s): Dong-Woo Seo, Hahn Yi, Hyun‐Jin Bae, Youn-Jung Kim, Cheol Ho Sohn, Won Young Kim, Kyung-Taek Lim, Namkug Kim, Youn-Jung Kim
Software Mentions: 13
Published: over 3 years ago
10.1186/s12859-020-03774-1
Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Cited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: about 4 years ago
10.1128/mSystems.00903-19
manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: almost 5 years ago
10.3390/ani11020485
Action Recognition Using a Spatial-Temporal Network for Wild Felines
Cited by: 9
Author(s): Liqi Feng, Yaqin Zhao, Yang Sun, Wenxuan Zhao, Jiaxi Tang
Software Mentions: 12
Published: almost 4 years ago
10.3389/fimmu.2020.00444
JunB Controls Intestinal Effector Programs in Regulatory T Cells
Cited by: 8
Author(s): Joshua D. Wheaton, Maria Ciofani
Software Mentions: 12
Published: over 4 years ago
10.1186/s12859-019-3096-7
Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues
Cited by: 9
Author(s): Jianya Huan, Hunter N. B. Moseley
Software Mentions: 12
Published: about 5 years ago
10.1371/journal.pcbi.1007753
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Cited by: 1
Author(s): Jacob Pfeil, Lauren Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 4 years ago
10.1186/s12868-017-0372-1
26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3
Cited by: 5
Author(s): Adam J. H. Newton, Alexandra H Seidenstein, Robert A. McDougal, Alberto Pérez-Cervera, Gemma Huguet, Tere M. Seara, Caroline Haimerl, David Angulo-García, Alessandro Torcini, Rosa Cossart, Arnaud Malvache, K. Skiker, Mounir Maouene, Gianmarco Ragognetti, Letizia Lorusso, Andrea Viggiano, Angelo Marcelli, Rosa Senatore, Antonio Parziale, Sebastiano Stramaglia, M. Pellicoro, Lucia Angelini, Enrico Amico, Hannelore Aerts, Jesús M. Cortés, Steven Laureys, Daniele Marinazzo, Iege Bassez, Luca Faes, Hannes Almgren, Adeel Razi, Frederik Van de Steen, Ruth M. Krebs, Hannelore Aerts, Lida Kanari, Paweł Dłotko, Martina Scolamiero, Ran Levi, Julian C. Shillcock, Christiaan Pj de Kock, Katharina Heß, Henry Markram, Cheng Ly, Gary Marsat, Tom Gillespie, Malin Sandström, Mathew Abrams, Jeffrey S. Grethe, Maryann E. Martone, Robin De Gernier, Sergio Solinas, Christian Rössert, Marc Haelterman, Serge Massar, Valentina Pasquale, Vito Paolo Pastore, Sergio Martinoia, Paolo Massobrio, Cristiano Capone, Núria Tort-Colet, María V. Sánchez-Vives, Maurizio Mattia, Ali Almasi, Shaun L. Cloherty, David B. Grayden, Yan T. Wong, M. Ibbotson, Hamish Meffin, Luke Y. Prince, Krasimira Tsaneva-Atanasova, Jack R. Mellor, Annalisa Mazzoni, Manuela Rosa, J. Carpaneto, Luigi Romito, Alberto Priori, Silvestro Micera, Rosanna Migliore, Carmen Alina Lupaşcu, Francesco Franchina, Luca Bologna, Armando Romani, Sára Sáray, Werner Van Geit, Szabolcs Káli, Alex Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Eilif Müller, Felix Schürmann, Dmitry Todorov, Robert Capps, William Barnett, Yaroslav I. Molkov, Federico Devalle, Diego Pazó, Ernest Montbrió, Gabriela Mochol, Habiba Azab, Benjamin Y. Hayden, Rubén Moreno‐Bote, Pragathi Priyadharsini Balasubramani, Srinivasa Chakravarthy, Vignayanandam Ravindernath Muddapu, Medorian D. Gheorghiu, Bartul Mimica, Jonathan Withlock, Raul C. Mureșan, Jennifer L. Zick, Kelsey Schultz, Rachael K. Blackman, Matthew V. Chafee, Theoden I. Netoff, Nicholas Roberts, Vivek Nagaraj, Andrew Lamperski, Logan L. Grado, Matthew D. Johnson, David Darrow, Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus, Marcel Stimberg, Dan