pypi: linux | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: over 3 years ago

10.1155/2014/348725

Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
Cited by: 6
Author(s): Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei P. Feinstein, Michał Bryliński, Shantenu Jha, Joohyun Kim
Software Mentions: 4
Published: almost 11 years ago

10.1186/1471-2105-8-344

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Cited by: 11
Author(s): Jeremiah J. Faith, Andrew Olson, Timothy S. Gardner, Ravi Sachidanandam
Software Mentions: 4
Published: about 17 years ago

10.1186/s13073-014-0125-z

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia
Cited by: 51
Author(s): Simone Ecker, Véra Pancaldi, Daniel Rico, Alfonso Valencia
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-015-0721-2

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
Cited by: 2,420
Author(s): David Emms, Steven Kelly
Software Mentions: 4
Published: over 9 years ago

10.1186/s12889-021-11790-w

Electronic data collection, management and analysis tools used for outbreak response in low- and middle-income countries: a systematic review and stakeholder survey
Cited by: 4
Author(s): Patrick Keating, Jillian Murray, Karl Schenkel, Laura Merson, Anna C. Seale
Software Mentions: 4
Published: about 3 years ago

10.1186/1471-2105-6-132

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
Cited by: 457
Author(s): Bjoern Peters, Alessandro Sette
Software Mentions: 4
Published: over 19 years ago

10.1186/1471-2105-12-83

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models
Cited by: 11
Author(s): Juliana Silva Bernardes, Alessandra Carbone, Gerson Zaverucha
Software Mentions: 4
Published: over 13 years ago

10.1186/gb-2008-9-1-r11

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships
Cited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: almost 17 years ago

10.1186/1471-2105-10-221

An introduction to scripting in Ruby for biologists
Cited by: 15
Author(s): Jan Aerts, Andy Law
Software Mentions: 4
Published: over 15 years ago

10.18632/oncotarget.24898

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets
Cited by: 17
Author(s): Rosemarie Weikard, Frieder Hadlich, H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Christa Kühn
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2018.01966

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data
Cited by: 12
Author(s): Ritwika Das, Vasu Arora, Sarika Jaiswal, Mir Asif Iquebal, U. B. Angadi, Samar Fatma, Rakesh Singh, Sandip Shil, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-5-60

POSA: Perl Objects for DNA Sequencing Data Analysis
Cited by: 5
Author(s): Jan Aerts, B.J. Jungerius, Martien A. M. Groenen
Software Mentions: 3
Published: about 20 years ago

10.1186/s12859-021-04192-7

A tool for analyzing and visualizing ribo-seq data at the isoform level
Cited by: 0
Author(s): Wei Wu, Yi Hong Tsao, Sheng Cian Shiue, Ting Yu Chen, Yan Yuan Tseng, Joseph T. Tseng
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-5210-z

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce
Cited by: 14
Author(s): Edita Jurak, Hitoshi Suzuki, Gijs van Erven, Julie-Anne Gandier, Pauline Wong, Kin Chan, Chi-Yip Ho, Yunchen Gong, Elisabeth R. M. Tillier, Marie‐Noëlle Rosso, Mirjam A. Kabel, Shingo Miyauchi, Emma R. Master
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-15-53

MafFilter: a highly flexible and extensible multiple genome alignment files processor
Cited by: 61
Author(s): Julien Dutheil, Sylvain Gaillard, Eva H. Stukenbrock
Software Mentions: 3
Published: almost 11 years ago

10.3389/fpls.2017.00969

Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing
Cited by: 14
Author(s): Muhammad Farooq, Shahid Mansoor, Hui Guo, Imran Amin, Peng W. Chee, M. Kamran Azim, Andrew H. Paterson
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-06858-7

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells
Cited by: 6
Author(s): Henning Onsbring, Alexander K. Tice, Brandon T. Barton, Matthew W. Brown, Thijs J. G. Ettema
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-11-S2-S6

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS
Cited by: 23
Author(s): Hwanjo Yu, Tae-Hoon Kim, Jinoh Oh, Ilhwan Ko, Sung‐Chul Kim, Wook-Shin Han
Software Mentions: 3
Published: over 14 years ago

10.1111/pbi.13305

Cytokinin dehydrogenase: a genetic target for yield improvement in wheat
Cited by: 84
Author(s): Lei Chen, Jingjing Zhao, Jiancheng Song, Paula E. Jameson
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-7-275

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
Cited by: 95
Author(s): Thomas J. Boyle, Zhirong Bao, John I. Murray, Carlos L. Araya, Robert H. Waterston
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pcbi.1008174

