pypi: seqtk | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.630542

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions
Cited by: 10
Author(s): Chandni Radhakrishnan, Mohit Kumar Divakar, Abhinav Jain, Prasanth Viswanathan, Rahul C. Bhoyar, Bani Jolly, Mohamed Imran, Disha Sharma, Mercy Rophina, Gyan Ranjan, Paras Sehgal, Beena Philomina Jose, R. Raman, Thulaseedharan Nallaveettil Kesavan, Kalpana George, Sheela Mathew, Jayesh Kumar Poovullathil, Sajeev Chakanalil Govindan, Priyanka Raveendranadhan Nair, Shameer Vadekkandiyil, Vineeth Gladson, Midhun Mohan, Fairoz Cheriyalingal Parambath, Mohit Mangla, Afra Shamnath, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-020-00937-3

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
Cited by: 25
Author(s): Lei Liu, Yulin Wang, Ying Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Kewei Chen, Tong Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep41498

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells
Cited by: 46
Author(s): Jean‐François Mangot, Ramiro Logares, Pablo Sánchez, Fran Latorre, Yoann Seeleuthner, Samuel Mondy, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Colomban de Vargas, Ramón Massana
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-020-1096-9

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Cited by: 27
Author(s): Austin B. Mudd, Jessen V. Bredeson, Rachel Baum, Dirk Hockemeyer, Daniel S. Rokhsar
Software Mentions: 3
Published: about 4 years ago

10.7150/thno.40798

CNTNAP4 deficiency in dopaminergic neurons initiates parkinsonian phenotypes
Cited by: 18
Author(s): Wenlong Zhang, Miaomiao Zhou, Weiye Lu, Junhua Gong, Feng Gao, Yuanquan Li, Xuandong Xu, Yuwan Lin, Xiaokang Zhang, Liuyan Ding, Zhiling Zhang, Guihua Liu, Xiang Chen, Xiangdong Sun, Xiaodong Zhu, Pingyi Xu, Yunlong Zhang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1007279

Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens
Cited by: 74
Author(s): Lyndal Henden, Stuart Lee, Ivo Müeller, Alyssa E. Barry, Melanie Bahlo
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12020144

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe
Cited by: 5
Author(s): Ulrike H. Taron, Johanna L. A. Paijmans, Axel Barlow, Michaela Preick, Arati Iyengar, Virgil Drăgușin, Ştefan Vasile, Adrian Marciszak, Martina Roblíčková, Michael Hofreiter
Software Mentions: 3
Published: over 3 years ago

10.1155/2019/4010764

LncRNA LEGLTBC Functions as a ceRNA to Antagonize the Effects of miR-34a on the Downregulation of SIRT1 in Glucolipotoxicity-Induced INS-1 Beta Cell Oxidative Stress and Apoptosis
Cited by: 26
Author(s): Kuanhui Xiang, Chongxiao Liu, Guodong Wang, Hui Yang, Xin-ming Yao, Qiang Hua, Xiaoyong Li, Hongmei Zhang, M. Anthony Moody, Qing Su, Kun Lv
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-020-3435-8

PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data
Cited by: 16
Author(s): Jian Bo Zhang, Dilip R. Panthee
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-018-2124-3

CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing
Cited by: 15
Author(s): Angel Mojarro, Julie Hachey, Gary Ruvkun, M. T. Zuber, Christopher E. Carr
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-367

Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries
Cited by: 26
Author(s): Anuj Srivastava, Vivek M. Philip, Ian Greenstein, Lucy B. Rowe, Mary Barter, Cathleen Lutz, Laura G. Reinholdt
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-019-6153-8

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data
Cited by: 3
Author(s): Raúl Y. Wijfjes, Sandra Smit, Dick de Ridder
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-4972-7

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken
Cited by: 25
Author(s): Stephen J. Bush, Lucy Freem, Amanda MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers, David Hume
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-016-3448-x

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
Cited by: 125
Author(s): Ole K. Tørresen, Bastiaan Star, Sissel Jentoft, William Brynildsen Reinar, Harald Grove, Jason R. Miller, Brian P. Walenz, James Knight, Jenny Ekholm, Paul Peluso, Rolf B. Edvardsen, Ave Tooming‐Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S. Jakobsen, Alexander J. Nederbragt
Software Mentions: 2
Published: over 7 years ago