F. M. Goodman, Thomas Nowotny, Veronika Koren, Valentin Dragoi, Klaus Obermayer, Samy Castro, Mariano Fernández, Wael El-Deredy, Ke Xu, Jean P. Maidana, Patricio Orio, Wei‐Liang Chen, Iain Hepburn, Francesco Casalegno, Adrien Devresse, A. G. Ovcharenko, Fernando Pereira, Fabien Delalondre, Erik De Schutter, Peter Bratby, Andrew R. Gallimore, Guido Klingbeil, Criseida Zamora, Yunliang Zang, Patrick Crotty, Eric Palmerduca, Alberto Antonietti, Claudia Casellato, Csaba Erö, Egidio D’Angelo, Marc‐Oliver Gewaltig, Alessandra Pedrocchi, Ilja Bytschok, Dominik Dold, Johannes Schemmel, K. Meier, Mihai A. Petrovici, Hui-An Shen, Simone Carlo Surace, Jean-Pascal Pfister, Baptiste Lefebvre, Olivier Marre, Pierre Yger, Athanasia Papoutsi, Jiyoung Park, Ryan T. Ash, Stelios M. Smirnakis, Panayiota Poirazi, Richard A. Felix, Alexander G. Dimitrov, Christine V. Portfors, Silvia Daun, Tibor Tóth, Joanna Jędrzejewska‐Szmek, Nadine Kabbani, Kim T. Blackwel, Bahar Moezzi, Natalie Schaworonkow, Lukas Plogmacher, Mitchell R. Goldsworthy, Brenton Hordacre, Mark D. McDonnell, Nicolangelo Iannella, Michael C. Ridding, Jochen Triesch, Reinoud Maex, Karen Safaryan, Volker Steuber, Rongxiang Tang, Yi‐Yuan Tang, Darya V. Verveyko, Alexey Brazhe, Andrey Yu. Verisokin, Dmitry E. Postnov, Cengiz Günay, Gabriella Panuccio, Michèle Giugliano, Astrid A. Prinz, Pablo Varona, M. I. Rabinovich, Jack E. Denham, Thomas Ranner, Netta Cohen, Maria Reva, Nelson Rebola, Tekla Kirizs, Zoltán Nusser, David A. DiGregorio, Eirini Mavritsaki, Panos Rentzelas, Nikul H. Ukani, Adam Tomkins, Chung-Heng Yeh, Wesley Bruning, Allison L. Fenichel, Yiyin Zhou, Yu-Chi Huang, Dorian Florescu, Carlos L. Ortiz, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann‐Shyn Chiang, Aurel A. Lazar, Jennifer Creaser, Congping Lin, Peter Ashwin, Jon T. Brown, Thomas Ridler, Daniel Levenstein, Brendon O. Watson, György Buzsáki, John Rinzel, Rodica Curtu, Anh Trung Nguyen, Sahand Assadzadeh, P. A. Robinson, Paula Sanz‐Leon, Caroline Garcia Forlim, Lírio Onofre Baptista de Almeida, Reynaldo D. Pinto, Francisco B. Rodríguez, Ángel Lareo, Aarón Montero, Thiago Mosqueiro, Ramón Huerta, Vinicio Changoluisa, Vinícius Lima Cordeiro, Cesar Ceballos, Nilton L. Kamiji, Antonio Roque, William W. Lytton, Andrew T. Knox, Joshua J. C. Rosenthal, Svitlana Popovych, Liqing Liu, Bin A. Wang, Christian Grefkes, Gereon R. Fink, Nils Rosjat, Abraham Perez-Trujillo, Andrés Espinal, Marco Aurelio Sotelo-Figueroa, Iván Cruz-Aceves, Horacio Rostro-González, Martin Zapotocky, Martina Hoskovcová, J Kopecká, Olga Ulmanová, Evžen Růžička, Matthias Gärtner, Sevil Duvarci, Jochen Roeper, Gerd‐Helge Schneider, Štefan Albert, Katharina Schmack, Michiel W. H. Remme, Susanne Schreiber, Michele Migliore, Stefano Maximiliano Antonel, Jean-Denis Courcol, Sami Utku Çelikok, Eva M. Navarro-López, Neslihan Serap Şengör, Rahmi Elibol, Mustafa Y. Özdemir, Tianyi Li, Angelo Arleo, Denis Sheynikhovich, Akihiro Nakamura, Masanori Shimono, Youngjo Song, Sol Park, Ilhwan Choi, Jaeseung Jeong, Hee‐Sup Shin, Sadra Sadeh, Padraig Gleeson, R. Angus Silver, Alexandra P. Chatzikalymniou, Frances K. Skinner, Francisco B. Rodríguez, Roberto C. Sotero, Loreen Hertäg, Owen Mackwood, Henning Sprekeler, Steffen Puhlmann, Simon Weber, David Higgins, Laura Naumann, Ramakrisnan Iyer, Ştefan Mihalaş, Valentina Ticcinelli, Tomislav Stankovski, Peter V. E. McClintock, Aneta Stefanovska, Predrag Janjić, Dimitar Solev, Gerald Seifert, Ljupčo Kocarev, Christian