pypi: ipython | Projects | Ecosyste.ms: Papers

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the Drosophila intestine
Cited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: over 3 years ago

10.3389/fninf.2017.00062

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography
Cited by: 78
Author(s): Liberty S. Hamilton, David L. Chang, Morgan B. Lee, Edward F. Chang
Software Mentions: 9
Published: almost 7 years ago

10.1002/pmic.201400377

Open source libraries and frameworks for biological data visualisation: A guide for developers
Cited by: 37
Author(s): Rui Wang, Yasset Perez‐Riverol, Henning Hermjakob, Juan Antonio Vizcaíno
Software Mentions: 8
Published: over 9 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: almost 9 years ago

10.1186/s13321-019-0332-0

Chemoinformatics and structural bioinformatics in OCaml
Cited by: 5
Author(s): Francois Berenger, Kam Y. J. Zhang, Yoshihiro Yamanishi
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.3944

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
Cited by: 24
Author(s): Ara S. Winter, Jennifer J.M. Hathaway, Jason C. Kimble, Debbie C. Buecher, Ernest W. Valdez, Andrea Porras-Alfaro, Jesse M. Young, Kaitlyn J. H. Read, Diana E. Northup
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0253411

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pone.0118442

Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence
Cited by: 2
Author(s): Enrico Giampieri, Marco De Cecco, Daniel Remondini, John M. Sedivy, Gastone Castellani
Software Mentions: 7
Published: about 9 years ago

10.3390/s21041072

A Do-It-Yourself Hyperspectral Imager Brought to Practice with Open-Source Python
Cited by: 8
Author(s): Kimmo A. Riihiaho, Matti A. Eskelinen, Ilkka Pölönen
Software Mentions: 7
Published: over 3 years ago

10.1016/j.cell.2016.09.027

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells
Cited by: 620
Author(s): Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Saltó, Amit Zeisel, Lars E. Borm, Simon Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, Sten Linnarsson
Software Mentions: 6
Published: almost 8 years ago

10.1093/gigascience/giaa152

Tool recommender system in Galaxy using deep learning
Cited by: 7
Author(s): Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1004384

Ten Simple Rules for Experiments’ Provenance
Cited by: 10
Author(s): Toni Kazic
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0081462

Estimation of the Horizon in Photographed Outdoor Scenes by Human and Machine
Cited by: 5
Author(s): Christian Herdtweck, Christian Wallraven
Software Mentions: 5
Published: almost 11 years ago

10.3389/fpls.2014.00406

Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus
Cited by: 27
Author(s): Allison Creason, Edward W. Davis, M. L. Putnam, Olivier M. Vandeputte, Jeff H. Chang
Software Mentions: 4
Published: about 10 years ago

10.3389/fninf.2014.00006

Equation-oriented specification of neural models for simulations
Cited by: 120
Author(s): Marcel Stimberg, Dan F. M. Goodman, Victor Benichoux, Romain Brette
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pcbi.1008256

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)
Cited by: 13
Author(s): Shuonan Chen, Jackson Loper, Xiaoyin Chen, Alex Vaughan, Anthony M. Zador, Liam Paninski
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.48779

An arbitrary-spectrum spatial visual stimulator for vision research
Cited by: 43
Author(s): Katrin Franke, André Maia Chagas, Zhijian Zhao, Maxime Zimmermann, Philipp Bartel, Yongrong Qiu, Klaudia P. Szatko, Tom Baden, Thomas Euler
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-019-2612-0

Barcode identification for single cell genomics
Cited by: 15
Author(s): Akshay Tambe, Lior Pachter
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0188511

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers
Cited by: 33
Author(s): Vanessa Sochat, Cameron J. Prybol, Gregory M. Kurtzer
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.ymeth.2017.09.010

Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data
Cited by: 30
Author(s): Dominic Waithe, Falk Schneider, Jakub Chojnacki, Mathias P. Clausen, Dilip Shrestha, Jorge Bernardino de la Serna, Christian Eggeling
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008732

Positive interactions within and between populations decrease the likelihood of evolutionary rescue
Cited by: 4
Author(s): Yaron Goldberg, Jonathan Friedman
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2007-8-8-r171

PyCogent: a toolkit for making sense from sequence
Cited by: 186
Author(s): Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J. Gregory Caporaso, Brett C Easton, Michael A. W. Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael S. Robeson, Raymond Sammut, Sandra Smit, Matthew J. Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie A. Wilson, Hua Ying, Gavin A. Huttley
Software Mentions: 3
Published: over 17 years ago

10.3389/fmicb.2021.637430

Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19
Cited by: 50
Author(s): María Paz Ventero, Rafael R C Cuadrat, Inmaculada Vidal, Bruno de Bezerril Andrade, Carmen Molina-Pardines, Jose M. Haro‐Moreno, Felipe H. Coutinho, Esperanza Merino, L. C. A. Regitano, Cynthia B. Silveira, Haithem Afli, Mario López‐Pérez, Juan Carlos Rodrı́guez
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-019-2686-8