10.1186/s12866-018-1171-2

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil
Cited by: 21
Author(s): Andrea Bagi, Even Sannes Riiser, Hilde Steine Molland, Bastiaan Star, Thomas Haverkamp, Magne O. Sydnes, Daniela M. Pampanin
Software Mentions: 2
Published: over 6 years ago

10.1186/s12867-018-0108-5

Laser capture microdissection for transcriptomic profiles in human skin biopsies
Cited by: 7
Author(s): Silvia Santoro, Ignazio Diego Lopez, Raffaella Lombardi, Andrea Zauli, Ana Maria Osiceanu, Melissa Sorosina, Ferdinando Clarelli, Silvia Peroni, Daniele Cazzato, Margherita Marchi, Angelo Quattrini, Gıancarlo Comı, Raffaele Calogero, Giuseppe Lauria, Filippo Martinelli Boneschi
Software Mentions: 2
Published: over 6 years ago

10.1111/1751-7915.13510

Modified clays alter diversity and respiration profile of microorganisms in long‐term hydrocarbon and metal co‐contaminated soil
Cited by: 10
Author(s): Bhabananda Biswas, Albert L. Juhasz, Mohammad Mahmudur Rahman, Ravi Naidu
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12934-021-01682-4

Multivalent poultry vaccine development using Protein Glycan Coupling Technology
Cited by: 7
Author(s): Marta Mauri, Thippeswamy H. Sannasiddappa, Prerna Vohra, Ricardo Corona-Torres, Adam Smith, Cosmin Chintoan-Uta, Abi Bremner, Vanessa S. Terra, Sherif Abouelhadid, Mark P. Stevens, A. Grant, Jon Cuccui, Brendan W. Wren
Software Mentions: 2
Published: almost 3 years ago

10.1128/MRA.00835-19

Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan
Cited by: 7
Author(s): Andreína I. Castillo, Shu‐Jen Tuan, Adam C. Retchless, Fei-Ting Hu, Hsun-Yin Chang, Rodrigo P. P. Almeida
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-019-0670-1

Identification and reconstruction of novel antibiotic resistance genes from metagenomes
Cited by: 76
Author(s): Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson, Erik Kristiansson
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms8081169

Microbiome Diversity and Community-Level Change Points within Manure-Based Small Biogas Plants
Cited by: 12
Author(s): Susanne Theuerl, Johanna Klang, Benedikt Hülsemann, Torsten Mächtig, Julia Hassa
Software Mentions: 2
Published: about 4 years ago

10.3390/v9120357

A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology
Cited by: 3
Author(s): Yuri V. Kravatsky, V. R. Chechetkin, Д. М. Федосеева, М. А. Горбачева, Galina I. Kravatskaya, О. В. Кретова, Nickolai A. Tchurikov
Software Mentions: 2
Published: almost 7 years ago

10.3390/v10040188

Characterizing Phage Genomes for Therapeutic Applications
Cited by: 109
Author(s): Casandra Philipson, Logan J. Voegtly, Matthew R. Lueder, Kyle A. Long, Gregory K. Rice, K. G. Frey, Biswajit Biswas, Regina Z. Cer, Theron Hamilton, Kimberly A. Bishop‐Lilly
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10796

Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing
Cited by: 2
Author(s): Lingling Liu, Chao Fang, YinZe Sun, Wujun Liu
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.8722

Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication
Cited by: 5
Author(s): Shinya Suzuki, Takuji Yamada
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0247115

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing
Cited by: 100
Author(s): Rahul C. Bhoyar, Abhinav Jain, Paras Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare, Swayamprabha Sahoo, Maheswata Sahoo, Ananya Nayak, Jatindra Nath Mohanty, Jayashankar Das, Sudhir Bhandari, Sandeep Kumar Mathur, Anshul Kumar, S G Rahul, Pallavali Rojarani, J Vijaya Lakshmi, A. Surekha, P. Chandra Sekhar, Siddharth Mahajan, Shet Masih, Pawan Kumar Singh, Vijayendra Kumar, Blessy Jose, Vidur Mahajan, V. Gupta, Rakesh Gupta, Prakash Arumugam, Anjali Singh, Aditya Nandy, P. V. Ragavendran, Rakesh Mohan Jha, Anupama Kumari, Sheetal Gandotra, V. Pandu Ranga Rao, Mohammed Faruq, Sanjeev Kumar, Betsy Reshma G, Narendra Varma G., Shuvra Shekhar Roy, A. K. Sengupta, Sabyasachi Chattopadhyay, Khushboo Singhal, Shalini Pradhan, Diksha Jha, Salwa Naushin, Saruchi Wadhwa, Nishu Tyagi, M. Damodara Poojary, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0139328

