pypi: bwa | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000221

Identification of novel adenovirus genotype 90 in children from Bangladesh
Cited by: 9
Author(s): Charlotte J. Houldcroft, Mathew A. Beale, Abu Sayeed, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Software Mentions: 3
Published: about 6 years ago

10.1016/j.dib.2020.105820

Multi-tissue Siberian sturgeon RNA sequencing data
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, Denise Vizziano-Cantonnet
Software Mentions: 3
Published: over 4 years ago

10.15252/emmm.202011987

Combined targeting of G protein‐coupled receptor and <scp>EGF</scp> receptor signaling overcomes resistance to <scp>PI</scp> 3K pathway inhibitors in <scp>PTEN</scp> ‐null triple negative breast cancer
Cited by: 17
Author(s): Davide Zecchin, Christopher Moore, Fanourios Michailidis, Stuart Horswell, Sareena Rana, Michael Howell, Julian Downward
Software Mentions: 3
Published: over 4 years ago

10.1186/s13028-018-0415-3

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging
Cited by: 33
Author(s): Marie Lisandra Zepeda Mendoza, Michael Roggenbuck, Karla Manzano Vargas, Lars Hestbjerg Hansen, Søren Brunak, M. Thomas P. Gilbert, Thomas Sicheritz-Pontén
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.2466

Dealing with paralogy in <scp>RAD</scp> seq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
Cited by: 26
Author(s): Cindy Verdu, Erwan Guichoux, Samuel Quevauvillers, Olivier De Thier, Yec’han Laizet, Adline Delcamp, Frédéric Gévaudant, Arnaud Monty, Annabel J. Porté, Philippe Lejeune, Ludivine Lassois, Stéphanie Mariette
Software Mentions: 3
Published: about 8 years ago

10.1111/eva.13231

Leveraging genomics to understand threats to migratory birds
Cited by: 4
Author(s): Brenda Larison, Alec R. Lindsay, Christen M. Bossu, Michael D. Sorenson, Jonas Kaplan, David C. Evers, James D. Paruk, Jeffrey M. DaCosta, Thomas B. Smith, Kristen Ruegg
Software Mentions: 3
Published: over 3 years ago

10.1111/eva.13086

Population genomic data in spider mites point to a role for local adaptation in shaping range shifts
Cited by: 11
Author(s): Lei Chen, Jing‐Tao Sun, Peng‐Yu Jin, Ary A. Hoffmann, Xiao‐Li Bing, Dian‐Shu Zhao, Xiao‐Feng Xue, Xiao‐Yue Hong
Software Mentions: 3
Published: about 4 years ago

10.1111/eva.13194

Standing genetic variation in laboratory populations of insecticide‐susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance
Cited by: 2
Author(s): David S. Denlinger, Spencer B. Hudson, Nadya S. Keweshan, Zachariah Gompert, Scott A. Bernhardt
Software Mentions: 3
Published: almost 4 years ago

10.1002/evl3.8

Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius
Cited by: 54
Author(s): Ann-Marie Oppold, Markus Pfenninger
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2148-13-48

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species
Cited by: 39
Author(s): Yeting Zhang, Mónica Fernández‐Aparicio, Eric Wafula, Mita Das, Yuannian Jiao, Norman J. Wickett, Loren Honaas, Paula E. Ralph, Martin F. Wojciechowski, Michael P. Timko, John I. Yoder, James H. Westwood, Claude W. dePamphilis
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2020.00876

Chromosome Genome Assembly of the Leopard Coral Grouper (Plectropomus leopardus) With Nanopore and Hi-C Sequencing Data
Cited by: 4
Author(s): Yongbo Wang, Xintian Wen, Xinhui Zhang, Shuyuan Fu, Jinye Liu, Wei Tan, Ming Luo, Longlong Liu, Hai Huang, Xinxin You, Jian Luo, Fuxiao Chen
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2018.00344

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis
Cited by: 11
Author(s): Anne Busch, Prasad Thomas, Eric Zuchantke, Holger Brendebach, Kerstin Neubert, Josephine Gruetzke, Sascha Al Dahouk, Martin C. Peters, Helmut Hotzel, Heinrich Neubauer, Herbert Tomaso
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.667718

Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy
Cited by: 13
Author(s): Xiangning Bai, Aswathy Narayanan, Piotr Nowak, Shilpa Ray, Ujjwal Neogi, Anders Sönnerborg
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-021-01064-3

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Cited by: 465
Author(s): Chang Liu, Meng‐Xuan Du, Rexiding Abuduaini, Haiying Yu, Dan‐Hua Li, Yujing Wang, Nan Zhou, Min-Zhi Jiang, Ping Niu, Shanshan Han, Hong-He Chen, Wenyu Shi, Linhuan Wu, Yu‐Hua Xin, Juncai Ma, Yu‐Guang Zhou, Cheng‐Ying Jiang, Hongwei Liu, Shuang‐Jiang Liu
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.647565

Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting
Cited by: 6
Author(s): Meshack O Juma, Arun Sankaradoss, Redcliff Ndombi, Patrick Mwaura, Tina Damodar, Junaid Nazir, Awadhesh Pandit, Rupsy Khurana, Moses Masika, Ruth Chirchir, John Gachie, Sudhir Krishna, Ramanathan Sowdhamini, Omu Anzala, Iyer Meenakshi
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.00302

CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma
Cited by: 7
Author(s): Robyn T. Sussman, Jo Lynne Rokita, Kevin Huang, Pichai Raman, Komal S. Rathi, Daniel Martı́nez, Kristopher R. Bosse, Maria Lane, Lori S. Hart, Tricia R. Bhatti, Bruce Pawel, John M. Maris
Software Mentions: 3
Published: over 4 years ago

10.3389/fphys.2015.00286

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution
Cited by: 30
Author(s): Anita Tripathi, Kavita Goswami, Neeti Sanan-Mishra
Software Mentions: 3
Published: about 9 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9051022

Genomics and Virulence of Klebsiella pneumoniae Kpnu95 ST1412 Harboring a Novel Incf Plasmid Encoding Blactx-M-15 and Qnrs1 Causing Community Urinary Tract Infection
Cited by: 3
Author(s): Ayala Gancz, Kira Kondratyeva, Dorit Cohen-Eli, Shiri Navon-Venezia
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.115.017277

Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome
Cited by: 39
Author(s): Flávia Krsticevic, Carlos G. Schrago, Antonio Bernardo Carvalho
Software Mentions: 3
Published: over 9 years ago

10.1186/s13100-017-0086-z

Considerations and complications of mapping small RNA high-throughput data to transposable elements
Cited by: 9
Author(s): Alexandros Bousios, Brandon S. Gaut, Nikos Darzentas
Software Mentions: 3
Published: almost 8 years ago

10.1534/g3.118.200030

Genomic Variation Among and Within SixJuglansSpecies
Cited by: 40
Author(s): Kristian Stevens, Keith Woeste, Sandeep Chakraborty, Marc W. Crepeau, Charles A. Leslie, Pedro J. Martínez-García, Daniela Puiu, Jeanne Romero‐Severson, Mark V. Coggeshall, Abhaya M. Dandekar, Daniel A. Kluepfel, David B. Neale, Steven L. Salzberg, Charles H. Langley
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.118.200308

Whole Genome Sequence of the Parasitoid Wasp Microplitis demolitor That Harbors an Endogenous Virus Mutualist
Cited by: 29
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 3
Published: about 6 years ago

10.1186/s12885-019-5628-y

The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution
Cited by: 5
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, José Ángel Díaz Arias, Nicolas Varela, Manuel Pérez‐Encinas, Catarina Allegue Toscano, Elena M. Seco, Ángel Carracedo, José Luis Bello López
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms20205047

Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies
Cited by: 5
Author(s): Jing Tu, Liang Chen, Shen Gao, Jun‐Yi Zhang, Changwei Bi, Yuhan Tao, Na Lü, Lu Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-13-S6-S8

High-resolution genetic mapping with pooled sequencing
Cited by: 55
Author(s): Matthew D. Edwards, David K. Gifford
Software Mentions: 2
Published: over 12 years ago

10.1038/s41416-018-0089-7

Somatic mutations in benign breast disease tissue and risk of subsequent invasive breast cancer
Cited by: 8
Author(s): Thomas E. Rohan, Christopher A. Miller, Tiandao Li, Yihong Wang, Olivier Loudig, Mindy Ginsberg, Andrew G. Glass, Elaine R. Mardis
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1009714

Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans
Cited by: 9
Author(s): Eric J. Foss, Smitha Sripathy, Tonibelle Gatbonton-Schwager, Hyunchang Kwak, Adam H. Thiesen, Uyen Lao, Antonio Bedalov
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0155760

Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing
Cited by: 89
Author(s): Prabin Bajgain, Matthew N. Rouse, Toi J. Tsilo, Godwin Macharia, Sridhar Bhavani, Yue Jin, James A. Anderson
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.08714

Genomic epidemiology of artemisinin resistant malaria
Cited by: 220
Author(s): Roberto Amato, Olivo Miotto, Charles J. Woodrow, Jacob Almagro-Garcia, Ipsita Sinha, Susana Campino, Daniel Mead, Eleanor Drury, Mihir Kekre, Mandy Sanders, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Voahangy Andrianaranjaka, Tobias O. Apinjoh, Elizabeth A. Ashley, Sarah Auburn, Gordon A. Awandare, Vito Baraka, Alyssa E. Barry, Maciej F. Boni, Steffen Borrmann, Teun Bousema, OraLee H. Branch, Peter C. Bull, Kesinee Chotivanich, David J. Conway, Alister G. Craig, Nicholas P. J. Day, AA Djimde, Christiane Dolecek, Arjen M. Dondorp, Chris Drakeley, Patrick E. Duffy
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.09945

RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits
Cited by: 40
Author(s): Lucas B. Carey
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12885-019-5650-0

Association of pathway mutation with survival after recurrence in colorectal cancer patients treated with adjuvant fluoropyrimidine and oxaliplatin chemotherapy
Cited by: 2
Author(s): Dae Won Lee, Sae Won Han, Yongjun Cha, Jeong Mo Bae, Hwang Phill Kim, Jaemyun Lyu, Hyojun Han, Hyoki Kim, Hoon Jang, Duhee Bang, Jae Kyung Won, Seung Yong Jeong, Kyu Joo Park, Gyeong Hoon Kang, Tae You Kim
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.61265

Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology
Cited by: 7
Author(s): Yijun Cheng, Luke Saville, Babita Gollen, Christopher Isaac, Abel Belay, Jogender Mehla, Krishna Patel, Nehal Thakor, Majid H. Mohajerani, Athanasios Zovoilis
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0157075

A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome
Cited by: 5
Author(s): Christopher M. Watson, Laura A. Crinnion, Sally M. Harrison, Carolina Lascelles, Agne Antanaviciute, Ian Carr, David T. Bonthron, Eamonn Sheridan
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.62765

Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity
Cited by: 13
Author(s): Chyi Yin Gwee, Kritika M. Garg, Balaji Chattopadhyay, Keren R. Sadanandan, Dewi M. Prawiradilaga, Martin Irestedt, Fumin Lei, Luke M. Bloch, Jessica G.H. Lee, Mohammad Irham, Tri Haryoko, Malcolm C. K. Soh, Kelvin S.‐H. Peh, Karen M. C. Rowe, Teuku Reza Ferasyi, Shaoyuan Wu, Guinevere O. U. Wogan, Rauri C. K. Bowie
Software Mentions: 2
Published: almost 4 years ago

10.1093/g3journal/jkaa018

Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei
Cited by: 12
Author(s): John W. Davey, Carolina Moura Costa Catta-Preta, Sally James, Sarah Forrester, Maria Cristina M. Motta, Peter D. Ashton, Jeremy C. Mottram
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.44812

Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community
Cited by: 11
Author(s): Samuel F.M. Hart, Jose Mario Bello Pineda, Chi‐Chun Chen, Robin Green, Wenying Shou
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0059850

Thermo-Regulation of Genes Mediating Motility and Plant Interactions in Pseudomonas syringae
Cited by: 65
Author(s): Kevin L. Hockett, Adrien Y. Burch, Steven E. Lindow
Software Mentions: 2
Published: over 11 years ago

10.1186/s40168-020-00849-2

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms
Cited by: 36
Author(s): Haohui Zhong, Laura E. Lehtovirta-Morley, Jiwen Liu, Yanfen Zheng, Heyu Lin, Delei Song, Jonathan D. Todd, Jie Tian, Xiao‐Hua Zhang
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-015-1456-x