Metabolic pathway inference using multi-label classification with rich pathway features
Cited by: 8
Author(s): Abdur Rahman M. A. Basher, Ryan J. McLaughlin, Steven J. Hallam
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2105-12-126

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology
Cited by: 9
Author(s): Szymon Stoma, Martina Fröhlich, Susanne Gerber, Edda Klipp
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2020.00003

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Cited by: 13
Author(s): Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil K. Raghav
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-15-85

Variant calling in low-coverage whole genome sequencing of a Native American population sample
Cited by: 31
Author(s): Chris Bizon, Michael Spiegel, Scott A. Chasse, Ian R. Gizer, Yun Li, Ewa Malc, Piotr A. Mieczkowski, Josh K Sailsbery, Xiaoshu Wang, Cindy L. Ehlers, Kirk C. Wilhelmsen
Software Mentions: 3
Published: almost 11 years ago

10.12688/f1000research.3-14.v2

mfSBA: Multifractal analysis of spatial patterns in ecological communities
Cited by: 6
Author(s): Leonardo A. Saravia
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-15-S1-S10

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units
Cited by: 4
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-6-219

Generalizations of Markov model to characterize biological sequences
Cited by: 12
Author(s): Junwen Wang, Sridhar Hannenhalli
Software Mentions: 3
Published: about 19 years ago

10.1371/journal.pcbi.1005851

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
Cited by: 29
Author(s): Ruolin Liu, Julie A. Dickerson
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2148-10-302

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Cited by: 562
Author(s): Liangliang Liu, Lili Yu, Scott V. Edwards
Software Mentions: 3
Published: almost 15 years ago

10.1038/s42003-021-02577-1

Machine learning-based real-time object locator/evaluator for cryo-EM data collection
Cited by: 19
Author(s): Koji Yonekura, Saori Maki-Yonekura, Hisashi Naitow, Tasuku Hamaguchi, Kiyotsugu Takaba
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1008697

FastTrack: An open-source software for tracking varying numbers of deformable objects
Cited by: 25
Author(s): Benjamin Gallois, Raphaël Candelier
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12885-017-3059-1

Stepwise addition of genetic changes correlated with histological change from “well-differentiated” to “sarcomatoid” phenotypes: a case report
Cited by: 24
Author(s): Taichiro Goto, Yosuke Hirotsu, Hitoshi Mochizuki, Takahiro Nakagomi, Toshio Oyama, Kenji Amemiya, Masao Omata
Software Mentions: 3
Published: almost 8 years ago

10.1186/1742-4682-3-13

A method for the generation of standardized qualitative dynamical systems of regulatory networks
Cited by: 212
Author(s): Luis Mendoza, Ioannis Xenarios
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0119289

Structure Determination of Feline Calicivirus Virus-Like Particles in the Context of a Pseudo-Octahedral Arrangement
Cited by: 11
Author(s): W.P. Burmeister, Marlyse Buisson, Leandro F. Estrozi, Guy Schoehn, Olivier Billet, Zahia Hannas, Cécile Sigoillot, Hervé Poulet
Software Mentions: 3
Published: over 9 years ago

10.1007/s00127-018-1487-0

The network structure of paranoia in the general population
Cited by: 49
Author(s): Vaughan Bell, Ciarán O’Driscoll
Software Mentions: 3
Published: almost 7 years ago

10.1186/1751-0473-8-3

FCC – An automated rule-based processing tool for life science data
Cited by: 17
Author(s): Simon Barkow-Oesterreicher, Can Türker, Christian Panse
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2105-8-268

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
Cited by: 138
Author(s): Michael J. Hickerson, Eli A. Stahl, Naoki Takebayashi
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-12-68

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
Cited by: 39
Author(s): Matthew E. Ritchie, Ruijie Liu, Benilton Carvalho, Rafael A. Irizarry
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0024210

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles
Cited by: 21
Author(s): Yingtao Bi, Hyunsoo Kim, Ravi P. Gupta, Ramana V. Davuluri
Software Mentions: 3
Published: about 13 years ago

10.12688/wellcomeopenres.14438.2

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum
Cited by: 5
Author(s): Mary Dias, Chitra Pattabiraman, Shilpa Siddappa, Malali Gowda, Anita Shet, Derek J. Smith, Barbara Muehlemann, Krishnapriya Tamma, Tom Solomon, Terry C. Jones, Sudhir Krishna
Software Mentions: 3
Published: almost 6 years ago