Exome Capture with Heterologous Enrichment in Pig (Sus scrofa)
Cited by: 1
Author(s): Denis Guiatti, Elena Pomari, Slobodanka Radović, Alessandro Spadotto, Bruno Stefanon
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0195481

Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet
Cited by: 58
Author(s): Martin Jensen Søe, Peter Nejsum, Frederik Valeur Seersholm, Brian L. Fredensborg, Ruben Habraken, Kirstine Haase, Mette Marie Hald, Rikke Kildevæld Simonsen, Flemming Højlund, Louise Blanke, Inga Merkytė, Eske Willerslev, Christian M. O. Kapel
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/7370350

Probe into the Target and Mechanism of Jianpi Xiaoke Prescription for Treating Type 2 Diabetes Mellitus through miRNA Expression Profiling
Cited by: 2
Author(s): Qinyue Guo, Yunsheng Xu, Jie Li, Dan Luo, Li Jun, Changwu Xu, Yanqin Huang
Software Mentions: 2
Published: almost 4 years ago

10.1002/2211-5463.12709

Profiling and functional analysis of differentially expressed circular RNAs in high glucose‐induced human umbilical vein endothelial cells
Cited by: 26
Author(s): Guoxi Jin, Qiong Wang, Xiaolei Hu, Xiaoli Li, Xiuying Pei, Erdi Xu, Minglong Li
Software Mentions: 2
Published: about 5 years ago

10.3389/fnagi.2017.00195

16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain
Cited by: 199
Author(s): David C. Emery, Deborah K. Shoemark, Thomas E Batstone, Christy Waterfall, Jane A. Coghill, Tanya L. Cerajewska, Malcolm Davies, Nicola West, Shelley J Allen
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.01883

Analytical Performance Validation of Next-Generation Sequencing Based Clinical Microbiology Assays Using a K-mer Analysis Workflow
Cited by: 12
Author(s): Sarah Lepuschitz, Thomas Weinmaier, Katharina Mrazek, Stephan Beisken, Johannes Weinberger, Andreas E. Posch
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2021.613529

Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
Cited by: 37
Author(s): Melissa E K Haines, Francesca E Hodges, Janet Y. Nale, Jennifer Mahony, Douwe van Sinderen, Joanna Kaczorowska, Bandar Alrashid, Mahmuda Akter, Nathan Brown, Dominic Sauvageau, Thomas Sicheritz-Pontén, Anisha M. Thanki, Andrew Millard, Edouard E. Galyov, Martha R.J. Clokie
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.02556

Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism
Cited by: 79
Author(s): Charlotte Peeters, Evelien De Canck, Margo Cnockaert, Evie De Brandt, Cindy Snauwaert, Bart Verheyde, Eliza Depoorter, Theodore Spilker, John J. LiPuma, Peter Vandamme
Software Mentions: 2
Published: almost 5 years ago

10.3389/fphar.2018.01570

High Throughput mRNA Sequencing Reveals Potential Therapeutic Targets of Tao-Hong-Si-Wu Decoction in Experimental Middle Cerebral Artery Occlusion
Cited by: 12
Author(s): Xianchun Duan, Lei Han, Daiyin Peng, Weidong Chen, Can Peng, Ling Xiao, Qiuyu Bao
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.119.400030

Diploid Genome Assembly of the Wine Grape Carménère
Cited by: 65
Author(s): Andrea Minio, Mélanie Massonnet, Rosa Figueroa‐Balderas, Álvaro Castro, Dario Cantu
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.119.400959

