pypi: pandas | Projects | Ecosyste.ms: Papers

10.1186/s13073-021-00910-1

Landscape and selection of vaccine epitopes in SARS-CoV-2
Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago

10.3389/fninf.2013.00052

A framework for streamlining research workflow in neuroscience and psychology
Cited by: 12
Author(s): Jonas Kubilius
Software Mentions: 25
Published: almost 11 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

10.1038/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

10.1371/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

10.3390/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

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: almost 7 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

10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 years ago

10.1186/s12864-016-3278-x

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Cited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: about 8 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

10.1039/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

10.1371/journal.pgen.1008405

Causal relationships between obesity and the leading causes of death in women and men
Cited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 years ago

10.15252/msb.20209498

Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans
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.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
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: almost 4 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: almost 7 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

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pone.0225900

PyRates—A Python framework for rate-based neural simulations
Cited by: 10
Author(s): Richard Gast, Daniel Rose, Christoph Salomon, Harald E. Möller, Nikolaus Weiskopf, Thomas R. Knösche
Software Mentions: 12
Published: about 5 years ago

10.1038/s42003-021-01941-5

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status
Cited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: almost 7 years ago

10.3389/fmicb.2019.02597

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: about 5 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/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: over 5 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

10.7717/peerj.11376

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pone.0195065

Dengue forecasting in São Paulo city with generalized additive models, artificial neural networks and seasonal autoregressive integrated moving average models
Cited by: 48
Author(s): Oswaldo Santos Baquero, Lidia Maria Reis Santana, Francisco Chiaravalloti Neto
Software Mentions: 12
Published: over 6 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

10.3390/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

10.7554/eLife.60474

The effect of hybridization on transposable element accumulation in an undomesticated fungal species
Cited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: over 4 years ago

10.1371/journal.pone.0243295

Polish is quantitatively different on quartzite flakes used on different worked materials
Cited by: 12
Author(s): Antonella Pedergnana, Ivan Calandra, Adrian Evans, Konstantin Bob, Andreas Hildebrandt, Andreu Ollé
Software Mentions: 12
Published: about 4 years ago

10.7554/eLife.65751

Visualizing anatomically registered data with brainrender
Cited by: 64
Author(s): Federico Claudi, Adam L. Tyson, Luigi Petrucco, Troy W. Margrie, Rubén Portugues, Tiago Branco
Software Mentions: 12
Published: almost 4 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

10.1038/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

10.1038/s41598-018-31154-6

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis
Cited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: over 6 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: over 3 years ago

10.3390/jcm9082591

Risk of Adverse Drug Events Following the Virtual Addition of COVID-19 Repurposed Drugs to Drug Regimens of Frail Older Adults with Polypharmacy
Cited by: 14
Author(s): Sweilem B. Al Rihani, Matt K. Smith, Ravil Bikmetov, Malavika Deodhar, Pamela Dow, Jacques Turgeon, Véronique Michaud
Software Mentions: 11
Published: over 4 years ago

10.12688/f1000research.18458.2

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: over 5 years ago

10.3389/fninf.2019.00012

A Serverless Tool for Platform Agnostic Computational Experiment Management
Cited by: 13
Author(s): Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
Software Mentions: 11
Published: almost 6 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: about 5 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: over 5 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

10.3390/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

10.3390/ijerph17031093

Teleconsultations between Patients and Healthcare Professionals in Primary Care in Catalonia: The Evaluation of Text Classification Algorithms Using Supervised Machine Learning
Cited by: 14
Author(s): Francesc López Seguí, Ricardo Ander Egg Aguilar, Gabriel de Maeztu, Anna García‐Altés, Francesc García Cuyàs, Sandra M. Walsh, Marta Sagarra Castro, Josep Vidal-Alaball
Software Mentions: 11
Published: almost 5 years ago