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data
Cited by: 48
Author(s): Richard Orton, Caroline F. Wright, Marco J. Morelli, David J. King, David Paton, Donald P. King, Daniel T. Haydon
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-015-1694-y

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation
Cited by: 73
Author(s): Michael Reck, Jürgen Tomasch, Zhi-Luo Deng, Michael Jarek, Peter Husemann, Irene Wagner‐Döbler
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0120585

Genetic Heterogeneity of Induced Pluripotent Stem Cells: Results from 24 Clones Derived from a Single C57BL/6 Mouse
Cited by: 11
Author(s): Li Cheng, Jeffery M. Klco, Nichole Helton, Daniel R. George, Jacqueline Mudd, Christopher A. Miller, Charles Lu, Robert S. Fulton, Michelle O’Laughlin, Catrina C. Fronick, Richard K. Wilson, Timothy J. Ley
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.117.300199

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower
Cited by: 21
Author(s): Patrick Thorwarth, Eltohamy A. A. Yousef, Karl Schmid
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.119.400930

High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
Cited by: 14
Author(s): Liang Lu, Jianmin Zhao, Chenhong Li
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.56450

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks
Cited by: 13
Author(s): Kelsey H. Elliott, Marc E. Rothenberg, Joseph Salomone, Praneet Chaturvedi, Preston A Schultz, Sai Keshavan Balchand, Jeffrey D Servetas, Aimée Zúñiga, Rolf Zeller, Brian Gebelein, Matthew T. Weirauch, Kevin A. Peterson, Samantha A. Brugmann
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2018.01223

Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation
Cited by: 33
Author(s): Gareth J. Norton, Anthony J. Travis, Alex Douglas, Susan Fairley, Eduardo Rodrigues Alves, Panthita Ruang-areerate, Elizabeth B. Naredo, Kenneth L. McNally, Mahmud Hossain, Rafiqul Islam, Adam H. Price
Software Mentions: 2
Published: about 6 years ago

10.1186/s40168-019-0717-3

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage
Cited by: 91
Author(s): Irina M. Velsko, James A. Fellows Yates, Franziska Aron, Richard Hagan, Laurent Frantz, Louise Loe, Juan Bautista Rodriguez Martinez, Eros Chaves, Chris Gosden, Greger Larson, Christina Warinner
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0197983

Gene expression to mitochondrial metabolism: Variability among cultured Trypanosoma cruzi strains
Cited by: 5
Author(s): Murat C. Kalem, Evgeny S. Gerasimov, Pamela K. Vu, Sara L. Zimmer
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.51407

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates
Cited by: 27
Author(s): Samantha G. Palace, Yi Wang, Daniel H. F. Rubin, Michael A. Welsh, Tatum D Mortimer, Kevin N. Cole, David W Eyre, Suzanne Walker, Yonatan H. Grad
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1008520

Hybridization promotes asexual reproduction in Caenorhabditis nematodes
Cited by: 11
Author(s): Piero Lamelza, Janet M. Young, Luke M. Noble, Lews Caro, Arielle Isakharov, Meenakshi Palanisamy, Matthew V. Rockman, Harmit S. Malik, Michael Ailion
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1005780

A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity
Cited by: 37
Author(s): Qingyun Li, Scott Barish, Sumie Okuwa, Abigail Maciejewski, Alicia Brandt, Dominik Reinhold, Corbin D. Jones, Pelin Volkan
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0063027

Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population
Cited by: 14
Author(s): Lionel Guy, Cecilia Jernberg, Jenny Arvén Norling, Sofie Ivarsson, Ingela Hedenström, Öjar Melefors, Ulrika Liljedahl, Lars Engstrand, Siv G. E. Andersson
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0144528

Mutation Screening of 1,237 Cancer Genes across Six Model Cell Lines of Basal-Like Breast Cancer
Cited by: 4
Author(s): Elin Olsson, Christof Winter, Anthony George, Yilun Chen, Therese Törngren, Pär‐Ola Bendahl, Åke Borg, Sofia K. Gruvberger-Saal, Lao H. Saal
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12885-020-07130-7

