pypi: Assembly | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: almost 8 years ago

10.1038/s41598-019-42310-x

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression
Cited by: 19
Author(s): Christian Kehlmaier, Xiuwen Zhang, Arthur Georges, Patrick D. Campbell, Scott Thomson, Uwe Fritz
Software Mentions: 9
Published: over 5 years ago

10.1590/1678-4685-GMB-2016-0230

Approaches for in silico finishing of microbial genome sequences
Cited by: 17
Author(s): Frederico Schmitt Kremer, Alan J. A. McBride, Luciano da Silva Pinto
Software Mentions: 8
Published: about 7 years ago

10.3389/fmicb.2020.01376

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?
Cited by: 28
Author(s): Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher Dean, Christina Boucher, Noelle Noyes
Software Mentions: 8
Published: over 4 years ago

10.1093/gigascience/giaa153

Significantly improving the quality of genome assemblies through curation
Cited by: 540
Author(s): Kerstin Howe, William Chow, Joanna Collins, Sarah Pelan, Damon-Lee Pointon, Ying Sims, James Torrance, Alan S. Tracey, Jonathan Wood
Software Mentions: 7
Published: almost 4 years ago

10.7717/peerj.8111

From command-line bioinformatics to bioGUI
Cited by: 4
Author(s): Markus Joppich, Ralf Zimmer
Software Mentions: 7
Published: almost 5 years ago

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0204076

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Cited by: 62
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Jong S. Leong, Cameron M. Nugent, Roy G. Danzmann, Moira M. Ferguson, Agnieszka Stadnik, Robert H. Devlin, Robin Muzzerall, Michael G. Edwards, William S. Davidson, Ben F. Koop
Software Mentions: 7
Published: about 6 years ago

10.1093/g3journal/jkaa043

Global translational landscape of the Candida albicans morphological transition
Cited by: 8
Author(s): Vasanthakrishna Mundodi, Saket Choudhary, Andrew D. Smith, David Kadosh
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.55159

Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons
Cited by: 9
Author(s): Amira Hassan, Pablo Araguas Rodriguez, Stefan Heidmann, Emma L Walmsley, Gabriel Aughey, Tony D. Southall
Software Mentions: 6
Published: over 4 years ago

10.1186/s40793-019-0342-6

The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers
Cited by: 46
Author(s): Axel Aigle, James I. Prosser, Cécile Gubry‐Rangin
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-018-2252-9

npInv: accurate detection and genotyping of inversions using long read sub-alignment
Cited by: 26
Author(s): Haojing Shao, Devika Ganesamoorthy, Tânia Duarte, Minh Duc Cao, Clive Hoggart, Lachlan Coin
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2164-11-571

Comparing de novo assemblers for 454 transcriptome data
Cited by: 240
Author(s): Sujai Kumar, Mark Blaxter
Software Mentions: 5
Published: about 14 years ago

10.1155/2019/4767354

GAAP: A Genome Assembly + Annotation Pipeline
Cited by: 5
Author(s): Jinhwa Kong, Sun Huh, Jung-Im Won, Jeehee Yoon, Baeksop Kim, Ki-Yong Kim
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.46070

Large protein organelles form a new iron sequestration system with high storage capacity
Cited by: 83
Author(s): Tobias W. Giessen, Benjamin J. Orlando, Andrew A Verdegaal, Melissa G. Chambers, Jules Gardener, David C. Bell, Gabriel Birrane, Maofu Liao, Pamela A. Silver
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-14-S11-S1

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
Cited by: 426
Author(s): Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao
Software Mentions: 5
Published: about 11 years ago

10.7554/eLife.71393

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies
Cited by: 18
Author(s): Angela M Phillips, Katherine R. Lawrence, Alief Moulana, Thomas Dupic, Jeffrey S. Chang, Milo S. Johnson, Ivana Cvijović, Thierry Mora, Aleksandra M. Walczak, Michael M. Desai
Software Mentions: 5
Published: about 3 years ago

10.1093/gbe/evab167

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene
Cited by: 2
Author(s): Mark Derbyshire, Lincoln A. Harper, Francisco J. López-Ruiz
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giaa027