10.3390/s19010001

Sii-Mobility: An IoT/IoE Architecture to Enhance Smart City Mobility and Transportation Services
Cited by: 53
Author(s): Claudio Badii, Pierfrancesco Bellini, Angelo Difino, Paolo Nesi
Software Mentions: 3
Published: almost 6 years ago

10.3390/s20123511

IoT Sensing Platform as a Driver for Digital Farming in Rural Africa
Cited by: 19
Author(s): Antônio Oliveira-Jr, Carlos Resende, André Alves Pereira, Pedro Madureira, João Gonçalves, Ruben Moutinho, Filipe Soares, Waldir Moreira
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-40659-7

Genome-wide Analysis of bZIP Transcription Factors in wheat and Functional Characterization of a TabZIP under Abiotic Stress
Cited by: 70
Author(s): Pragya Agarwal, Vinay Kumar Baranwal, Paramjit Khurana
Software Mentions: 3
Published: over 5 years ago

10.1038/srep11534

Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data
Cited by: 35
Author(s): Michael Förster, Silke Szymczak, David Ellinghaus, Georg Hemmrich, Malte Rühlemann, Lars Kraemer, Sören Mucha, Lars Wienbrandt, Martin Stanulla, André Franke
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-10-35

The Genome Reverse Compiler: an explorative annotation tool
Cited by: 13
Author(s): Andrew S. Warren, João Carlos Setúbal
Software Mentions: 3
Published: almost 16 years ago

10.1038/srep12062

Differential and coherent processing patterns from small RNAs
Cited by: 21
Author(s): Sachin Pundhir, Jan Gorodkin
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-020-61857-8

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-15-237

Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes
Cited by: 24
Author(s): Shea N. Gardner, Tom Slezak
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.ppat.1005576

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae
Cited by: 15
Author(s): Joshua Chang Mell, Cristina Viadas, Javier Moleres, Sunita Sinha, Ariadna Fernández-Calvet, Eric A. Porsch, Joseph W. St. Geme, Corey Nislow, Rosemary J. Redfield, Junkal Garmendia
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-11-138

An optimized TOPS+ comparison method for enhanced TOPS models
Cited by: 2
Author(s): Mallika Veeramalai, David Gilbert, Gabriel Valiente
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-020-03887-7

Inferring time-dependent population growth rates in cell cultures undergoing adaptation
Cited by: 9
Author(s): H. Jonathan G. Lindström, Ran Friedman
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-8-307

Protein structural similarity search by Ramachandran codes
Cited by: 45
Author(s): Wei-Cheng Lo, Po-Jung Huang, Chih Hung Chang, Ping Lyu
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-14-220

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
Cited by: 15
Author(s): Xinyun Ma, Xuegong Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-018-1449-6

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments
Cited by: 153
Author(s): Viktor Petukhov, Jimin Guo, Ninib Baryawno, Nicolas Sévère, David T. Scadden, Maria Samsonova, Peter V. Kharchenko
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0136718

Accelerating Neuroimage Registration through Parallel Computation of Similarity Metric
Cited by: 6
Author(s): Yungang Luo, Ping Liu, Lin Shi, Yishan Luo, Lei Yi, Ang Li, Jing Qin, Pheng‐Ann Heng, Defeng Wang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12929-014-0088-9

Identifying rare and common disease associated variants in genomic data using Parkinson's disease as a model
Cited by: 6
Author(s): Ying Lin, Ai-Ru Hsieh, Ching Lin Hsiao, Shang Jung Wu, Hui‐Min David Wang, Ie Bin Lian, Cathy S.J. Fann
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2229-13-228

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing
Cited by: 40
Author(s): Jin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12859-018-2315-y

bioSyntax: syntax highlighting for computational biology
Cited by: 2
Author(s): Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Jeffrey Kam, Gherman Novakovsky, Jasper Wong, Dylan Aïssi, Yao Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-014-0468-1

The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment
Cited by: 81
Author(s): Seung Chul Shin, Do Hwan Ahn, Su Jin Kim, Chul Woo Pyo, Yongrok Choi, Mi-Kyeong Kim, Jung-Eun Lee, Jong Eun Lee, H. William Detrich, John H. Postlethwait, David Edwards, Sung Gu Lee, Hyun Park
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1003942

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
Cited by: 122
Author(s): Krystyna Nadachowska‐Brzyska, Reto Burri, Pall I. Olason, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren
Software Mentions: 3
Published: about 11 years ago