Whole Genome Sequences of 23 Species from the Drosophila montium Species Group (Diptera: Drosophilidae): A Resource for Testing Evolutionary Hypotheses
Cited by: 15
Author(s): Michael J. Bronski, Ciera C. Martinez, Holli A. Weld, Michael B. Eisen
Software Mentions: 2
Published: over 4 years ago

10.3390/genes11060617

Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids
Cited by: 9
Author(s): Anatolie Marta, Dmitrij Dedukh, Oldřich Bartoš, Zuzana Majtánová, Karel Janko
Software Mentions: 2
Published: over 4 years ago

10.3390/genes12071055

Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity
Cited by: 7
Author(s): Romy Petroll, Mona Schreiber, Hermann Finke, J. Mark Cock, Sven B. Gould, Stefan A. Rensing
Software Mentions: 2
Published: about 3 years ago

10.1186/s13059-020-01981-w

Obstacles to detecting isoforms using full-length scRNA-seq data
Cited by: 32
Author(s): Jennifer Westoby, Pavel Artemov, Martin Hemberg, Anne C. Ferguson‐Smith
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-020-02143-8

Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs
Cited by: 20
Author(s): Chongwei Bi, Lin Wang, Baolei Yuan, Xuan Zhou, Li Yu, Sheng Wang, Yuhong Pang, Xin Gao, Yanyi Huang, Mo Li
Software Mentions: 2
Published: about 4 years ago

10.1093/gbe/evz165

Intraspecific Diversity of Fission Yeast Mitochondrial Genomes
Cited by: 21
Author(s): Yu‐Tian Tao, Fang Suo, Sergio Tusso, Yankai Wang, Song Huang, Jochen B. W. Wolf, Li-Lin Du
Software Mentions: 2
Published: about 5 years ago

10.1186/s13073-018-0528-3

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
Cited by: 50
Author(s): Amit A. Upadhyay, Robert C. Kauffman, Amber N. Wolabaugh, Alice Cho, Nirav Patel, Samantha M. Reiss, Colin Havenar-Daughton, Reem A. Dawoud, Gregory K. Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F. Eun-Hyung Lee, Jens Wrammert, Steven E. Bosinger
Software Mentions: 2
Published: over 6 years ago

10.1186/s41065-020-00120-6

STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
Cited by: 4
Author(s): Dong Wang, Ruiyang Tao, Zhiqiang Li, Dun Pan, Zhuo Wang, Chengtao Li, Yongyong Shi
Software Mentions: 2
Published: over 4 years ago

10.1007/s13353-020-00603-2

European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients
Cited by: 15
Author(s): Szymon Hryhorowicz, Adam Ustaszewski, Marta Kaczmarek-Ryś, Emilia Lis, Michał Witt, Andrzej Pławski, Ewa Ziętkiewicz
Software Mentions: 2
Published: over 3 years ago

10.3390/jcm9113656

Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale
Cited by: 12
Author(s): Ana Díaz-de Usera, José M. Lorenzo-Salazar, Luis A. Rubio-Rodríguez, Adrián Muñoz-Barrera, Beatriz Guillén‐Guío, Itahisa Marcelino-Rodríguez, Víctor García‐Olivares, Alejandro Mendoza-Álvarez, Almudena Corrales, Antonio Íñigo-Campos, Rafaela González-Montelongo, Carlos Flores
Software Mentions: 2
Published: almost 4 years ago

10.1126/sciadv.abg6424

Disruption of paternal circadian rhythm affects metabolic health in male offspring via nongerm cell factors
Cited by: 10
Author(s): Maximilian Lassi, Archana Tomar, Gemma Comas-Armangué, Rebekka Vogtmann, Dorieke J. Dijkstra, David Corujo, Raffaele Gerlini, Jonatan Darr, F. Scheid, Jan Rozman, Antonio Aguilar-Pimentel, Omry Koren, Marcus Buschbeck, Helmut Fuchs, Susan Marschall, Valérie Gailus‐Durner, Martin Hrabě de Angelis, Torsten Plösch, Alexandra Gellhaus, Raffaele Teperino
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-09089-1

Accelerating next generation sequencing data analysis with system level optimizations
Cited by: 14
Author(s): Nagarajan Kathiresan, Ramzi Temanni, Hakeem Almabrazi, Najeeb Syed, Puthen V. Jithesh, Rashid Al‐Ali
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-11466-9