10.1186/s41044-019-0043-6

A substrate for modular, extensible data-visualization
Cited by: 6
Author(s): Jordan Matelsky, Joseph Downs, Hannah Cowley, Brock Wester, William Gray-Roncal
Software Mentions: 11
Published: almost 5 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

10.1038/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

10.1186/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: about 5 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.dnarep.2021.103158

Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution
Cited by: 1
Author(s): Aldo S. Bader, Martin Bushell
Software Mentions: 10
Published: over 3 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

10.3390/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

10.1016/j.dib.2020.105195

Dataset of depressive posts in Russian language collected from social media
Cited by: 12
Author(s): Sergazy Narynov, Daniyar Mukhtarkhanuly, Batyrkhan Omarov
Software Mentions: 10
Published: over 4 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.3390/ijms22157974

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice
Cited by: 4
Author(s): Yu Te Lin, Yong Shiou Lin, Wen Cheng, Jui-Chih Chang, Yi Chun Chao, Chin San Liu, An-Chi Wei
Software Mentions: 10
Published: over 3 years ago

10.1093/bioinformatics/btaa073

Coolpup.py: 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

10.15252/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

10.3389/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

10.1371/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: over 3 years ago

10.1186/s12859-021-04093-9

Machine learning predicts nucleosome binding modes of transcription factors
Cited by: 1
Author(s): K C Kishan, Sridevi K. Subramanya, Rui Li, Feng Cui
Software Mentions: 9
Published: over 3 years ago

10.3390/s19122772

Extracting Value from Industrial Alarms and Events: A Data-Driven Approach Based on Exploratory Data Analysis
Cited by: 16
Author(s): Aguinaldo Bezerra, Ivanovitch Silva, Luiz Affonso Guedes, Diego R. C. Silva, Gustavo Bezerra Paz Leitão, Kaku Saito
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-016-1442-6

Unboxing cluster heatmaps
Cited by: 25
Author(s): Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard
Software Mentions: 9
Published: almost 8 years ago

10.1186/s12911-021-01459-0

Transformers-sklearn: a toolkit for medical language understanding with transformer-based models
Cited by: 14
Author(s): Feihong Yang, Xuwen Wang, Hetong Ma, Jiao Li
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

10.1111/1755-0998.13030

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Cited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: over 5 years ago

10.1038/s41597-020-00638-4

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance
Cited by: 117
Author(s): Sebastiaan P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper Welzel Andersen, Francisco Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro, Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola Marzari, Boris Kozinsky, Giovanni Pizzi
Software Mentions: 9
Published: over 4 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: almost 4 years ago

10.1128/AEM.00121-20

Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i
Cited by: 15
Author(s): Cody Glickman, Ravleen Virdi, Nabeeh A. Hasan, L. Elaine Epperson, Leeza Brown, Stephanie N. Dawrs, James Crooks, Edward D. Chan, Michael Strong, Stephen T. Nelson, Jennifer R. Honda
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-020-02165-2

iMOKA: k-mer based software to analyze large collections of sequencing data
Cited by: 6
Author(s): Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
Software Mentions: 9
Published: about 4 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: 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/s12864-020-06892-5

Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices
Cited by: 15
Author(s): Ananya Bhattacharjee, Md. Shamsuzzoha Bayzid
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pcbi.1008982

Predicting mean ribosome load for 5’UTR of any length using deep learning
Cited by: 14
Author(s): Alexander Karollus, Žiga Avsec, Julien Gagneur
Software Mentions: 9
Published: over 3 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: about 5 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: about 4 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: about 10 years ago

10.1111/tpj.15190

Subgenome evolution in allotetraploid plants
Cited by: 19
Author(s): Matteo Schiavinato, Alexandrina Bodrug‐Schepers, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 9
Published: over 3 years ago

10.1099/mgen.0.000511

Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Cited by: 12
Author(s): Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Iréna Kukavica-Ibrulj, Nicholas P. Tucker, D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter M. Hawkey, Kevin W Southern, Martin Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pcbi.1008126