Steinhäuser, Mehrdad Salmasi, Stefan Glasauer, Martin B. Stemmler, Danke Zhang, Chi Zhang, Armen Stepanyants, Julia Goncharenko, Lieke Kros, Neil Davey, Chris I. De Zeeuw, Freek E. Hoebeek, Ankur Sinha, Roderick Adams, Michael Schmuker, Maria Psarrou, Maria J. Schilstra, Benjamin Torben‐Nielsen, Christoph Metzner, Achim Schweikard, Tuomo Mäki‐Marttunen, Bartosz Zurowski, Daniele Marinazzo, Luca Faes, Sebastiano Stramaglia, H Jordan, Simon M. Stringer, Elżbieta Gajewska-Dendek, Piotr Suffczyński, Nicoladie D. Tam, George Zouridakis, Luca Pollonini, Mojtaba Madadi Asl, Alireza Valizadeh, Peter A. Tass, Andreas Nold, Wei Fan, Sara Konrad, Heiko Endle, Johannes Vogt, Tatjana Tchumatchenko, Juliane Herpich, Christian Tetzlaff, Jannik Luboeinski, Timo Nachstedt, Manuel Ciba, Andreas Bahmer, Christiane Thielemann, Eric S. Kuebler, Joseph S. Tauskela, Jean-Philippe Thivierge, Rembrandt Bakker, María García‐Amado, Marian Evangelio, Francisco Clascá, Paul Tiesinga, Christopher L. Buckley, Taro Toyoizumi, Alexis Dubreuil, Rémi Monasson, Alessandro Treves, Davide Spalla, Sophie Rosay, Florence I. Kleberg, Willy Wong, Bruno de Oliveira Floriano, Toshihiko Matsuo, Tetsuya Uchida, D. Dibenedetto, Kâmil Uludağ, Abdorreza Goodarzinick, Maximilian Schmidt, Claus C. Hilgetag, Markus Diesmann, Sacha J. van Albada, Michael Fauth, Mark C. W. van Rossum, Manuel Reyes-Sánchez, Rodrigo Amaducci, Carlos Múñiz, Irene Elices, David Arroyo, Rafael Levi, Ben Cohen, Carson C. Chow, Shashaank Vattikuti, Elena Bertolotti, Raffaella Burioni, Matteo di Volo, A. Vezzani, Bayar Menzat, Tim P. Vogels, Nobuhiko Wagatsuma, Susmita Saha, Reena Kapoor, Robert R. Kerr, John Wagner, Luis C. G. del Molino, Guangyu Robert Yang, Jorge F. Mejías, Xiaojing Wang, Hanbing Song, Joseph W. Goodliffe, Jennifer I. Luebke, Christina M. Weaver, John Thomas, Nishant Sinha, Nikhita Shaju, Tomasz Maszczyk, Jing Jin, Sydney S. Cash, Justin Dauwels, M. Brandon Westover, Maryam Karimian, Michelle Moerel, Peter De Weerd, Thomas Burwick, Ronald L. Westra, Romesh Abeysuriya, Jonathan Hadida, Stamatios N. Sotiropoulos, Saâd Jbabdi, Mark W. Woolrich, Chama Bensmail, Borys Wróbel, Xiaolong Zhou, Zilong Ji, Xiao Liu, Xin Yan, Si Wu, Wang Xiao, Mingsha Zhang, Netanel Ofer, Orit Shefi, Gur Yaari, Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Elena Y. Smirnova, Dmitry V. Amakhin, Sergey L. Malkin, Aleksey V. Zaitsev, Anton V. Chizhov, Margarita Zaleshina, Alexander Zaleshin, Victor J. Barranca, George Zhu, Quinton M. Skilling, Daniel Maruyama, Nicolette Ognjanovski, Sara J. Aton, Michal Zochowski, Jiaxing Wu, Sara J. Aton, Scott Rich, Victoria Booth, Maral Budak, Salvador Dura‐Bernal, Samuel A. Neymotin, Benjamin A. Suter, Gordon M. Shepherd, Melvin Felton, Alfred B. Yu, David L. Boothe, Kelvin S. Oie, Piotr J. Franaszczuk, Sergey A. Shuvaev, Batuhan Başerdem, Anthony M. Zador, Alexei A. Koulakov, Víctor J. López‐Madrona, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Stefano Masoli, Udaya Bhaskar Rongala, Anton Spanne, Henrik Jörntell, Calogero Maria Oddo, A. Vartanov, Anastasia Neklyudova, S. Kozlovskiy, A. Kiselnikov, J. Marakshina, Maria Teleńczuk, Bartosz Teleńczuk, Alain Destexhe, Paula T. Kuokkanen, Anna Kraemer, Thomas McColgan, Catherine Carr, Richard Kempter
Software Mentions: 12
Published: over 7 years ago
10.3389/fninf.2018.00092
Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0
Cited by: 96
Author(s): Espen Hagen, Solveig Næss, Torbjørn V. Ness, Gaute T. Einevoll
Software Mentions: 12