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
Cited by: 19
Author(s): Lior David, Xavier Grau‐Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-41235-9

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples
Cited by: 24
Author(s): Shambhavi Singh, Lixin Wang, Dylan L. Schaff, Matthew D. Sutcliffe, Alexander F. Koeppel, Jung-Eun Kim, Suna Önengüt-Gümüşcü, Kwon-Sik Park, Hui Zong, Kevin A. Janes
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-61989-x

Benchmarking the MinION: Evaluating long reads for microbial profiling
Cited by: 26
Author(s): Robert Maximilian Leidenfrost, Dierk-Christoph Pöther, Udo Jäckel, Röbbe Wünschiers
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-66331-z

Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length
Cited by: 5
Author(s): Barbara Iadarola, Luciano Xumerle, Denise Lavezzari, Marta Paterno, Luca Marcolungo, Cristina Beltrami, Elisabetta Fortunati, Davide Mei, Annalisa Vetro, Renzo Guerrini, Elena Parrini, Marzia Rossato, Massimo Delledonne
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.01917-20

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome
Cited by: 25
Author(s): Bridget L. Hansen, Rita de Cássia Pessotti, Monika Fischer, Alyssa Collins, Laila El-Hifnawi, Mira D. Liu, Matthew F. Traxler
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00648-20

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
Cited by: 7
Author(s): María Isabel Rojas, Giselle S. Cavalcanti, Katelyn McNair, Sean Benler, Amanda T. Alker, Ana G Cobián-Güemes, Melissa Giluso, Kyle Levi, Forest Rohwer, Barbara Bailey, Sinem Beyhan, Robert A. Edwards, Nicholas J. Shikuma
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00392-21

Catching SARS-CoV-2 by Sequence Hybridization: a Comparative Analysis
Cited by: 7
Author(s): Alexandra Rehn, Peter Braun, Mandy Knüpfer, Roman Wölfel, Markus Antwerpen, Mathias C. Walter
Software Mentions: 2
Published: about 3 years ago

10.1128/mSystems.00552-21

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing
Cited by: 3
Author(s): Matthew Y Cho, Marc Oliva, Anna Spreafico, Bin Chen, Wei Xu, Yoojin Choi, Rupert Kaul, Lillian L. Siu, Bryan Coburn, Pierre H. H. Schneeberger
Software Mentions: 2
Published: about 3 years ago

10.1186/s12866-018-1336-z

USA300 Staphylococcus aureus persists on multiple body sites following an infection
Cited by: 11
Author(s): Timothy D. Read, Robert A. Petit, Yin Zhen, Tuyaa Montgomery, Moira McNulty, Michael Z. David
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.fsigen.2019.01.008

Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region
Cited by: 7
Author(s): Tunde I. Huszar, Jon H. Wetton, Mark A. Jobling
Software Mentions: 1
Published: over 5 years ago

10.1128/mSphere.00571-17

Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages
Cited by: 25
Author(s): Michael B. Frisch, Santiago Castillo-Ramírez, Robert A. Petit, Monica M. Farley, Susan M. Ray, Valérie Albrecht, Brandi Limbago, Jeranfel Hernandez, Isaac See, Sarah W. Satola, Timothy D. Read
Software Mentions: 1
Published: about 6 years ago

10.1111/eva.13249

The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species
Cited by: 10
Author(s): Lídia Escoda, José Castresana
Software Mentions: 1
Published: over 3 years ago

10.1016/j.celrep.2021.109746

Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state
Cited by: 4
Author(s): Frank J. Piscotta, Shawn T. Whitfield, Toshiki G. Nakashige, Andréia Bergamo Estrela, Thahmina Ali, Sean F. Brady
Software Mentions: 1
Published: about 3 years ago

