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: cran: SLIDE
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SLIDE
Single Cell Linkage by Distance Estimation is SLIDE
1 version
Latest release: over 6 years ago
104 downloads last month
Papers Mentioning SLIDE 50
10.1186/s13059-016-0881-8
A survey of best practices for RNA-seq data analysisCited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago
10.1186/1471-2105-16-S6-S3
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteinsCited by: 42
Author(s): Hossam M. Ashtawy, Nihar R. Mahapatra
Software Mentions: 9
Published: over 9 years ago
10.1177/1177932219899051
Multi-omics Data Integration, Interpretation, and Its ApplicationCited by: 527
Author(s): Indhupriya Subramanian, Srikant Verma, Sanjiv Kumar, Abhay Jere, Krishanpal Anamika
Software Mentions: 8
Published: almost 5 years ago
10.1186/1471-2105-15-S9-S6
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq dataCited by: 10
Author(s): Jin Gu, Wang Xiao, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 5
Published: about 10 years ago
10.1186/s12864-017-4002-1
Evaluation and comparison of computational tools for RNA-seq isoform quantificationCited by: 132
Author(s): Chi Zhang, Baohong Zhang, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pgen.1000456
Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated MarkersCited by: 170
Author(s): Buhm Han, Hyun Min Kang, Eleazar Eskin
Software Mentions: 4
Published: over 15 years ago
10.3390/molecules24030378
Approaches to the Structure-Based Design of Antivirulence Drugs: Therapeutics for the Post-Antibiotic EraCited by: 19
Author(s): Nolan Neville, Zongchao Jia
Software Mentions: 3
Published: almost 6 years ago
10.3389/fmicb.2018.02313
Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host InvasionCited by: 32
Author(s): Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Software Mentions: 3
Published: about 6 years ago
10.12688/f1000research.2-188.v2
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissuesCited by: 215
Author(s): Liliana Florea, Li Song, Steven L. Salzberg
Software Mentions: 3
Published: about 11 years ago
10.1186/1471-2164-16-S2-S15
Accurate inference of isoforms from multiple sample RNA-Seq dataCited by: 12
Author(s): Masruba Tasnim, Shuping Ma, Ei-Wen Yang, Tao Jiang, Wei Li
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12859-021-04107-6
Optimized permutation testing for information theoretic measures of multi-gene interactionsCited by: 2
Author(s): James Kunert-Graf, Nikita A. Sakhanenko, David J. Galas
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2105-15-135
Computational approaches for isoform detection and estimation: good and bad newsCited by: 26
Author(s): Claudia Angelini, Daniela De Canditiis, Italia De Feis
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2105-16-S4-S8
BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexesCited by: 49
Author(s): Hossam M. Ashtawy, Nihar R. Mahapatra
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-14-S5-S15
A novel min-cost flow method for estimating transcript expression with RNA-SeqCited by: 67
Author(s): Alexandru I. Tomescu, Anna Kuosmanen, Roméo Rizzi, Veli Mäkinen
Software Mentions: 2
Published: over 11 years ago
10.1186/s12859-021-04296-0
Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancerCited by: 4
Author(s): Erica Ponzi, Magne Thoresen, Therese Haugdahl Nøst, Kajsa Møllersen
Software Mentions: 2
Published: over 3 years ago
10.3390/life10050057
Targeting the C-Terminal Domain Small Phosphatase 1Cited by: 10
Author(s): Harikrishna Reddy Rallabandi, Palanivel Ganesan, Young Jun Kim
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pbio.2005821
Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunityCited by: 48
Author(s): Tadeusz Wróblewski, Laurentiu N. Spiridon, Eliza C. Martin, Andrei-José Petrescu, Keri Cavanaugh, María José Truco, Haiping Xu, Dariusz Gozdowski, Krzysztof Pawłowski, Richard W. Michelmore, Frank L. W. Takken
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0028428
Discovery of Novel MDR-Mycobacterium tuberculosis Inhibitor by New FRIGATE Computational ScreenCited by: 11
Author(s): Christoph Scheich, Zoltan Szabadka, Beáta G. Vértessy, Vera Pütter, Vince Grolmusz, Markus Schade