Published: almost 6 years ago
10.1186/s13059-019-1900-3
Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
Cited by: 60
Author(s): Koki Tsuyuzaki, Hiroyuki Sato, K. Sato, Itoshi Nikaido
Software Mentions: 12
Published: almost 5 years ago
10.1186/s40679-018-0060-y
An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 6 years ago
10.3390/ani11072131
Predicting Subclinical Ketosis in Dairy Cows Using Machine Learning Techniques
Cited by: 7
Author(s): Alicja Satoła, Edyta Bauer
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pone.0238835
Analyzing the fine structure of distributions
Cited by: 35
Author(s): Michael C. Thrun, Tino Gehlert, Alfred Ultsch
Software Mentions: 12
Published: about 4 years ago
10.1186/s13059-018-1563-5
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: about 6 years ago
10.3389/fnins.2020.00919
HYGRIP: Full-Stack Characterization of Neurobehavioral Signals (fNIRS, EEG, EMG, Force, and Breathing) During a Bimanual Grip Force Control Task
Cited by: 10
Author(s): Pablo Ortega, Tong Zhao, A. Aldo Faisal
Software Mentions: 11
Published: about 4 years ago
10.1371/journal.pone.0256339
Sex-specific spatial use of the winter foraging areas by Magellanic penguins and assessment of potential conflicts with fisheries during winter dispersal
Cited by: 6
Author(s): Samanta Dodino, Nicolás A. Lois, Luciana Riccialdelli, Michael J. Polito, Klemens Pütz, Andrea Raya Rey
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-020-65015-y
Toffee – a highly efficient, lossless file format for DIA-MS
Cited by: 9
Author(s): Brett Tully
Software Mentions: 11
Published: over 4 years ago
10.1371/journal.pone.0225734
PyLandStats: An open-source Pythonic library to compute landscape metrics
Cited by: 19
Author(s): Martí Bosch
Software Mentions: 11
Published: almost 5 years ago
10.1242/bio.018713
3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software
Cited by: 65
Author(s): Brandon E. Jackson, Dennis Evangelista, Dylan D. Ray, Tyson L. Hedrick
Software Mentions: 11
Published: over 8 years ago
10.1098/rsif.2010.0230
Multi-camera real-time three-dimensional tracking of multiple flying animals
Cited by: 164
Author(s): Andrew Straw, Kristin Branson, Titus R. Neumann, Michael H. Dickinson
Software Mentions: 11
Published: over 14 years ago
10.1107/S1600577518016570
Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Cited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: almost 6 years ago
10.3390/nu12020302
The Role of Glycemic Index and Glycemic Load in the Development of Real-Time Postprandial Glycemic Response Prediction Models for Patients with Gestational Diabetes
Cited by: 14
Author(s): Evgenii Pustozerov, Aleksandra Tkachuk, Elena Vasukova, А. В. Дронова, Ekaterina S. Shilova, Anna D. Anopova, Faina Piven, Tatiana Pervunina, Elena Vasilieva, Elena Grineva, Polina Popova
Software Mentions: 11
Published: almost 5 years ago
10.1038/s41598-021-82043-4
PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: almost 4 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: about 3 years ago
10.1128/mSystems.00065-20
Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk
Cited by: 19
Author(s): Justine W. Debelius, Tingting Huang, Yonglin Cai, Alexander Ploner, Donal Barrett, Xiaoying Zhou, Xue Xiao, Yancheng Li, Jian Liao, Yuming Zheng, Guangwu Huang, Hans‐Olov Adami, Yi Xin Zeng, Zhe Zhang, Ye W
Software Mentions: 10
Published: about 4 years ago
10.1186/s13062-018-0214-9
Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach
Cited by: 13
Author(s): Léon-Charles Tranchevent, Petr V. Nazarov, Tony Kaoma, Georges Pierre Schmartz, Arnaud Muller, Sang Yoon Kim, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 10
Published: almost 7 years ago
10.1038/s41598-021-89904-y
Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Cited by: 5
Author(s): Zhenhua Zhang, Freerk van Dijk, Nigel Klein, Mariëlle van Gijn, Lude Franke, Richard J. Sinke, Morris A. Swertz, K. Joeri van der Velde
Software Mentions: 10
Published: over 3 years ago
10.1016/j.cell.2021.07.017
Whole-body integration of gene expression and single-cell morphology
Cited by: 59
Author(s): Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
Software Mentions: 10
Published: about 3 years ago
10.1038/s41597-020-00725-6
An annotated dataset of bioacoustic sensing and features of mosquitoes
Cited by: 5
Author(s): Dinarte Vasconcelos, Nuno Nunes, João Gomes
Software Mentions: 10
Published: about 4 years ago
10.15252/msb.202010108
Joint cell segmentation and cell type annotation for spatial transcriptomics
Cited by: 40
Author(s): Russell Littman, Zachary Hemminger, Robert T. Foreman, Douglas Arneson, Guanglin Zhang, Fernando Gómez‐Pinilla, Xia Yang, Roy Wollman
Software Mentions: 10
Published: over 3 years ago
10.3390/md18100515
Applying a Chemogeographic Strategy for Natural Product Discovery from the Marine Cyanobacterium Moorena bouillonii
Cited by: 6
Author(s): Christopher A. Leber, C. Benjamin Naman, Lena Keller, Jehad Almaliti, Eduardo J. E. Caro‐Diaz, Evgenia Glukhov, V. Joseph, Sajeevan Thavarool Puthiyedathu, Andres Joshua Reyes, Jason S. Biggs, Te Li, Ye Yuan, Shan He, Xiaojun Yan, William H. Gerwick
Software Mentions: 10
Published: about 4 years ago
10.1186/s12920-019-0628-y
A deep neural network approach to predicting clinical outcomes of neuroblastoma patients
Cited by: 14
Author(s): Léon-Charles Tranchevent, Francisco Azuaje, Jagath C. Rajapakse
Software Mentions: 10
Published: almost 5 years ago
10.1038/s41598-020-80308-y
A novel retinal ganglion cell quantification tool based on deep learning
Cited by: 22
Author(s): Luca Masin, Marie Claes, Steven Bergmans, Lien Cools, Lien Andries, Benjamin Davis, Lieve Moons, Lies De Groef
Software Mentions: 10
Published: almost 4 years ago
10.1093/bioinformatics/btaa073
<i>Coolpup.py:</i> versatile pile-up analysis of Hi-C data
Cited by: 86
Author(s): Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore
Software Mentions: 10
Published: almost 5 years ago
10.1186/s13059-019-1647-x
Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
Cited by: 48
Author(s): Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli, Angela Gallo
Software Mentions: 10
Published: almost 6 years ago
10.3389/fgene.2018.00461
TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: about 6 years ago
10.1029/2019EA001004
Open‐Source Software Analysis Tool to Investigate Space Plasma Turbulence and Nonlinear DYNamics (ODYN)
Cited by: 6
Author(s): E. Teodorescu, Marius Echim
Software Mentions: 10
Published: over 4 years ago
10.1371/journal.pbio.3001319
A flexible framework for multi-particle refinement in cryo-electron tomography
Cited by: 29
Author(s): Alister Burt, Lorenzo Gaifas, Tom Dendooven, Irina Gutsche
Software Mentions: 10
Published: about 3 years ago
10.1186/s12859-021-04037-3
InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
Cited by: 8
Author(s): Dominik J. E. Waibel, Sayedali Shetab Boushehri, Carsten Marr
Software Mentions: 10
Published: over 3 years ago