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C
Cited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 4 years ago

10.1186/1755-8794-8-S2-S13

SeedsGraph: an efficient assembler for next-generation sequencing data
Cited by: 2
Author(s): Chuyu Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Quan Zou
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pbio.3000123

Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF
Cited by: 22
Author(s): E.J. Waldron, Donald R. Snyder, Nicolas L. Fernandez, Emily Sileo, Daigo Inoyama, Joel S. Freundlich, Christopher M. Waters, Vaughn S. Cooper, Matthew B. Neiditch
Software Mentions: 4
Published: almost 6 years ago

10.3390/cells9081776

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore
Cited by: 22
Author(s): Mourdas Mohamed, Nguyet Thi-Minh Dang, Yuki Ogyama, Nelly Burlet, Bruno Mugat, Matthieu Boulesteix, Vincent Mérel, Philippe Veber, Judit Salces-Ortiz, Dany Séverac, Alain Pélisson, Cristina Vieira, François Sabot, Marie Fablet, Séverine Chambeyron
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0010141

Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae
Cited by: 43
Author(s): Fangqing Zhao, Jie Bai, Jinyu Wu, Jing Liu, Ming‐Ming Zhou, Shilin Xia, Shanjin Wang, Xiaoding Yao, Huiguang Yi, Meili Lin, Shengjie Gao, Tieli Zhou, Zitong Xu, Yuxin Niu, Qiyu Bao
Software Mentions: 3
Published: over 14 years ago

10.3390/s21061987

Efficient Implementation of NIST LWC ESTATE Algorithm Using OpenCL and Web Assembly for Secure Communication in Edge Computing Environment
Cited by: 2
Author(s): BoSun Park, Seog Chung Seo
Software Mentions: 3
Published: over 3 years ago

10.1111/j.1742-4658.2009.06893.x

Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms
Cited by: 58
Author(s): Emmanuel Debrand, Yasmine El Jai, Lorraine Spence, Neil Bate, Uta Praekelt, Catrin Pritchard, Susan J. Monkley, David R. Critchley
Software Mentions: 3
Published: over 15 years ago

10.3390/genes10050382

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations
Cited by: 12
Author(s): Himansu Kumar, Woncheol Park, Krishnamoorthy Srikanth, Bong-Hwan Choi, Eun Seok Cho, Kyung-Tai Lee, Junmo Kim, Kwangmin Kim, Jun Hyung Park, Dajeong Lim
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0015392

Identification of De Novo Copy Number Variants Associated with Human Disorders of Sexual Development
Cited by: 133
Author(s): Mounia Tannour‐Louet, Shuo Han, Sean T. Corbett, Jean-François Louet, Svetlana A. Yatsenko, Lindsay Meyers, Chad A. Shaw, Sung-Hae L. Kang, Sau Wai Cheung, Dolores J. Lamb
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2164-11-692

A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening
Cited by: 11
Author(s): Frank M. You, Ming Luo, Kenong Xu, Karin R. Deal, Olin D. Anderson, Jan Dvořák
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12934-021-01509-2

Engineering Escherichia coli for the utilization of ethylene glycol
Cited by: 11
Author(s): Aditya Vikram Pandit, Emma Harrison, Radhakrishnan Mahadevan
Software Mentions: 3
Published: almost 4 years ago

10.1093/gigascience/giy162

A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert
Cited by: 116
Author(s): Marta Farré, Qiye Li, Yang Zhou, Joana Damas, Leona G. Chemnick, Jaebum Kim, Oliver A. Ryder, Jian Ma, Guojie Zhang, Denis M. Larkin, Harris A. Lewin
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-019-1710-7

Bridging the gap between reference and real transcriptomes
Cited by: 34
Author(s): Antonin Morillon, Daniel Gautheret
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-021-04004-y

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Cited by: 7
Author(s): Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0038657

Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron-5 of the Sheep SCF Gene: A Novel Splice Variant
Cited by: 6
Author(s): Siva Arumugam Saravanaperumal, Dario Pediconi, Carlo Renieri, Antonietta La Terza
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0173300

Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut
Cited by: 12
Author(s): Alix Armero, Luc Baudouin, Stéphanie Bocs, Dominique This
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0017418

A De Novo Expression Profiling of Anopheles funestus, Malaria Vector in Africa, Using 454 Pyrosequencing
Cited by: 51
Author(s): Richard I. Gregory, Alistair C. Darby, Helen Irving, Mamadou B. Coulibaly, Margaret Hughes, Lizette L. Koekemoer, Maureen Coetzee, Hilary Ranson, Janet Hemingway, Neil Hall, Charles S. Wondji
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-12-95

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Cited by: 53
Author(s): Joshua L. Wetzel, Carl Kingsford, Mihai Pop
Software Mentions: 2
Published: over 13 years ago

10.1186/s13015-016-0064-x

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage
Cited by: 6
Author(s): Jean Zukurov, Sieberth do Nascimento-Brito, Ângela Volpini, Guilherme Oliveira, Luiz Mário Janini, Fernando Antoneli
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-014-0381-3

CAR: contig assembly of prokaryotic draft genomes using rearrangements
Cited by: 35
Author(s): Chin Lung Lu, Kun Tze Chen, Shong Huang, Hsien Tai Chiu
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-12-S1-S24

Strobe sequence design for haplotype assembly
Cited by: 19
Author(s): Christine Lo, Ali Kashif Bashir, Vikas Bansal, Vineet Bafna
Software Mentions: 2
Published: over 13 years ago

10.1016/j.crbiot.2020.03.001

Restoration of wild-type motility to flagellin-knockout Escherichia coli by varying promoter, copy number and induction strength in plasmid-based expression of flagellin
Cited by: 3
Author(s): Nicholas M. Thomson, Mark J. Pallen
Software Mentions: 2
Published: about 4 years ago

10.3390/pathogens3020258

High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology
Cited by: 25
Author(s): Ségolène Caboche, Christophe Audebert, David Hot
Software Mentions: 2
Published: over 10 years ago

10.12688/f1000research.25148.2

First draft genome assembly of the desert locust, Schistocerca gregaria
Cited by: 13
Author(s): Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Ho‐Jun Song, Spencer T. Behmer, Gregory A. Sword, Troy Matheson, Swidbert R. Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de Peer, Jozef Vanden Broeck
Software Mentions: 2
Published: over 3 years ago

10.1186/s13040-014-0035-z

Identifying genetic interactions associated with late-onset Alzheimer’s disease
Cited by: 17
Author(s): Charalampos S. Floudas, Nara Um, M. Ilyas Kamboh, M. Michael Barmada, Shyam Visweswaran
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmicb.2020.519169

Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic
Cited by: 2
Author(s): Víctor V. Calderón, Roberto Bonnelly, Camila Del Rosario, Albert Duarte, Rafael A. Baraúna, Rommel Thiago Jucá Ramos, Omar Paíno Perdomo, Luis Francisco, Edian F. Franco
Software Mentions: 2
Published: almost 4 years ago

10.26508/lsa.201900593

Mylk3null C57BL/6N mice develop cardiomyopathy, whereasNntnull C57BL/6J mice do not
Cited by: 18
Author(s): Jack Williams, Anju Paudyal, Sherine Awad, James Nicholson, Dominika Grzesik, Joaquín Botta, Eirini Meimaridou, Avinaash Maharaj, Michelle Stewart, Andrew Tinker, Roger Cox, Louise A. Metherell
Software Mentions: 2
Published: over 4 years ago

10.1007/s41116-018-0015-3

Solar UV and X-ray spectral diagnostics
Cited by: 150
Author(s): G. Del Zanna, H. E. Mason
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2020.571104

Recirculation of Giardia lamblia Assemblage A After Metronidazole Treatment in an Area With Assemblages A, B, and E Sympatric Circulation
Cited by: 7
Author(s): Maria Fantinatti, Luiz Antonio Pimentel Lopes-Oliveira, Tiara Cascais-Figueredo, Phelipe Austriaco-Teixeira, Erika Verissimo, Alexandre Ribeiro Bello, Alda Maria Da‐Cruz
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2018.01800