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
Cited by: 4
Author(s): Hamed Khakzad, Johan Malmström, Lars Malmström
Software Mentions: 2
Published: over 5 years ago

10.1186/s12918-018-0557-y

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Cited by: 53
Author(s): Erol Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Jonathan M. Monk
Software Mentions: 2
Published: over 6 years ago

10.1080/21505594.2019.1637699

Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum
Cited by: 14
Author(s): Marina Muñoz, Daniel Restrepo-Montoya, Nitin Kumar, Gregorio Iraola, Giovanny Herrera, Dora I. Ríos-Chaparro, Diana Díaz-Arévalo, Manuel A. Patarroyo, Trevor D. Lawley, Juan David Ramírez
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0155574

Cognitive and Ocular Factors Jointly Determine Pupil Responses under Equiluminance
Cited by: 119
Author(s): Tomas Knapen, Jan Willem de Gee, Jan W. Brascamp, Stijn Adriaan Nuiten, Sylco S. Hoppenbrouwers, Jan Theeuwes
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0145199

Genetic Mapping of Novel Loci Affecting Canine Blood Phenotypes
Cited by: 9
Author(s): Mary H. White, Jessica J. Hayward, Tracy Stokol, Adam R. Boyko
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpsyg.2020.01594

Modeling the Mental Lexicon as Part of Long-Term and Working Memory and Simulating Lexical Access in a Naming Task Including Semantic and Phonological Cues
Cited by: 7
Author(s): Catharina Marie Stille, Trevor Bekolay, Peter Blouw, Bernd J. Kröger
Software Mentions: 2
Published: about 4 years ago

10.1038/srep31965

H3.3 demarcates GC-rich coding and subtelomeric regions and serves as potential memory mark for virulence gene expression in Plasmodium falciparum
Cited by: 22
Author(s): Sabine Anne‐Kristin Fraschka, Rob Henderson, Richárd Bártfai
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.117.1125

Sequence-Based Mapping and Genome Editing Reveal Mutations in Stickleback Hps5 Cause Oculocutaneous Albinism and the casper Phenotype
Cited by: 10
Author(s): James C. Hart, Craig T. Miller
Software Mentions: 1
Published: about 7 years ago

10.3389/fncir.2015.00090

Precise Synaptic Efficacy Alignment Suggests Potentiation Dominated Learning
Cited by: 8
Author(s): Christoph Hartmann, Daniel Miner, Jochen Triesch
Software Mentions: 1
Published: over 8 years ago

10.12688/f1000research.6230.1

Portrayed emotions in the movie "Forrest Gump"
Cited by: 26
Author(s): Annika Labs, Theresa Reich, Helene Schulenburg, Manuel Boennen, Gehrke Mareike, Madleen Golz, Benita Hartigs, Nico Hoffmann, Sebastian Keil, Malú Perlow, Anne Katrin Peukmann, Lea Noell Rabe, Franca-Rosa von Sobbe, Michael Hanke
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0176945

Target-distractor synchrony affects performance in a novel motor task for studying action selection
Cited by: 1
Author(s): Sebastian S. James, Olivia A. Bell, Muhammed A. M. Nazli, Rachel Pearce, Jonathan Spencer, Katie Tyrrell, Phillip J. Paine, Timothy J Heaton, Sean Anderson, Mauro Da Lio, Kevin Gurney
Software Mentions: 1
Published: over 7 years ago

10.1186/s40170-020-0208-9

Metabolic models predict bacterial passengers in colorectal cancer
Cited by: 28
Author(s): Daniel Garza, Rahwa Taddese, Jakob Wirbel, Georg Zeller, Annemarie Boleij, Martijn Huynen, Bas E. Dutilh
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.65459

Spike frequency adaptation supports network computations on temporally dispersed information
Cited by: 23
Author(s): Darjan Salaj, Anand Subramoney, Ceca Kraišniković, Guillaume Bellec, Robert Legenstein, Wolfgang Maass
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-017-15411-8

SensorFRET: A Standardless Approach to Measuring Pixel-based Spectral Bleed-through and FRET Efficiency using Spectral Imaging
Cited by: 14
Author(s): Paul T. Arsenovic, Carl R. Mayer, Daniel E. Conway
Software Mentions: 1
Published: almost 7 years ago

10.1093/bioinformatics/btaa959

HRIBO: high-throughput analysis of bacterial ribosome profiling data
Cited by: 9
Author(s): Rick Gelhausen, Sarah L. Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M Sharma, Florian Eggenhofer, Rolf Backofen
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-019-3018-8

A multiscale mathematical model of cell dynamics during neurogenesis in the mouse cerebral cortex
Cited by: 10
Author(s): Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider‐Maunoury, Frédérique Clément
Software Mentions: 1
Published: about 5 years ago

10.3389/frobt.2019.00062

Natural Language Processing in Large-Scale Neural Models for Medical Screenings
Cited by: 1
Author(s): Catharina Marie Stille, Trevor Bekolay, Peter Blouw, Bernd J. Kröger
Software Mentions: 1
Published: about 5 years ago

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