Ten simple rules to power drug discovery with data science
Cited by: 10
Author(s): Enrico Ferrero, Sophie Brachat, Jeremy L. Jenkins, Philippe Marc, Peter Skewes-Cox, Robert C. Altshuler, Caroline Gubser Keller, Audrey Kauffmann, Erik K Sassaman, Jason M. Laramie, Birgit Schoeberl, Mark Borowsky, Nikolaus Stiefl
Software Mentions: 9
Published: over 4 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-018-2287-y

miRge 2.0 for comprehensive analysis of microRNA sequencing data
Cited by: 54
Author(s): Yin Lu, Alexander S. Baras, Marc K. Halushka
Software Mentions: 9
Published: over 6 years ago

10.7554/eLife.61834

SpikeInterface, a unified framework for spike sorting
Cited by: 96
Author(s): Alessio Paolo Buccino, Cole Hurwitz, Samuel Garcia, Jeremy F. Magland, Joshua H. Siegle, Roger Hurwitz, Matthias H. Hennig
Software Mentions: 9
Published: about 4 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

10.1007/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

10.1186/s12859-021-04275-5

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
Cited by: 2
Author(s): Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Chi Yang
Software Mentions: 8
Published: over 3 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

10.3389/fgene.2021.602196

AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2
Cited by: 4
Author(s): Giovanni Mazzocco, Iga Niemiec, Alexander Myronov, Piotr Skoczylas, Jan Kaczmarczyk, Anna Sanecka-Duin, Katarzyna Gruba, Paulina Król, Michał Drwal, Marian Szczepanik, Krzysztof Pyrć, Piotr Stępniak
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-020-73978-1

Data based predictive models for odor perception
Cited by: 27
Author(s): Rinu Chacko, Deepak Jain, Manasi Patwardhan, Abhishek Puri, Shirish Karande, Beena Rai
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pgen.1009324

Virus-derived variation in diverse human genomes
Cited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 3 years ago

10.1016/j.patter.2021.100270

ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles
Cited by: 1
Author(s): Chinedu Anthony Anene, Faraz Khan, Findlay Bewicke-Copley, Eleni Maniati, Jun Wang
Software Mentions: 8
Published: over 3 years ago

10.26508/lsa.202101113

Statistical guidelines for quality control of next-generation sequencing techniques
Cited by: 1
Author(s): Maximilian Sprang, Matteo Krüger, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pntd.0008755

Combining natural language processing and metabarcoding to reveal pathogen-environment associations
Cited by: 2
Author(s): David Molik, DeAndre Tomlinson, Shane Davitt, Eric Lease Morgan, Matthew Sisk, Benjamin Roche, Natalie Meyers, Michael E. Pfrender
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers13071734

Role for the Histone Demethylase KDM4B in Rhabdomyosarcoma via CDK6 and CCNA2: Compensation by KDM4A and Apoptotic Response of Targeting Both KDM4B and KDM4A
Cited by: 5
Author(s): Zoë S. Walters, Ewa Aładowicz, Bárbara Villarejo-Balcells, Gary Nugent, Joanna Selfe, Paul D. Eve, Julian Blagg, Olivia W. Rossanese, Janet Shipley
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: almost 4 years ago

10.3390/biom10060878

High-Throughput Identification of Adapters in Single-Read Sequencing Data
Cited by: 3
Author(s): Asan M. S. H. Mohideen, Steinar Johansen, Igor Babiak
Software Mentions: 8
Published: over 4 years ago

10.3390/plants10050840

Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field
Cited by: 1
Author(s): Willem Q. M. van de Koot, Larissa J. J. van Vliet, Wei‐Lun Chen, John Doonan, Cândida Nibau
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pbio.3001172

Perception of biological motion by jumping spiders
Cited by: 16
Author(s): Massimo De Agrò, Daniela C. Rößler, Kris Kim, Paul S. Shamble
Software Mentions: 8
Published: over 3 years ago

Projects: pypi: pandas

Papers Mentioning pandas 640