10.3389/fneur.2021.681140
Using Base-ml to Learn Classification of Common Vestibular Disorders on DizzyReg Registry Data
Cited by: 3
Author(s): Gerome Vivar, Ralf Strobl, Eva Grill, Nassir Navab, Andreas Zwergal, Seyed-Ahmad Ahmadi
Software Mentions: 9
Published: over 3 years ago
10.1186/s12859-014-0408-9
Kiwi: a tool for integration and visualization of network topology and gene-set analysis
Cited by: 12
Author(s): Leif Väremo, Francesco Gatto, Jens Nielsen
Software Mentions: 9
Published: almost 10 years ago
10.3389/fneur.2021.713794
Seizure Forecasting Using a Novel Sub-Scalp Ultra-Long Term EEG Monitoring System
Cited by: 35
Author(s): Rachel E Stirling, Matias I. Maturana, Philippa J Karoly, Ewan S. Nurse, Kate McCutcheon, David B. Grayden, Steven G. Ringo, John M. Heasman, R. J. Hoare, Alan Lai, Wendyl D’Souza, Udaya Seneviratne, Linda Seiderer, Karen J. McLean, Kristian J Bulluss, Michael A. Murphy, Benjamin H. Brinkmann, Mark P. Richardson, Dean R. Freestone, Mark Cook
Software Mentions: 9
Published: about 3 years ago
10.3390/metabo11030133
Correlation of Metabolic Profiles of Plasma and Cerebrospinal Fluid of High-Grade Glioma Patients
Cited by: 9
Author(s): Artem D. Rogachev, Н. А. Алемасов, В. А. Иванисенко, Nikita V. Ivanisenko, E. V. Gaisler, Olga Oleshko, С. В. Чересиз, С. В. Мишинов, В. В. Ступак, Andrey G. Pokrovsky
Software Mentions: 9
Published: over 3 years ago
10.3390/s19224824
Validation of Wireless Sensors for Psychophysiological Studies
Cited by: 9
Author(s): Pedro Silva Moreira, Pedro Chaves, Rúben Dias, Nuno Dias, Pedro R. Almeida
Software Mentions: 9
Published: about 5 years ago
10.1371/journal.pcbi.1008724
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
Cited by: 81
Author(s): Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, F. Diblen, Simon Rogers, Justin J. J. van der Hooft
Software Mentions: 9
Published: almost 4 years ago
10.1534/genetics.119.302662
Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait
Cited by: 47
Author(s): Kevin R. Thornton
Software Mentions: 9
Published: almost 5 years ago
10.1371/journal.pone.0235930
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Cited by: 3
Author(s): Achim Werckenthin, Jannik Huber, Thordis Arnold, Susanne Koziarek, Marcus J. A. Plath, Jenny Aino Plath, Olaf Stursberg, Hanspeter Herzel, Monika Stengl
Software Mentions: 9
Published: over 4 years ago
10.15252/msb.20209819
Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration
Cited by: 17
Author(s): Nader Morshed, William T. Ralvenius, Alexi Nott, L. Ashley Watson, Felicia H. Rodriguez, Leyla Anne Akay, Brian A. Joughin, Ping‐Chieh Pao, Jay Penney, Lauren M. LaRocque, Diego Mastroeni, Li Huei Tsai, Forest M. White
Software Mentions: 9
Published: almost 4 years ago
10.1371/journal.pone.0078009
Frequency Response and Gap Tuning for Nonlinear Electrical Oscillator Networks
Cited by: 0
Author(s): Harish S. Bhat, Garnet J. Vaz
Software Mentions: 9
Published: about 11 years ago
10.3389/fmed.2021.640515
Performance of Different Diagnostic PD-L1 Clones in Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Julika Ribbat‐Idel, Frederick A. Dressler, Rosemarie Krupar, Christian Watermann, F. Paulsen, Patrick Kuppler, Luise Klapper, Anne Offermann, Barbara Wollenberg, Dirk Rades, Simon Laban, Markus Reischl, Karl‐Ludwig Bruchhage, Christian Idel, Sven Perner
Software Mentions: 9
Published: over 3 years ago
10.26508/lsa.202000658
Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago
10.1172/jci.insight.141683
CD84 is a regulator of the immunosuppressive microenvironment in Multiple Myeloma
Cited by: 15
Author(s): Hadas Lewinsky, Emine Gulsen Gunes, Keren David, Lihi Radomir, Matthias P. Kramer, Bianca Pellegrino, Michal Perpinial, Jing Chen, Ting He, Anthony G. Mansour, Kun yu Teng, Supriyo Bhattacharya, Enrico Caserta, Estelle Troadec, Peter Lee, Mingye Feng, Jonathan J. Keats, Amrita Krishnan, Michael Rosenzweig, Jianhua Yu, Michael A. Caligiuri, Yosef Cohen, Olga Shevetz, Shirly Becker-Herman, Flavia Pichiorri, Steven T. Rosen, Idit Shachar
Software Mentions: 9
Published: almost 4 years ago
10.20900/immunometab20210022
Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pgen.1009773
Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline
Cited by: 7
Author(s): Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A. Louwé, Gonneke S. K. Pilgram, Károly Szuhai, Roberto Matorras, Cristina Eguizábal, Lucette van der Westerlaken, Hailiang Mei, Susana M. Chuva de Sousa Lopes
Software Mentions: 9
Published: about 3 years ago
10.3389/fcimb.2020.00137
Microbiotyping the Sinonasal Microbiome
Cited by: 15
Author(s): Ahmed Bassiouni, S. Paramasivan, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S. Bleier, Claudio Callejas, Marjolein Cornet, Richard Douglas, Daniel Lorena Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter John Wormald, J. Gregory Caporaso, Alkis James Psaltis
Software Mentions: 9
Published: over 4 years ago
10.7717/peerj-cs.227
Component-oriented acausal modeling of the dynamical systems in Python language on the example of the model of the sucker rod string
Cited by: 5
Author(s): Volodymyr Kopei, Oleh Onysko, Vitalii Panchuk
Software Mentions: 9
Published: about 5 years ago
10.3389/fninf.2013.00026
Spyke Viewer: a flexible and extensible platform for electrophysiological data analysis
Cited by: 15
Author(s): Robert Pröpper, Klaus Obermayer
Software Mentions: 9
Published: almost 12 years ago
10.1186/s13040-019-0201-4
Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
Cited by: 3
Author(s): Elisabetta Manduchi, Patryk Orzechowski, Marylyn D. Ritchie, Jason H. Moore
Software Mentions: 9
Published: over 5 years ago
10.1371/journal.pcbi.1008364
pyTFM: A tool for traction force and monolayer stress microscopy
Cited by: 19
Author(s): Andreas Bauer, Magdalena Přechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry
Software Mentions: 9
Published: over 3 years ago
10.1007/s13755-020-00105-9
Predicting risk of stillbirth and preterm pregnancies with machine learning
Cited by: 43
Author(s): Aki Koivu, Mikko Sairanen
Software Mentions: 9
Published: over 4 years ago
10.3389/fninf.2016.00008
PyRhO: A Multiscale Optogenetics Simulation Platform
Cited by: 20
Author(s): Benjamin D. Evans, Sarah Jarvis, Simon R. Schultz, Konstantin Nikolić
Software Mentions: 9
Published: over 8 years ago
10.7717/peerj.10670
Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics
Cited by: 8
Author(s): Sergii Domanskyi, Alex Hakansson, T. J. Bertus, Giovanni Paternostro, Carlo Piermarocchi
Software Mentions: 8
Published: almost 4 years ago
10.1016/j.ymeth.2015.07.012
Construction of an instant structured illumination microscope
Cited by: 30
Author(s): Alistair Curd, Alexa Cleasby, Katarzyna Makowska, Andrew G. York, Hari Shroff, Michelle Peckham
Software Mentions: 8
Published: about 9 years ago
10.1186/1751-0473-8-2
Knowledge Driven Variable Selection (KDVS) – a new approach to enrichment analysis of gene signatures obtained from high–throughput data