10.1002/gepi.22345

A framework for pathway knowledge driven prioritization in genome‐wide association studies
Cited by: 2
Author(s): Shrayashi Biswas, Suresh Pal, Partha P. Majumder, Samsiddhi Bhattacharjee
Software Mentions: 3
Published: over 4 years ago

10.1186/s12913-021-06798-2

Empirically identified networks of healthcare providers for adults with mental illness
Cited by: 2
Author(s): Joshua Breslau, Beth Dana, Harold Alan Pincus, Marcela Horvitz-Lennon, Luke J. Matthews
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-9-330

An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
Cited by: 43
Author(s): Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J. Siezen, Christof Francke
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-10-469

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades
Cited by: 60
Author(s): Frank Förster, Chunguang Liang, Alexander V. Shkumatov, Daniela Beißer, Julia C. Engelmann, Martina Schnölzer, Marcus Frohme, Tobias Müller, Ralph O. Schill, Thomas Dandekar
Software Mentions: 2
Published: about 15 years ago

10.3389/fpls.2020.00688

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)
Cited by: 14
Author(s): Do Yoon Hyun, Sebastin Raveendar, Kyung Jun Lee, Gi-An Lee, Myoung-Jae Shin, Seong Hoon Kim, Jung-Ro Lee, Gyu‐Taek Cho
Software Mentions: 2
Published: over 4 years ago

10.3389/fnins.2020.590029

Changes in Day/Night Activity in the 6-OHDA-Induced Experimental Model of Parkinson’s Disease: Exploring Prodromal Biomarkers
Cited by: 7
Author(s): Catalina Requejo, Karmele López de Ipiña, José Ángel Ruiz-Ortega, Elsa Fernández, Pilar M. Calvo, Teresa Morera-Herreras, Cristina Miguélez, Laura Cardona-Grifoll, Hodei Cepeda, Luisa Ugedo, José Vicente Lafuente
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-10-198

A Bayesian approach to efficient differential allocation for resampling-based significance testing
Cited by: 6
Author(s): Shane T. Jensen, Sameer Soi, Li-San Wang
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-13-417

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing
Cited by: 6
Author(s): Abdou ElSharawy, Michael Förster, Nadine Schracke, Andreas Keller, Ingo Thomsen, Britt‐Sabina Petersen, Björn Stade, Peer F. Stähler, Stefan Schreiber, Philip Rosenstiel, André Franke
Software Mentions: 2
Published: over 12 years ago

10.3389/frobt.2020.00098

Efficacy of Modern Neuro-Evolutionary Strategies for Continuous Control Optimization
Cited by: 19
Author(s): Paolo Pagliuca, Nicola Milano, Stefano Nolfi
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-016-3208-y

De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water
Cited by: 11
Author(s): Peter A. Bain, Adrienne Gregg, Anu Kumar
Software Mentions: 2
Published: about 8 years ago

10.3389/fninf.2013.00032

Brain extraction using the watershed transform from markers
Cited by: 33
Author(s): Richard Beare, Jian Chen, Christopher Adamson, Tim Silk, Deanne K. Thompson, Joseph Yuan-Mou Yang, Vladyslav Anderson, Marc L. Seal, Amanda G. Wood
Software Mentions: 2
Published: almost 12 years ago

10.3389/fninf.2013.00050

Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease
Cited by: 330
Author(s): Denis P. Shamonin, Esther E. Bron, Boudewijn P. F. Lelieveldt, Marion Smits, Stefan Klein, Marius Staring
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2105-11-317

Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences
Cited by: 32
Author(s): Amber Hartman, Sean Riddle, Timothy M. McPhillips, Bertram Ludäscher, Jonathan A. Eisen
Software Mentions: 2
Published: over 14 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: almost 10 years ago

10.3389/fimmu.2019.02367

Minimizing Batch Effects in Mass Cytometry Data
Cited by: 73
Author(s): Ronald P. Schuyler, Conner Jackson, Josselyn E. Garcia-Perez, Ryan M. Baxter, Sidney Ogolla, Rosemary Rochford, Debashis Ghosh, Pratyaydipta Rudra, Elena W.Y. Hsieh
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.631603

IL-33 Gene Polymorphisms as Potential Biomarkers of Disease Susceptibility and Response to TNF Inhibitors in Rheumatoid Arthritis, Ankylosing Spondylitis, and Psoriatic Arthritis Patients
Cited by: 17
Author(s): Milena Iwaszko, Joanna Wielińska, Jerzy Świerkot, Katarzyna Kolossa, Renata Sokolik, Bartosz Bugaj, Monika Chaszczewska-Markowska, Sławomir Jeka, Katarzyna Bogunia‐Kubik
Software Mentions: 2
Published: over 3 years ago

