cran: SLIDE | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited 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: over 8 years ago

10.1186/1471-2105-16-S6-S3

Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
Cited 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 Application
Cited by: 527
Author(s): Indhupriya Subramanian, Srikant Verma, Sanjiv Kumar, Abhay Jere, Krishanpal Anamika
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-15-S9-S6

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
Cited 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 quantification
Cited by: 132
Author(s): Chi Zhang, Baohong Zhang, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1000456

Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers
Cited 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 Era
Cited by: 19
Author(s): Nolan Neville, Zongchao Jia
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2018.02313

Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion
Cited by: 32
Author(s): Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Software Mentions: 3
Published: almost 6 years ago

10.12688/f1000research.2-188.v2

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
Cited by: 215
Author(s): Liliana Florea, Li Song, Steven L. Salzberg
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-16-S2-S15

Accurate inference of isoforms from multiple sample RNA-Seq data
Cited by: 12
Author(s): Masruba Tasnim, Shuping Ma, Ei-Wen Yang, Tao Jiang, Wei Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-021-04107-6

Optimized permutation testing for information theoretic measures of multi-gene interactions
Cited 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 news
Cited 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 complexes
Cited 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-Seq
Cited 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 cancer
Cited by: 4
Author(s): Erica Ponzi, Magne Thoresen, Therese Haugdahl Nøst, Kajsa Møllersen
Software Mentions: 2
Published: about 3 years ago

10.3390/life10050057

Targeting the C-Terminal Domain Small Phosphatase 1
Cited 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 immunity
Cited 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 Screen
Cited 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 Alignment
Cited by: 278
Author(s): Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0010126

Discovery of Selective Inhibitors Against EBNA1 via High Throughput In Silico Virtual Screening
Cited 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 vivo
Cited 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 spread
Cited 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 Inhibitors
Cited by: 15
Author(s): Yulan Zhao, Qingqing Meng, Linquan Bai, Huchen Zhou
Software Mentions: 2
Published: over 10 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 structures
Cited by: 44
Author(s): Jordan Clark, Mark L. Benson, Richard Smith, Heather A. Carlson
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-015-0695-9

A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples
Cited by: 7
Author(s): Elsa Bernard, Laurent Jacob, Julien Mairal, Éric Viara, Jean-Philippe Vert
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-016-0903-6

Multiple testing correction in linear mixed models
Cited 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 1
Cited 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: about 8 years ago

10.7150/ijbs.59191

<i>In silico</i> structure-based discovery of a SARS-CoV-2 main protease inhibitor
Cited 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: over 3 years ago

10.7554/eLife.57849

Whole-genome sequencing analysis of semi-supercentenarians
Cited 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 Traits
Cited 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 Individuals
Cited by: 3
Author(s): Aleš Kvasnička, David Friedecký, Alena Tichá, R. Hyšpler, Hana Janečková, Radana Brumarová, Lukáš Najdekr, Z Zadák
Software Mentions: 1
Published: about 3 years ago

10.1039/c5sc00473j

Using the gravitational energy of water to generate power by separation of charge at interfaces
Cited by: 59
Author(s): Yiping Sun, Xu Huang, Siowling Soh
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-15-S9-S5

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly
Cited 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 Review
Cited by: 128
Author(s): Federico Cabitza, Angela Locoro, Giuseppe Banfi
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-15-S9-S3

Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq
Cited 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 Lymphotropism
Cited by: 1
Author(s): Nandini Sen, Gourab Mukherjee, Ann M. Arvin
Software Mentions: 1
Published: about 4 years ago

10.1534/g3.115.023275

Diversity and Divergence of Dinoflagellate Histone Proteins
Cited by: 30
Author(s): Georgi K. Marinov, Michael Lynch
Software Mentions: 1
Published: over 8 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 study
Cited 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 analysis
Cited by: 16
Author(s): Ali Toosi, Rohan L. Fernando, Jack C. M. Dekkers
Software Mentions: 1
Published: about 6 years ago

10.1186/s13059-014-0501-4

Bayesian transcriptome assembly
Cited by: 52
Author(s): Lasse Maretty, Jonas Andreas Sibbesen, Anders Krogh
Software Mentions: 1
Published: almost 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 flows
Cited 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 reads
Cited 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 data
Cited 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 DNA
Cited by: 9
Author(s): Yuichi Yoshimura, Hiroki Takahata
Software Mentions: 1
Published: almost 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 data
Cited by: 10
Author(s): Yuting Ye, Jingyi Jessica Li
Software Mentions: 1
Published: over 8 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 genus
Cited 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 estimation
Cited by: 41
Author(s): Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1004586

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Cited 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

Projects: cran: SLIDE

Papers Mentioning SLIDE 50