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation
Cited by: 11
Author(s): Álvaro M. Plominsky, Carlos Henríquez‐Castillo, Nathalie Delherbe, Sheila Podell, Salvador Ramírez-Flandes, Juan A. Ugalde, Juan F. Santibáñez, Ger van den Engh, Kurt Hanselmann, Osvaldo Ulloa, Rodrigo De la Iglesia, Eric E. Allen, Nicole Trefault
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2018.03038

Intracellular pHluorin as Sensor for Easy Assessment of Bacteriocin-Induced Membrane-Damage in Listeria monocytogenes
Cited by: 13
Author(s): Peter Crauwels, Leonie Schäfer, Dominik Weixler, Nadav Bar, Dzung B. Diep, Christian U. Riedel, Gerd M. Seibold
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1005483

Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish
Cited by: 49
Author(s): Diana Mitchell, Craig B. Stevens, Ruth A. Frey, Samuel S. Hunter, Ryuichi Ashino, Shoji Kawamura, Deborah L. Stenkamp
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1008931

Impact of insertion sequences on convergent evolution of Shigella species
Cited by: 37
Author(s): Jane Hawkey, Jonathan M. Monk, Helen Billman‐Jacobe, Jaehyung Kim, Kathryn E. Holt
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1000260

Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression
Cited by: 98
Author(s): Khyobeni Mozhui, Daniel C. Ciobanu, Thomas Schikorski, Xusheng Wang, Lu Lu, Robert W. Williams
Software Mentions: 2
Published: almost 16 years ago

10.1534/g3.114.010264

Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations
Cited by: 34
Author(s): Matthew W. Hahn, Simo V. Zhang, Leonie C. Moyle
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1001070

The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation
Cited by: 134
Author(s): Brian B. Tuch, Quinn M. Mitrovich, Oliver Homann, Aaron D. Hernday, Cinna K. Monighetti, Francisco Vega, Alexander D. Johnson
Software Mentions: 2
Published: about 14 years ago

10.1186/s12711-016-0182-4

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array
Cited by: 49
Author(s): Marina Atlija, J. J. Arranz, María Martínez Valladares, Beatriz Gutiérrez-Gil
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1648-4

The venomous cocktail of the vampire snail Colubraria reticulata (Mollusca, Gastropoda)
Cited by: 40
Author(s): Maria Vittoria Modica, Fabrizio Lombardo, Paolo Franchini, Marco Oliverio
Software Mentions: 2
Published: over 9 years ago

10.3390/metabo10060250

Photosynthetic Co-production of Succinate and Ethylene in a Fast-Growing Cyanobacterium, Synechococcus elongatus PCC 11801
Cited by: 30
Author(s): Annesha Sengupta, Prem Pritam, Damini Jaiswal, Anindita Bandyopadhyay, Himadri B. Pakrasi, Pramod P. Wangikar
Software Mentions: 2
Published: over 4 years ago

10.1186/gb-2007-8-4-r52

Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes
Cited by: 152
Author(s): Marco van het Hoog, Timothy J. Rast, Mikhail Martchenko, Suzanne Grindle, Daniel Dignard, Hervé Hogues, Christina A. Cuomo, Matthew Berriman, Stewart Scherer, B. B. Magee, Malcolm Whiteway, Hiroji Chibana, André Nantel, Patrick Magee
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2013-14-9-r97

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure
Cited by: 112
Author(s): Dale Muzzey, Katja Schwartz, Jonathan S. Weissman, Gavin Sherlock
Software Mentions: 2
Published: almost 12 years ago

10.2196/10336

A Platform to Record Patient Events During Physiological Monitoring With Wearable Sensors: Proof-of-Concept Study
Cited by: 0
Author(s): Jonathan Duc Vinh Vo, Alexander M. Gorbach
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jbc.2021.100353

The molecular basis of OH-PCB estrogen receptor activation
Cited by: 5
Author(s): Ting Wang, Ian Cook, Thomas S. Leyh
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-12-466

