pypi: grep | Projects | Ecosyste.ms: Papers

10.1016/j.cell.2019.09.035

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Cited by: 322
Author(s): Chrysothemis C. Brown, Herman Gudjonson, Yuri Pritykin, Deeksha Deep, Vincent Philippe Lavallée, Alejandra Mendoza, Rachel M. Fromme, Linas Mažutis, Charlotte E. Ariyan, Christina Leslie, Dana Pe’er, Alexander Y. Rudensky
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pcbi.1008645

Ten simple rules for getting started with command-line bioinformatics
Cited by: 7
Author(s): Parice A. Brandies, Carolyn J. Hogg
Software Mentions: 7
Published: almost 4 years ago

10.7717/peerj.5299

BTW—Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data
Cited by: 2
Author(s): Daniel Morais, Luiz Fernando Würdig Roesch, Marc Redmile‐Gordon, Fausto G. dos Santos, Petr Baldrián, Fernando Dini Andreote, Victor Satler Pylro
Software Mentions: 7
Published: over 6 years ago

10.1093/gbe/evz245

The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)
Cited by: 42
Author(s): Valerie L. Soza, Dale Lindsley, Adam Waalkes, Elizabeth Ramage, Rupali P Patwardhan, Joshua N. Burton, Andrew Adey, Akash Kumar, Ruolan Qiu, Jay Shendure, Benjamin D. Hall
Software Mentions: 6
Published: about 5 years ago

10.1074/jbc.RA120.014598

The nuclear factor CECR2 promotes somatic cell reprogramming by reorganizing the chromatin structure
Cited by: 2
Author(s): Linlin Wu, Guoqing Zhao, Xu Shou, Jinqiang Kuang, Ming Jin, Guiying Wu, Tao Wang, Bo Wang, Ping Zhu, Duanqing Pei, Jing Liu
Software Mentions: 6
Published: almost 4 years ago

10.1186/1472-6947-5-30

Automation of a problem list using natural language processing
Cited by: 93
Author(s): Stéphane M. Meystre, Peter J. Haug
Software Mentions: 6
Published: over 19 years ago

10.1128/mBio.02146-20

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System
Cited by: 20
Author(s): Charlotte B. Francoeur, Lily Khadempour, Rolando D. Moreira-Soto, Kirsten Gotting, Adam J. Book, Adrián A. Pinto‐Tomás, Ken Keefover‐Ring, Cameron R. Currie
Software Mentions: 6
Published: about 4 years ago

10.26508/lsa.202000731

Exploiting somatic piRNAs in Bemisia tabaci enables novel gene silencing through RNA feeding
Cited by: 18
Author(s): Mosharrof Mondal, Judith K. Brown, Alex S. Flynt
Software Mentions: 6
Published: over 4 years ago

10.1016/j.dib.2020.105757

The molecular entities in linked data dataset
Cited by: 1
Author(s): Dominik Tomaszuk, Łukasz Szeremeta
Software Mentions: 6
Published: over 4 years ago

10.3390/v12070695

Ross River Virus Provokes Differentially Expressed MicroRNA and RNA Interference Responses in Aedes aegypti Mosquitoes
Cited by: 10
Author(s): J. B. Sinclair, Sassan Asgari
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-017-14650-z

Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females
Cited by: 18
Author(s): Louise Pease, Peter Clegg, Carole J. Proctor, Daryl P. Shanley, Simon Cockell, Mandy J. Peffers
Software Mentions: 5
Published: about 7 years ago

10.1186/s12885-020-6616-y

Epigenetic loss of heterozygosity of Apc and an inflammation-associated mutational signature detected in Lrig1+/−-driven murine colonic adenomas
Cited by: 1
Author(s): Jessica L. Preston, Nicholas Stiffler
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13321-018-0312-9

MER: a shell script and annotation server for minimal named entity recognition and linking
Cited by: 27
Author(s): Francisco M. Couto, André Lamúrias
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2164-8-191

C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families
Cited by: 15
Author(s): Ryan E Austin, Nicholas J. Provart, Sean R. Cutler
Software Mentions: 5
Published: over 17 years ago

10.12688/f1000research.16301.2

Increasing workflow development speed and reproducibility with Vectools
Cited by: 0
Author(s): Tyler Weirick, Raphael Müller, Shizuka Uchida
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0192858

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets
Cited by: 1
Author(s): Piotr Madanecki, Magdalena Bałut, Patrick G. Buckley, J. Renata Ochocka, Rafał Bartoszewski, David K. Crossman, Ludwine Messiaen, Arkadiusz Piotrowski
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-018-2446-1

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
Cited by: 26
Author(s): Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O’Connor, Michael R. Crusoe, Don Armstrong, Shaun Aron, Fourie Joubert, Azza E. Ahmed, Mamana Mbiyavanga, Peter van Heusden, Lerato E Magosi, Jennie Zermeno, Liudmila Sergeevna Mainzer, Faisal M. Fadlelmola, C V Jongeneel, Nicola Mulder
Software Mentions: 4
Published: about 6 years ago