10.1093/gigascience/gix125

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree
Cited by: 21
Author(s): Orzenil B. Silva‐Junior, Dário Grattapaglia, Evandro Novaes, Rosane Garcia Collevatti
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-017-0141-1

iPSC modeling of severe aplastic anemia reveals impaired differentiation and telomere shortening in blood progenitors
Cited by: 24
Author(s): Dario Melguizo‐Sanchis, Yaobo Xu, Dheraj K. Taheem, Min Yu, Katarzyna Tilgner, Tomáš Bárta, Katja Gassner, George Anyfantis, Tengfei Wan, Ramu Elango, Sameer E. Al-Harthi, Ashraf A. El‐Harouni, Stefan Przyborski, Soheir Adam, Gabriele Saretzki, Sujith Samarasinghe, Lyle Armstrong, Majlinda Lako
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers12082089

Comprehensive Cohort Analysis of Mutational Spectrum in Early Onset Breast Cancer Patients
Cited by: 9
Author(s): Mohit Midha, Yu-Feng Huang, Hsiao-Hsiang Yang, Tan‐Chi Fan, Nai‐Chuan Chang, Tzu-Han Chen, Yutai Wang, Wen‐Hung Kuo, King‐Jen Chang, Chen‐Yang Shen, Alice L. Yu, King-Wah Chiu, Chien-Jen Chen
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0130673

Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy
Cited by: 2
Author(s): Yu-Feng Huang, Mohit Midha, Tzu-Han Chen, Yutai Wang, David Glenn Smith, Kurtis Jai‐Chyi Pei, Kuo Ping Chiu
Software Mentions: 1
Published: about 9 years ago

10.1093/gigascience/giz158

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
Cited by: 35
Author(s): Mitsutaka Kadota, Osamu Nishimura, Hisashi Miura, Kaori Tanaka, Ichiro Hiratani, Shigehiro Kuraku
Software Mentions: 1
Published: over 4 years ago

10.1093/gigascience/giaa100

Construction of a chromosome-scale long-read reference genome assembly for potato
Cited by: 119
Author(s): Gina M. Pham, John Hamilton, Joshua C. Wood, Joseph Burke, Hainan Zhao, Brieanne Vaillancourt, Shujun Ou, Jiming Jiang, C. Robin Buell
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0119812

Genomic, Proteomic and Morphological Characterization of Two Novel Broad Host Lytic Bacteriophages ΦPD10.3 and ΦPD23.1 Infecting Pectinolytic Pectobacterium spp. and Dickeya spp.
Cited by: 68
Author(s): Robert Czajkowski, Zofia Ozymko, Victor de Jager, Joanna Siwinska, Anna Smolarska, Adam Ossowicki, Magdalena Narajczyk, Ewa Łojkowska
Software Mentions: 1
Published: over 9 years ago

10.1128/AEM.01999-18

Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline
Cited by: 18
Author(s): Wesley Morovic, Paige Roos, Bryan Zabel, Claudio Hidalgo-Cantabrana, Anthony Kiefer, Rodolphe Barrangou
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41437-018-0070-5

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra)
Cited by: 24
Author(s): Silvia Fuselli, Rodrigo P. Baptista, Alex Panziera, Alberto Magi, S. Guglielmi, Rita Tonin, Andrea Benazzo, Luíz Guilherme Soares da Rocha Bauzer, Camila J. Mazzoni, Giorgio Bertorelle
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-019-1649-6

Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)
Cited by: 23
Author(s): Deane N Woruba, Jennifer L. Morrow, Olivia L. Reynolds, Toni A. Chapman, Damian Collins, Markus Riegler
Software Mentions: 1
Published: almost 5 years ago

10.1128/mSystems.00497-21

VB 12 Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways
Cited by: 3
Author(s): Jiayin Zhou, Xiaoli Yu, Jihua Liu, Wei Qin, Zhili He, David A. Stahl, Nianzhi Jiao, Jizhong Zhou, Qichao Tu
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.ppat.1005701

CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections
Cited by: 211
Author(s): Ferdy R. van Diemen, Elisabeth Kruse, Marjolein J. G. Hooykaas, Carlijn E. Bruggeling, Anita C. Schürch, Petra M. van Ham, Saskia M. Imhof, Monique Nijhuis, Emmanuel J. H. J. Wiertz, Robert Jan Lebbink
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1007445

Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
Cited by: 38
Author(s): Yolande Grobler, Chi Young Yun, David J. Kahler, Casey M. Bergman, Hangnoh Lee, Brian Oliver, Ruth Lehmann
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0113036

Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing
Cited by: 17
Author(s): Szabolcs Szelinger, Ivana Malenica, Jason J. Corneveaux, Ashley L. Siniard, Ahmet Kurdoglu, Keri Ramsey, Isabelle Schrauwen, Jeffrey M. Trent, Vinodh Narayanan, Matthew J. Huentelman, David W. Craig
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms221910359

Saturation Mutagenesis of the Transmembrane Region of HokC in Escherichia coli Reveals Its High Tolerance to Mutations
Cited by: 1
Author(s): María Teresa Lara Ortiz, Víctor M. Petrone García, Gabriel del Río
Software Mentions: 1
Published: almost 3 years ago

10.1371/journal.pone.0105585

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods
Cited by: 253
Author(s): Charles F. A. de Bourcy, Iwijn De Vlaminck, Jad Kanbar, Jianbin Wang, Charles Gawad, Stephen R. Quake
Software Mentions: 1
Published: about 10 years ago

10.1038/srep05597

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)
Cited by: 23
Author(s): Bart J. G. Broeckx, Frank Coopman, Geert Verhoeven, Valérie Bavegems, Sarah De Keulenaer, Ellen De Meester, Filip Van Niewerburgh, Dieter Deforce
Software Mentions: 1
Published: about 10 years ago

10.1038/srep21597

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
Cited by: 124
Author(s): Shailesh Kumar, Angie Duy Vo, Fujun Qin, Hui Li
Software Mentions: 1
Published: over 8 years ago

10.1038/srep31175

Fetal Bovine Serum RNA Interferes with the Cell Culture derived Extracellular RNA
Cited by: 116
Author(s): Zengxin Wei, Arsen O. Batagov, David R. F. Carter, Anna M. Krichevsky
Software Mentions: 1
Published: about 8 years ago

10.1186/s13007-019-0445-5

Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3
Cited by: 15
Author(s): Charlotte Prodhomme, Danny Esselink, Theo Borm, R.G.F. Visser, H.J. van Eck, Jack H. Vossen
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10030384

WGS of Commensal Neisseria Reveals Acquisition of a New Ribosomal Protection Protein (MsrD) as a Possible Explanation for High Level Azithromycin Resistance in Belgium
Cited by: 16
Author(s): Tessa de Block, Jolein Laumen, Christophe Van Dijck, Saïd Abdellati, Irith De Baetselier, Sheeba Santhini Manoharan-Basil, Dorien Van den Bossche, Chris Kenyon
Software Mentions: 1
Published: over 3 years ago

10.1128/AAC.01324-19

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes
Cited by: 55
Author(s): Allison K Guitor, Amogelang R. Raphenya, Jennifer Klunk, Melanie Kuch, Brian Alcock, Michael G. Surette, Andrew G. McArthur, Hendrik N. Poinar, Gerard D. Wright
Software Mentions: 1
Published: over 4 years ago

10.1093/hmg/ddx140

Induced pluripotent stem cell modelling of HLHS underlines the contribution of dysfunctional NOTCH signalling to impaired cardiogenesis
Cited by: 50
Author(s): Chunbo Yang, Yaobo Xu, Min Yu, David Lee, Sameer Alharti, Nicola Hellen, Noor Ahmad Shaik, Babajan Banaganapalli, Hussein Sheikh Ali Mohamoud, Stefan Przyborski, Gennadiy Tenin, Simon G. Williams, John O’Sullivan, Osman O. Al‐Radi, Jameel Atta, Siân E. Harding, Bernard Keavney, Majlinda Lako, Lyle Armstrong
Software Mentions: 1
Published: over 7 years ago

10.1128/MRA.00121-19

Complete Genome Sequence of a Bioactive Pseudomonas sp. Strain, DTU12.3, Isolated from Soil in Denmark
Cited by: 0
Author(s): Pavelas Sazinas, May Iren Aune, Marie Højmark Fischer, Jonas Greve Lauritsen, Lone Gram, Lars Jelsbak
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-20015-x

Use of whole genome sequencing to investigate an increase in Neisseria gonorrhoeae infection among women in urban areas of Australia
Cited by: 22
Author(s): Cameron Buckley, Brian M. Forde, Ella Trembizki, Monica M Lahra, Scott A. Beatson, David M. Whiley
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-018-0092-2