Nucleosome-coupled expression differences in closely-related species
Cited by: 7
Author(s): Yuanfang Guan, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya J. Dunham, Corey Nislow, Olga G. Troyanskaya
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0100948

HomeRun Vector Assembly System: A Flexible and Standardized Cloning System for Assembly of Multi-Modular DNA Constructs
Cited by: 12
Author(s): Ming V. Li, Dip Shukla, Brian H. Rhodes, Anjali Lall, Jingmin Shu, Branden S. Moriarity, David A. Largaespada
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-2007-1

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation
Cited by: 77
Author(s): Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kanazawa, Shigehiro Kuraku
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0067222

Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p
Cited by: 10
Author(s): Pontus Eriksson, Mattias Aine, Gottfrid Sjödahl, Johan Staaf, David Lindgren, Mattias Höglund
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-018-34457-w

Dynamic evolution of inverted repeats in Euglenophyta plastid genomes
Cited by: 15
Author(s): Anna Karnkowska, Matthew S. Bennett, Richard E. Triemer
Software Mentions: 2
Published: about 6 years ago

10.1128/MRA.00881-19

Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the Secoviridae Family Recovered from a Japanese Apricot ( Prunus mume ) Metagenome Data Set
Cited by: 2
Author(s): Andrea M. Fetters, Paul G. Cantalupo, Tia‐Lynn Ashman, James M. Pipas
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-15-216

The Xenopusalcohol dehydrogenase gene family: characterization and comparative analysis incorporating amphibian and reptilian genomes
Cited by: 5
Author(s): Emma Borràs, Ricard Albalat, Gregg Duester, Xavier Parés, Jaume Farrés
Software Mentions: 2
Published: over 10 years ago

10.1186/1751-0473-7-4

Scaffolder - software for manual genome scaffolding
Cited by: 17
Author(s): Michael D. Barton, Hazel A. Barton
Software Mentions: 1
Published: over 12 years ago

10.1186/1742-4682-9-30

Zinc finger arrays binding human papillomavirus types 16 and 18 genomic DNA: precursors of gene-therapeutics for in-situ reversal of associated cervical neoplasia
Cited by: 8
Author(s): Misaki Wayengera
Software Mentions: 1
Published: over 12 years ago

10.1128/mBio.00349-20

Lipid Anchoring of Archaeosortase Substrates and Midcell Growth in Haloarchaea
Cited by: 30
Author(s): Mohd Farid Abdul Halim, Stefan Schulze, Anthony DiLucido, Friedhelm Pfeiffer, Alexandre W. Bisson‐Filho, Mechthild Pohlschröder
Software Mentions: 1
Published: over 4 years ago

10.3390/jof6040314

Targeted Disruption of Scytalone Dehydratase Gene Using Agrobacterium tumefaciens-Mediated Transformation Leads to Altered Melanin Production in Ascochyta lentis
Cited by: 1
Author(s): Johannes Wolfram Debler, Bernadette M. Henares
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.ijpara.2010.08.008

Whole genome re-sequencing identifies a mutation in an ABC transporter (mdr2) in a Plasmodium chabaudi clone with altered susceptibility to antifolate drugs
Cited by: 18
Author(s): Axel Martinelli, Gisela Henriques, Pedro Vitor Lemos Cravo, Paul Hunt
Software Mentions: 1
Published: almost 14 years ago

10.7554/eLife.26067

Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide
Cited by: 36
Author(s): Erik L. Snapp, Nicholas McCaul, Matthias Quandte, Zuzana Cabartova, Ilja Bontjer, Carolina Källgren, IngMarie Nilsson, Aafke Land, Gunnar von Heijne, Rogier W. Sanders, Ineke Braakman
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.39723

Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria
Cited by: 73
Author(s): Joshua S. MacCready, Pusparanee Hakim, Eric J. Young, Longhua Hu, Jian Liu, Katherine W. Osteryoung, Anthony G. Vecchiarelli, Daniel C. Ducat
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.27417