10.3389/frobt.2019.00022

Model-Based Control of Soft Actuators Using Learned Non-linear Discrete-Time Models
Cited by: 40
Author(s): Phillip Hyatt, David Wingate, Marc D. Killpack
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-13-299

PePPER: a webserver for prediction of prokaryote promoter elements and regulons
Cited by: 133
Author(s): Anne de Jong, Hilco Pietersma, Martijn Cordes, Oscar P. Kuipers, Jan Kok
Software Mentions: 2
Published: over 12 years ago

10.3389/fchem.2017.00100

Discovering Novel Alternaria solani Succinate Dehydrogenase Inhibitors by in Silico Modeling and Virtual Screening Strategies to Combat Early Blight
Cited by: 13
Author(s): Sehrish Iftikhar, Ahmad Ali Shahid, Sobia Ahsan Halim, Pieter J. Wolters, Vivianne G. A. A. Vleeshouwers, Ajmal Khan, Ahmed Al‐Harrasi, Shahbaz Ahmad
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-018-4891-7

Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing
Cited by: 6
Author(s): Shengru Wu, Yan Li Liu, Wei Guo, Xi Cheng, Xiaochun Ren, Si Chen, Xueyuan Li, Yongle Duan, Qingzhu Sun, Xiaojun Yang
Software Mentions: 2
Published: over 6 years ago

10.3389/fchem.2018.00189

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
Cited by: 5
Author(s): Mingyuan Xu, Tong Zhu, John Z. H. Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4771-1

Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
Cited by: 41
Author(s): Jake A. Lacey, Theo R. Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas L. Stent, Xiaoyan Han, Julian I. Rood, Ben Wade, Anthony L. Keyburn, Torsten Seemann, Honglei Chen, Volker Häring, Priscilla Johanesen, Dena Lyras, Robert J. Moore
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-14-200

Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies
Cited by: 22
Author(s): Katherine Thompson, Laura Kubatko
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-11-398

Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training
Cited by: 78
Author(s): Beatrice A. McGivney, Paul A. McGettigan, John A. Browne, A.C.O. Evans, R. Fonseca, Brendan J. Loftus, Amanda J. Lohan, David E. MacHugh, Barbara A. Murphy, Lisa Katz, E. W. Hill
Software Mentions: 2
Published: over 14 years ago

10.3389/fcell.2014.00070

Integrative workflows for metagenomic analysis
Cited by: 31
Author(s): Efthymios Ladoukakis, Fragiskos N. Kolisis, Aristotelis Chatziioannou
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-11-S12-S6

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
Cited by: 7
Author(s): Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al‐Ouran, Lev Neiman, L Nau, Joshua D. Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank A. Drews, Stephen Sauchi Lee, Lonnie R. Welch
Software Mentions: 2
Published: almost 14 years ago

10.1107/S1399004713029817

Experiences with making diffraction image data available: what metadata do we need to archive?
Cited by: 24
Author(s): Loes M. J. Kroon-Batenburg, John R. Helliwell
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-9-457

CoGemiR: A comparative genomics microRNA database
Cited by: 37
Author(s): Vincenza Maselli, Diego di Bernardo, Sandro Banfi
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2105-7-461

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons
Cited by: 9
Author(s): Chunguang Liang, Thomas Dandekar
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pcbi.1008565

Online analysis of microendoscopic 1-photon calcium imaging data streams
Cited by: 22
Author(s): Johannes Friedrich, Andrea Giovannucci, Eftychios A. Pnevmatikakis
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-13-324

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
Cited by: 53
Author(s): Steven M. Lewis, Attila Csordás, Sarah Killcoyne, Henning Hermjakob, Michael R. Hoopmann, Robert L. Moritz, Eric W. Deutsch, John P. Boyle
Software Mentions: 2
Published: almost 12 years ago

10.12688/f1000research.2-217.v2

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
Cited by: 16
Author(s): Guillermo Barturen, Antonio Rueda, José Luis Tejera Oliver, Michael Hackenberg
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1005494

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Cited by: 79
Author(s): Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J. Lercher
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2148-9-207

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family
Cited by: 47
Author(s): William J. Gillis, John St. John, Bruce Bowerman, Stephan Schneider
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pcbi.1003792

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Cited by: 19
Author(s): Brian Y. Chen
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pcbi.1005897

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
Cited by: 24
Author(s): Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert C. Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris
Software Mentions: 2
Published: over 6 years ago

Projects: pypi: linux

Papers Mentioning linux 450