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0046679
Improving PacBio Long Read Accuracy by Short Read AlignmentCited by: 278
Author(s): Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0010126
Discovery of Selective Inhibitors Against EBNA1 via High Throughput In Silico Virtual ScreeningCited by: 58
Author(s): Ning Li, Scott B. Thompson, D. Schultz, Weiliang Zhu, Hualiang Jiang, Cheng Luo, Paul M. Lieberman
Software Mentions: 2
Published: over 14 years ago
10.1016/j.celrep.2021.109038
Characterization of HIV-induced remodeling reveals differences in infection susceptibility of memory CD4+ T cell subsets in vivoCited by: 13
Author(s): Guorui Xie, Xiaoyu Luo, Tongcui Ma, Julie Frouard, Jason Neidleman, Rebecca Hoh, Steven G. Deeks, Warner C. Greene, Nadia R. Roan
Software Mentions: 2
Published: over 3 years ago
10.7554/eLife.55487
HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spreadCited by: 31
Author(s): Tongcui Ma, Xiaoyu Luo, Ashley F George, Gourab Mukherjee, Nandini Sen, Trimble Spitzer, Linda C. Giudice, Warner C. Greene, Nadia R. Roan
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms15011358
In Silico Discovery of Aminoacyl-tRNA Synthetase InhibitorsCited by: 15
Author(s): Yulan Zhao, Qingqing Meng, Linquan Bai, Huchen Zhou
Software Mentions: 2
Published: almost 11 years ago
10.3390/ijms17040525
Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?Cited by: 99
Author(s): David Ramírez, Julio Caballero
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pcbi.1006705
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structuresCited by: 44
Author(s): Jordan Clark, Mark L. Benson, Richard Smith, Heather A. Carlson
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12859-015-0695-9
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samplesCited by: 7
Author(s): Elsa Bernard, Laurent Jacob, Julien Mairal, Éric Viara, Jean-Philippe Vert
Software Mentions: 1
Published: over 9 years ago
10.1186/s13059-016-0903-6
Multiple testing correction in linear mixed modelsCited by: 61
Author(s): Jong Wha J. Joo, Farhad Hormozdiari, Buhm Han, Eleazar Eskin
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0159397
High Specificity in Circulating Tumor Cell Identification Is Required for Accurate Evaluation of Programmed Death-Ligand 1Cited by: 54
Author(s): Jennifer L. Schehr, Zachery D. Schultz, Jay W. Warrick, David J. Guckenberger, Hannah M. Pezzi, Jamie M. Sperger, Erika Héninger, Anwaar Saeed, Ticiana Leal, Kara Mattox, Anne M. Traynor, Toby C. Campbell, Scott M. Berry, David J. Beebe, Joshua M. Lang
Software Mentions: 1
Published: over 8 years ago
10.7150/ijbs.59191
<i>In silico</i> structure-based discovery of a SARS-CoV-2 main protease inhibitorCited by: 9
Author(s): Lei Wen, Kaiming Tang, Kenn Ka-Heng Chik, Chris Chun-Yiu Chan, Jessica Oi-Ling Tsang, Ronghui Liang, Jianli Cao, Yaoqiang Huang, Cuiting Luo, Jian‐Piao Cai, Zi‐Wei Ye, Feifei Yin, Hin Chu, Dong-Yan Jin, Kwok‐Yung Yuen, Shuofeng Yuan, Jasper Fuk‐Woo Chan
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.57849
Whole-genome sequencing analysis of semi-supercentenariansCited by: 34
Author(s): Paolo Garagnani, Julien Marquis, Massimo Delledonne, Chiara Pirazzini, Elena Marasco, Katarzyna Malgorzata Kwiatkowska, Vincenzo Iannuzzi, Maria Giulia Bacalini, Armand Valsesia, Jérôme Carayol, Frédéric Raymond, Alberto Ferrarini, Luciano Xumerle, Sebastiano Collino, Daniela Mari, Beatrice Arosio, Martina Casati, Evelyn Ferri, Daniela Monti, Benedetta Nacmias, Sandro Sorbi, Donata Luiselli, Davide Pettener, Gastone Castellani, Claudia Sala, Giuseppe Passarino, Francesco De Rango, Patrizia D’Aquila, Luca Bertamini, Nicola Martinelli, Domenico Girelli, Oliviero Olivieri, Cristina Giuliani, Patrick Descombes, Claudio Franceschi
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0033851
The GTPase Activating Rap/RanGAP Domain-Like 1 Gene Is Associated with Chicken Reproductive TraitsCited by: 17
Author(s): Xu Shen, Hua Zeng, Liang Xie, Jun He, Jian Li, Xiujuan Xie, Chenglong Luo, Haiping Xu, Min Zhou, Qinghua Nie, Xiquan Zhang
Software Mentions: 1
Published: over 12 years ago
10.3390/ijms22158054
SLIDE—Novel Approach to Apocrine Sweat Sampling for Lipid Profiling in Healthy IndividualsCited by: 3