Kinetochore inactivation by expression of a repressive mRNA
Cited by: 63
Author(s): Jingxun Chen, Amy Tresenrider, Minghao Chia, David McSwiggen, Gianpiero Spedale, Victoria Jorgensen, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms21176188

Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops
Cited by: 3
Author(s): Christina Bergonzo, Andrea L. Szakal
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.17391

Increased S100A15 expression and decreased DNA methylation of its gene promoter are involved in high metastasis potential and poor outcome of lung adenocarcinoma
Cited by: 13
Author(s): Yung‐Che Chen, Chang‐Chun Hsiao, Yixin Zheng, Kuang‐Den Chen, Ming-Tse Sung, Chung‐Jen Chen, Ting‐Ya Wang, Yann-Sheng Lin, Hsien‐Kun Chang, Jen‐Chieh Chang
Software Mentions: 1
Published: over 7 years ago

10.1007/s00253-019-09707-0

The role of the acyl-CoA thioesterase “YciA” in the production of (R)-3-hydroxybutyrate by recombinant Escherichia coli
Cited by: 16
Author(s): Mónica Guevara-Martínez, Mariel Pérez-Zabaleta, Martin Gustavsson, Jorge Quillaguamán, Gen Larsson, Antonius J. A. van Maris
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-14-322

3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape
Cited by: 13
Author(s): Qi Wang, Biao Tang, Lifu Song, Baiping Ren, Qun Liang, Feng Xie, Ying Zhuo, Xueting Liu, Lixin Zhang
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2148-9-180

The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage
Cited by: 60
Author(s): Scot Libants, Kevin M. Carr, Hong Wu, John H. Teeter, Yu Wen Chung-Davidson, Ziping Zhang, Curt Wilkerson, Weiming Li
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-12-65

Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations
Cited by: 14
Author(s): Pamela Wiener, M. A. Edriss, J. L. Williams, David Waddington, Andrew Law, John Woolliams, Beatriz Gutiérrez-Gil
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-015-1479-3

Assessing structural variation in a personal genome—towards a human reference diploid genome
Cited by: 142
Author(s): Adam C. English, William Salerno, Oliver A. Hampton, Claudia Gonzaga‐Jauregui, Shruthi Ambreth, Deborah Ritter, Christine R. Beck, Caleb Davis, Mahmoud Dahdouli, Xiaotu Ma, Andrew Carroll, Narayanan Veeraraghavan, Jeremy Bruestle, Becky Drees, Alex Hastie, Ernest T. Lam, Simon White, Pamela Mishra, Min Wang, Yi Han, Feng Zhang, Paweł Stankiewicz, David A. Wheeler, Jeffrey G. Reid, Donna M. Muzny, Jeffrey Rogers, Aniko Sabo, Kim C. Worley, James R. Lupski, Eric Boerwinkle, Richard A. Gibbs
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-14-875

A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
Cited by: 31
Author(s): Andrezza Campos Chagas, Eric Calvo, Claudia Maria Ríos-Velásquez, Felipe Arley Costa Pessoa, Jansen Fernandes Medeiros, José M. C. Ribeiro
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-15-S1-S12

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
Cited by: 42
Author(s): Yi Wang, Ho-fung Leung, Siu Ming Yiu, Francis Y. L. Chin
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12866-019-1554-z

Inference from the analysis of genetic structure of Helicobacter pylori strains isolates from two paediatric patients with recurrent infection
Cited by: 13
Author(s): Sandra Mendoza-Elizalde, Ana Caren Cortés-Márquez, Gerardo Zúñiga, René Cerritos, Pedro Valencia‐Mayoral, Alejandra Consuelo Sánchez, Héctor Olivares-Clavijo, Norma Velázquez-Guadarrama
Software Mentions: 1
Published: about 5 years ago

10.1186/s12866-021-02247-6

SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus
Cited by: 5
Author(s): Colin Wood, Jason W. Sahl, Sara Maltinsky, Briana Coyne, Benjamin Russakoff, David Panisello Yagüe, Jolene R. Bowers, Talima Pearson
Software Mentions: 1
Published: over 3 years ago