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate
Cited by: 113
Author(s): Michael W. Henson, V. Celeste Lanclos, Brant C. Faircloth, J. Cameron Thrash
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-43600-0

Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures
Cited by: 42
Author(s): Mari Kamitani, Makoto Kashima, Ayumi Tezuka, Atsushi J. Nagano
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00158-21

Draft Genome Sequence of the Type Strain Bacillus subtilis subsp. subtilis DSM10
Cited by: 2
Author(s): Lars Lilge, Robert Hertel, Kambiz Morabbi Heravi, Marius Henkel, Fabian M. Commichau, Rudolf Hausmann
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-58300-3

Analysis of Plasmodium falciparum Rh2b deletion polymorphism across different transmission areas
Cited by: 3
Author(s): Yaw Aniweh, Jonathan Suurbaar, Collins M. Morang’a, Prince B. Nyarko, Katherine E. Wright, Kwadwo Asamoah Kusi, Felix Ansah, Eric Kyei-Baafour, Evelyn Quansah, Jessica Asante, Laty G. Thiam, M.K. Higgins, Gordon A. Awandare
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-015-1412-9

Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions
Cited by: 14
Author(s): Martin Urban, Robert C. King, Keywan Hassani‐Pak, K. E. Hammond‐Kosack
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.36389

The cJUN NH2-terminal kinase (JNK) signaling pathway promotes genome stability and prevents tumor initiation
Cited by: 26
Author(s): Nomeda Girnius, Yvonne J. K. Edwards, David S. Garlick, Roger J. Davis
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2020.00124

Unearthing the Plant Growth-Promoting Traits of Bacillus megaterium RmBm31, an Endophytic Bacterium Isolated From Root Nodules of Retama monosperma
Cited by: 42
Author(s): Malika Affaf Dahmani, Antoine Desrut, Bouziane Moumen, Julien Verdon, Lamia Mermouri, Kacem Mourad, Pierre Coutos-Thévenot, Meriem Kaïd-Harche, Thierry Bergès, Cécile Vriet
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2018.00388

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes
Cited by: 76
Author(s): Byron C. Crump, John Michael Adrian Wojahn, Fiona Tomàs, Robert F. Mueller
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2014.00505

Bacteria in Ostreococcus tauri cultures â€“ friends, foes or hitchhikers?
Cited by: 27
Author(s): Sophie S. Abby, Marie Touchon, Aurélien De Jode, Nigel Grimsley, Gwenaël Piganeau
Software Mentions: 1
Published: almost 10 years ago

10.1534/g3.118.200729

RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3′ Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species
Cited by: 5
Author(s): Jordan R. Silke, Yulong Wei, Xuhua Xia
Software Mentions: 1
Published: almost 6 years ago

10.1128/MRA.01339-19

Complete Genome Sequences for Two Myoviridae Strains Infecting Cyanobacteria in a Subarctic Lake
Cited by: 3
Author(s): Alice V. Lévesque, Mary Thaler, Simon J. Labrie, Catherine Marois, Antony T. Vincent, Anne-Marie Lapointe, Alexander I. Culley
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01375-20

Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in Malta
Cited by: 2
Author(s): Manuele Biazzo, Silvia Madeddu, Elfath M. Elnifro, Tessabella Sultana, Josie Muscat, Christian Scerri, Francesco Santoro, David Pinzauti
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2017.01525

iRAGu: A Novel Inducible and Reversible Mouse Model for Ubiquitous Recombinase Activity
Cited by: 1
Author(s): Marie-Laure Bonnet, Leonor M. Sarmento, Ana Martins, Daniel Sobral, Joana Silva, Jocelyne Demengeot
Software Mentions: 1
Published: almost 7 years ago

10.1128/MRA.01015-19

Draft Genome Sequence of an Escherichia coli Strain Harboring bla CTX-M-115 , bla CMY-2 , Aminoglycoside, Tetracycline, and Sulfonamide Resistance Genes, Isolated from a Costa Rican Wastewater Treatment Plant
Cited by: 1
Author(s): Kenia Barrantes, Luz Chacón, Eric Morales Mora, Lisbeth Ramírez-Carvajal
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: seqtk

Papers Mentioning seqtk 213