10.1093/bioinformatics/btaa950

RepeatFS: a file system providing reproducibility through provenance and automation
Cited by: 0
Author(s): Anthony Westbrook, Elizabeth Varki, W. Kelley Thomas
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1005422

Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation
Cited by: 11
Author(s): David M. Truong, F. Curtis Hewitt, Joseph H. Hanson, Xiaoxia Cui, Alan M. Lambowitz
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0242708

Multi-objective regression test suite optimization using three variants of adaptive neuro fuzzy inference system
Cited by: 5
Author(s): Ayesha Kiran, Wasi Haider Butt, Arslan Shaukat, Muhammad Umar Farooq, Urooj Fatima, Farooque Azam, Zeeshan Anwar
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2019.00549

Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks
Cited by: 32
Author(s): Pavel Loskot, Komlan Atitey, Lyudmila Mihaylova
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.00496

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
Cited by: 55
Author(s): HueyTyng Lee, Harmeet Singh Chawla, Christian Obermeier, Felix Dreyer, Amine Abbadi, Rod J. Snowdon
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02248-0

The variant call format provides efficient and robust storage of GWAS summary statistics
Cited by: 55
Author(s): M. Lyon, Shea J. Andrews, Benjamin Elsworth, Tom R. Gaunt, Gibran Hemani, Edoardo Marcora
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.67615

Local adaptation and archaic introgression shape global diversity at human structural variant loci
Cited by: 27
Author(s): Shouqing Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N Bortvin, Michael C. Schatz, Rajiv C. McCoy
Software Mentions: 4
Published: over 3 years ago

10.1016/j.omtm.2021.07.001

High throughput screening of novel AAV capsids identifies variants for transduction of adult NSCs within the subventricular zone
Cited by: 15
Author(s): Lukas P.M. Kremer, Santiago Cerrizuela, Sascha Dehler, Thomas Stiehl, Jonas Weinmann, Heike Abendroth, Susanne Kleber, Alexander Laure, Jihad El Andari, Simon Anders, Anna Marciniak‐Czochra, Dirk Grimm, Ana Martin‐Villalba
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2105-9-532

Extended Newick: it is time for a standard representation of phylogenetic networks
Cited by: 90
Author(s): Gabriel Cardona, Francesc Rosselló, Gabriel Valiente
Software Mentions: 3
Published: about 16 years ago

10.1128/mSphere.00482-19

Genomic Variation among Strains of Crithidia bombi and C. expoeki
Cited by: 7
Author(s): Evgeny S. Gerasimov, Niklaus Zemp, Regula Schmid‐Hempel, Paul Schmid‐Hempel, Vyacheslav Yurchenko
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1007066

Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni
Cited by: 44
Author(s): David Roquis, Aaron Taudt, Kathrin K. Geyer, Gilda Padalino, Karl F. Hoffmann, Nancy Holroyd, Matthew Berriman, Benoît Aliaga, Cristian Chaparro, Christoph Grunau, Ronaldo de Carvalho Augusto
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: over 3 years ago

10.1002/pld3.60

Expression of FLOWERING LOCUS C and a frameshift mutation of this gene on chromosome 20 differentiate a summer and winter annual biotype of Camelina sativa
Cited by: 23
Author(s): James V. Anderson, David P. Horvath, Münevver Doğramacı, Kevin M. Dorn, Wun S. Chao, Erin E. Watkin, Alvaro G. Hernandez, M. David Marks, Russ W. Gesch
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0100864

Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions Using RNA-Seq Data
Cited by: 10
Author(s): Yongsheng Bai, Justin Hassler, Ahdad Ziyar, Hui Li, Zachary C. Wright, Rajasree Menon, Gilbert S. Omenn, James D. Cavalcoli, Randal J. Kaufman, Maureen A. Sartor
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-015-1975-5

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Cited by: 32
Author(s): Elizabeth Hénaff, Luís Zapata, Josep M. Casacuberta, Stephan Ossowski
Software Mentions: 3
Published: about 9 years ago

10.1093/molbev/msz176

Discovery of Novel Sequences in 1,000 Swedish Genomes
Cited by: 23
Author(s): Jesper Eisfeldt, Gustaf Mårtensson, Adam Ameur, Daniel Nilsson, Anna Wedell
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2017.00079

LMNA Sequences of 60,706 Unrelated Individuals Reveal 132 Novel Missense Variants in A-Type Lamins and Suggest a Link between Variant p.G602S and Type 2 Diabetes
Cited by: 14
Author(s): Alyssa Florwick, Tejas Dharmaraj, Julie A Jurgens, David Valle, Katherine L. Wilson
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-016-1080-3

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes
Cited by: 35
Author(s): Anthony J. Studer, James C. Schnable, S. Weissmann, Allison R. Kolbe, Michael R. McKain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell
Software Mentions: 2
Published: about 8 years ago

10.1093/bioinformatics/btx007

ASCIIGenome: a command line genome browser for console terminals
Cited by: 3
Author(s): Dario Beraldi
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.mcpro.2021.100102

Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins
Cited by: 5
Author(s): Fatemeh Mazloumi Gavgani, Malene Skuseth Slinning, Andrea Papdiné Morovicz, Victoria Smith Arnesen, Diana Cornelia Turcu, Sandra Ninzima, Clive S. D’Santos, Aurélia E. Lewis
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41421-018-0074-6

Hemi-methylated CpG sites connect Dnmt1-knockdown-induced and Tet1-induced DNA demethylation during somatic cell reprogramming
Cited by: 10
Author(s): Songbing He, Fuhui Wang, Yixin Zhang, Jinlong Chen, Lining Liang, Yuan Li, Mengdan Zhang, Xiao Yang, Hongshen Pang, Yingying Li, Xiaofen Huang, Dajiang Qin, Duanqing Pei, Hao Sun, Hui Zheng
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-015-0871-y

NOBLE – Flexible concept recognition for large-scale biomedical natural language processing
Cited by: 84
Author(s): Eugene Tseytlin, Kevin J. Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan, Rebecca S. Jacobson
Software Mentions: 2
Published: almost 9 years ago

10.1098/rstb.2012.0103

Artificial grammar learning meets formal language theory: an overview
Cited by: 151
Author(s): W. Tecumseh Fitch, Angela D. Friederici
Software Mentions: 2
Published: over 12 years ago

10.1038/s41598-021-92834-4

In Silico identification of a common mobile element insertion in exon 4 of RP1
Cited by: 0
Author(s): Dongju Won, Joo-Yeon Hwang, Yeeun Shim, Suk Ho Byeon, Junwon Lee, Christopher S. Lee, Min Kim, Hyun Taek Lim, Jong Rak Choi, Seung Tae Lee, Jinu Han
Software Mentions: 2
Published: over 3 years ago

10.1186/s13601-018-0193-z

7th International Symposium on Molecular Allergology (ISMA 2017)
Cited by: 1
Author(s):
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0241306

Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets
Cited by: 2
Author(s): Ben Vezina, Guillaume A. Petit, Jennifer L. Martin, Maria A. Halili
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0099439

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)
Cited by: 54
Author(s): Ioannis Panagopoulos, Ludmila Gorunova, Bodil Bjerkehagen, Sverre Heim
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0116040

Generation of Silver Standard Concept Annotations from Biomedical Texts with Special Relevance to Phenotypes
Cited by: 16
Author(s): Anika Oellrich, Nigel Collier, Damian Smedley, Tudor Groza
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0164085

Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells
Cited by: 15
Author(s): Winston Koh, Veronica D. Gonzalez, Sivaraman Natarajan, Caroline Robert, Patrick O. Brown, Charles Gawad
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj-cs.653

Toward IoT fog computing-enabled system energy consumption modeling and optimization by adaptive TCP/IP protocol
Cited by: 0
Author(s): Aladdin Masri, Muhannad Al-Jabi
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0117010

Novel KAT6B-KANSL1 Fusion Gene Identified by RNA Sequencing in Retroperitoneal Leiomyoma with t(10;17)(q22;q21)
Cited by: 33
Author(s): Ioannis Panagopoulos, Ludmila Gorunova, Bodil Bjerkehagen, Sverre Heim
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0132736

Novel ZEB2-BCL11B Fusion Gene Identified by RNA-Sequencing in Acute Myeloid Leukemia with t(2;14)(q22;q32)
Cited by: 15
Author(s): Synne Torkildsen, Ludmila Gorunova, Klaus Beiske, Geir E. Tjønnfjord, Sverre Heim, Ioannis Panagopoulos
Software Mentions: 1
Published: over 9 years ago

10.3758/s13428-020-01507-z

Implicit consequentiality bias in English: A corpus of 300+ verbs
Cited by: 5
Author(s): Alan Garnham, Svenja Vorthmann, Karolina Kaplanova
Software Mentions: 1
Published: about 4 years ago

10.1186/s13326-015-0019-z

Concept selection for phenotypes and diseases using learn to rank
Cited by: 10
Author(s): Nigel Collier, Anika Oellrich, Tudor Groza
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-9-442

Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data
Cited by: 10
Author(s): Michael J. Gilchrist, Mikkel Christensen, Richard M. Harland, Nicolas Pollet, James C. Smith, Naoto Ueno, Nancy Papalopulu
Software Mentions: 1
Published: about 16 years ago

10.1186/s41039-018-0073-0

Text analytics approach to extract course improvement suggestions from students’ feedback
Cited by: 34
Author(s): Swapna Gottipati, Venky Shankararaman, Jeff Rongsheng Lin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0142614

Efficient In Silico Identification of a Common Insertion in the MAK Gene which Causes Retinitis Pigmentosa
Cited by: 13
Author(s): Kinga Bujakowska, Joseph A. White, Emily Place, Mark Consugar, Jason Comander
Software Mentions: 1
Published: about 9 years ago

10.3390/s21041528

Generating Datasets for Anomaly-Based Intrusion Detection Systems in IoT and Industrial IoT Networks
Cited by: 26
Author(s): Ismael Essop, José Carlos Ribeiro, Μαρία Παπαϊωάννου, Georgios Zachos, Γεώργιος Μαντάς, Jonathan Rodrı́guez
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: grep

Papers Mentioning grep 57