Cited by: 7
Author(s): Grzegorz Zycinski, Annalisa Barla, Margherita Squillario, Tiziana Sanavia, Barbara Di Camillo, Alessandro Verri
Software Mentions: 8
Published: almost 12 years ago
10.1186/s12870-019-1693-2
A k-mer grammar analysis to uncover maize regulatory architecture
Cited by: 32
Author(s): Maria Katherine Mejía‐Guerra, Edward S. Buckler
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pcbi.1006907
Ten quick tips for effective dimensionality reduction
Cited by: 164
Author(s): Linh P. Nguyen, Susan Holmes
Software Mentions: 8
Published: over 5 years ago
10.1099/mgen.0.000168
Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages
Cited by: 73
Author(s): Apostolos Almpanis, Martin Swain, Derek Gatherer, Neil McEwan
Software Mentions: 8
Published: over 6 years ago
10.7717/peerj.2674
jicbioimage: a tool for automated and reproducible bioimage analysis
Cited by: 6
Author(s): Tjelvar S. G. Olsson, Matthew Hartley
Software Mentions: 8
Published: about 8 years ago
10.3390/s20226666
Blood Stain Classification with Hyperspectral Imaging and Deep Neural Networks
Cited by: 18
Author(s): Kamil Książek, Michał Romaszewski, Przemysław Głomb, Bartosz Grabowski, Michał Cholewa
Software Mentions: 8
Published: about 4 years ago
10.1371/journal.pcbi.1007832
Flux-based hierarchical organization of Escherichia coli’s metabolic network
Cited by: 2
Author(s): Semidán Robaina-Estévez, Zoran Nikoloski
Software Mentions: 8
Published: over 4 years ago
10.3389/fninf.2014.00014
Machine learning for neuroimaging with scikit-learn
Cited by: 1,186
Author(s): A. Alexandre, Fabián Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi, Alexandre Gramfort, Bertrand Thirion, Gaël Varoquaux
Software Mentions: 8
Published: almost 11 years ago
10.1186/s12866-021-02222-1
Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang
Cited by: 7
Author(s): Shanshan Zhu, Yonghui Lei, Chong Wang, Yu‐Mei Wei, Chuncheng Wang, Yanfei Sun
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pcbi.1008605
Machine learning based CRISPR gRNA design for therapeutic exon skipping
Cited by: 5
Author(s): Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
Software Mentions: 8
Published: almost 4 years ago
10.3389/fninf.2014.00063
A flexible, interactive software tool for fitting the parameters of neuronal models
Cited by: 25
Author(s): Péter Friedrich, M.C. Vella, Attila I. Gulyás, Tamás F. Freund, Szabolcs Káli
Software Mentions: 8
Published: over 10 years ago
10.1371/journal.pbio.3001341
Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain
Cited by: 3
Author(s): Shaina Lu, Cantin Ortiz, Daniel Fürth, Stephan Fischer, Konstantinos Meletis, Anthony M. Zador, Jesse Gillis
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pcbi.1005727
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: about 7 years ago
10.1186/s13321-018-0270-2
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 6 years ago
10.1186/s12859-016-1003-z
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Cited by: 26
Author(s): Niklaus Johner, Daniel Harries, George Khelashvili
Software Mentions: 8
Published: over 8 years ago
10.1371/journal.pgen.1009094
Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: over 3 years ago
10.1186/s12864-021-07760-6
UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Cited by: 31
Author(s): Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime A Castro-Mondragón, Anthony Mathelier
Software Mentions: 8
Published: over 3 years ago