Author(s): Aleš Kvasnička, David Friedecký, Alena Tichá, R. Hyšpler, Hana Janečková, Radana Brumarová, Lukáš Najdekr, Z Zadák
Software Mentions: 1
Published: over 3 years ago
10.1039/c5sc00473j
Using the gravitational energy of water to generate power by separation of charge at interfacesCited by: 59
Author(s): Yiping Sun, Xu Huang, Siowling Soh
Software Mentions: 1
Published: almost 10 years ago
10.1186/1471-2105-15-S9-S5
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assemblyCited by: 20
Author(s): Roméo Rizzi, Alexandru I. Tomescu, Veli Mäkinen
Software Mentions: 1
Published: about 10 years ago
10.3389/fbioe.2018.00075
Machine Learning in Orthopedics: A Literature ReviewCited by: 128
Author(s): Federico Cabitza, Angela Locoro, Giuseppe Banfi
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2105-15-S9-S3
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seqCited by: 2
Author(s): Yan Huang, Yin Hu, Jinze Liu
Software Mentions: 1
Published: about 10 years ago
10.3389/fmicb.2020.01224
The Use of Single Cell Mass Cytometry to Define the Molecular Mechanisms of Varicella-Zoster Virus LymphotropismCited by: 1
Author(s): Nandini Sen, Gourab Mukherjee, Ann M. Arvin
Software Mentions: 1
Published: over 4 years ago
10.1534/g3.115.023275
Diversity and Divergence of Dinoflagellate Histone ProteinsCited by: 30
Author(s): Georgi K. Marinov, Michael Lynch
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12263-018-0597-3
Analysis of circulating angiopoietin-like protein 3 and genetic variants in lipid metabolism and liver health: the DiOGenes studyCited by: 16
Author(s): Anne Lundby Hess, Jérôme Carayol, Trine Blædel, Jörg Hager, Alessandro Di Cara, Arne Astrup, Wim H. M. Saris, Lesli H. Larsen, Armand Valsesia
Software Mentions: 1
Published: over 6 years ago
10.1186/s12711-018-0402-1
Genome-wide mapping of quantitative trait loci in admixed populations using mixed linear model and Bayesian multiple regression analysisCited by: 16
Author(s): Ali Toosi, Rohan L. Fernando, Jack C. M. Dekkers
Software Mentions: 1
Published: over 6 years ago
10.1186/s13059-014-0501-4
Bayesian transcriptome assemblyCited by: 52
Author(s): Lasse Maretty, Jonas Andreas Sibbesen, Anders Krogh
Software Mentions: 1
Published: about 10 years ago
10.1186/1471-2164-11-724
Accounting for multiple comparisons in a genome-wide association study (GWAS)Cited by: 248
Author(s): Randall C. Johnson, George W. Nelson, Jennifer L. Troyer, James A. Lautenberger, Bailey Kessing, Cheryl A. Winkler, Stephen J. O’Brien
Software Mentions: 1
Published: almost 14 years ago
10.1093/bioinformatics/btu317
Efficient RNA isoform identification and quantification from RNA-Seq data with network flowsCited by: 69
Author(s): Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert
Software Mentions: 1
Published: over 10 years ago
10.1186/1471-2105-14-S5-S14
CLASS: constrained transcript assembly of RNA-seq readsCited by: 29
Author(s): Li Song, Liliana Florea
Software Mentions: 1
Published: over 11 years ago
10.1007/s11306-019-1622-2
Common and distinct variation in data fusion of designed experimental dataCited by: 11
Author(s): Masoumeh Alinaghi, Hanne Christine Bertram, Anders Brunse, Age K. Smilde, Johan A. Westerhuis
Software Mentions: 1
Published: almost 5 years ago
10.3390/molecules171011630
Recent Advances in Cyclonucleosides: C-Cyclonucleosides and Spore Photoproducts in Damaged DNACited by: 9
Author(s): Yuichi Yoshimura, Hiroki Takahata
Software Mentions: 1
Published: about 12 years ago
10.1186/s12864-015-2304-8
NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq dataCited by: 10
Author(s): Yuting Ye, Jingyi Jessica Li
Software Mentions: 1
Published: almost 9 years ago
10.3897/zookeys.1024.60393
Review of the North American fauna of Drymeia Meigen (Diptera, Muscidae) and evaluation of DNA barcodes for species-level identification in the genusCited by: 2
Author(s): Jade Savage, Vera S. Sorokina
Software Mentions: 1
Published: over 3 years ago
10.1186/s13059-015-0865-0
CIDANE: comprehensive isoform discovery and abundance estimationCited by: 41
Author(s): Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pcbi.1004586
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site FlexibilityCited by: 256
Author(s): Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner
Software Mentions: 1
Published: almost 9 years ago