10.1016/j.meteno.2017.01.001

Overexpression of the primary sigma factor gene sigA improved carotenoid production by Corynebacterium glutamicum : Application to production of β-carotene and the non-native linear C50 carotenoid bisanhydrobacterioruberin
Cited by: 32
Author(s): H Taniguchi, Nadja A. Henke, Sabine A. E. Heider, Volker F. Wendisch
Software Mentions: 1
Published: over 7 years ago

10.1186/s12934-019-1162-5

Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110
Cited by: 12
Author(s): Lena Schaffert, Camilla März, Lisa Burkhardt, Julian Droste, David Brandt, Tobias Busche, Winfried Rosen, Susanne Schneiker-Bekel, Marcus Persicke, Alfred Pühler, Jörn Kalinowski
Software Mentions: 1
Published: over 5 years ago

10.1186/1475-2859-13-72

Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing
Cited by: 86
Author(s): Jan Kjølhede Vester, Mikkel A. Glaring, Peter Stougaard
Software Mentions: 1
Published: over 10 years ago

10.1002/mbo3.251

Alternative modes of biofilm formation by plant‐associated Bacillus cereus
Cited by: 63
Author(s): Tantan Gao, Lucy Foulston, Yunrong Chai, Qi Wang, Richard Losick
Software Mentions: 1
Published: over 9 years ago

10.1099/mic.0.000559

MtlR negatively regulates mannitol utilization by Vibrio cholerae
Cited by: 10
Author(s): Tanner Byer, Jessica Wang, Mark Zhang, Naomi Vather, Anna Blachman, Bryan J. Visser, Jane M. Liu
Software Mentions: 1
Published: almost 7 years ago

10.1128/MRA.01142-20

Complete Genome Sequences of Two Streptococcus suis Strains Isolated from Asymptomatic Pigs
Cited by: 0
Author(s): Atsuko Minowa‐Nozawa, Takashi Nozawa, Daisuke Takamatsu, Akemi Yoshida, Kazunori Murase, Taisei Kikuchi, Kasumi Ishida-Kuroki, Yoshihiro Nitta, Tsutomu Sekizaki, Ichirô Nakagawa
Software Mentions: 1
Published: almost 4 years ago

10.3390/microorganisms8081232

Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy
Cited by: 3
Author(s): Vittoria Mattioni Marchetti, Ibrahim Bitar, Aurora Piazza, Alessandra Mercato, Elena Fogato, Jaroslav Hrabák, Roberta Migliavacca
Software Mentions: 1
Published: about 4 years ago

10.3390/microorganisms8050693

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution
Cited by: 4
Author(s): Wen‐Lang Lin, Chee Kent Lim, Martin G. Klotz
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8030339

Complete Genome and Plasmids Sequences of a Clinical Proteus mirabilis Isolate Producing Plasmid Mediated NDM-1 From Italy
Cited by: 17
Author(s): Ibrahim Bitar, Vittoria Mattioni Marchetti, Alessandra Mercato, Elisabetta Nucleo, Adriano Anesi, Silvia Bracco, Vanina Rognoni, Jaroslav Hrabák, Roberta Migliavacca
Software Mentions: 1
Published: over 4 years ago

10.1111/mpp.12443

An Epichloë festucae homologue of MOB3, a component of the STRIPAK complex, is required for the establishment of a mutualistic symbiotic interaction with Lolium perenne
Cited by: 19
Author(s): Kimberly Green, Yvonne Becker, Helen L. Fitzsimons, Barry Scott
Software Mentions: 1
Published: about 8 years ago

10.1111/mpp.12805

A homologue of the fungal tetraspanin Pls1 is required for Epichloë festucae expressorium formation and establishment of a mutualistic interaction with Lolium perenne
Cited by: 8
Author(s): Kimberly Green, Carla J. Eaton, Matthew S. Savoian, Barry Scott
Software Mentions: 1
Published: over 5 years ago

10.3897/zookeys.932.48532

Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species
Cited by: 18
Author(s): Avery S Hatch, Haebin Liew, Stéphane Hourdez, Greg W. Rouse
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: Assembly

Papers Mentioning Assembly 147