Defective migration and dysmorphology of neutrophil granulocytes in atypical chronic myeloid leukemia treated with ruxolitinib
Cited by: 6
Author(s): Lea Bornemann, Marc Schuster, Saskia Schmitz, Charlyn Sobczak, Clara Bessen, Simon F. Merz, Karl‐Heinz Jöckel, Thomas Haverkamp, Matthias Gunzer, Joachim R. Göthert
Software Mentions: 2
Published: over 4 years ago

10.1093/gbe/evz011

Small Segmental Duplications inDrosophila—High Rate of Emergence and Elimination
Cited by: 2
Author(s): Juan Li, Lan Jiang, Chung‐I Wu, Xuemei Lu, Shu Fang, Chau‐Ti Ting
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.42014

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice
Cited by: 58
Author(s): João Pl Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William Beluch, Ronald Naumann, Isabella Skuplik, James C. Cobb, Nicholas H. Barton, Campbell Rolian, Yingguang Frank Chan
Software Mentions: 2
Published: over 5 years ago

10.1093/gbe/evv079

Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees
Cited by: 48
Author(s): Daniel Tamarit, Kirsten Ellegaard, Johan Wikander, Tobias Olofsson, Alejandra Vásquez, Siv G. E. Andersson
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0172903

Domestication drive the changes of immune and digestive system of Eurasian perch (Perca fluviatilis)
Cited by: 12
Author(s): Xiaowen Chen, Chenghui Wang, Long Qian, Sarah Gaughan, Wei Xiang, Tao Ai, Zhenming Fan
Software Mentions: 2
Published: over 7 years ago

10.1007/s00109-019-01792-y

Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing
Cited by: 2
Author(s): Ulrike Fischer, Christina Backes, Tobias Fehlmann, Valentina Galata, Andreas Keller, Eckart Meese
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0209523

elPrep 4: A multithreaded framework for sequence analysis
Cited by: 16
Author(s): Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Wilfried Verachtert
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0249930

Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions
Cited by: 0
Author(s): Aziz Belkadi, Gaurav Thareja, Darshana Dadhania, John Y.K. Lee, Thangamani Muthukumar, Catherine Snopkowski, Carol Li, Anna Halama, Sara Abdelkader, Silvana A Abdulla, Yasmin Mahmoud, Joel A. Malek, Manikkam Suthanthiran, Karsten Suhre
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-021-02285-3

Comprehensive identification of somatic nucleotide variants in human brain tissue
Cited by: 23
Author(s): Yifan Wang, Taejeong Bae, Jeremy Thorpe, Maxwell A. Sherman, Attila Jones, Sean Cho, Kenneth Daily, Yanmei Dou, Javier Ganz, Alon Galor, Irene Lobón, Reenal Pattni, Chaggai Rosenbluh, Simone Tomasi, Livia Tomasini, Xiaoxu Yang, Bo Zhou, Schahram Akbarian, Laurel Ball, Sara Bizzotto, Sarah B. Emery, Ryan Doan, Liana Fasching, Yeongjun Jang, David Juan, Esther Lizano, Lovelace J. Luquette, John B. Moldovan, Rujuta Narurkar, Matthew T. Oetjens, Rachel E. Rodin, Shobana Sekar, Joo Heon Shin, Eduardo Soriano, Richard E. Straub, Weichen Zhou, Andrew Chess, Joseph G. Gleeson, Tomàs Marquès-Bonet, Peter J. Park, Mette A. Peters, Jonathan Pevsner, Christopher A. Walsh, Daniel R. Weinberger, Flora M. Vaccarino, John V. Moran, Alexander Urban, Jeffrey M. Kidd, Ryan E. Mills, Alexej Abyzov
Software Mentions: 2
Published: over 3 years ago

10.1093/infdis/jiw323

Genomic Analysis Reveals a Common Breakpoint in Amplifications of thePlasmodium vivaxMultidrug Resistance 1 Locus in Thailand
Cited by: 26
Author(s): Sarah Auburn, David Serre, Richard D. Pearson, Roberto Amato, Kanlaya Sriprawat, Sheren To, Irene Handayuni, Rossarin Suwanarusk, Bruce Russell, Eleanor Drury, Jim Stalker, Olivo Miotto, Dominic P. Kwiatkowski, François Nosten, Ric N. Price
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-14-191

Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family
Cited by: 33
Author(s): Gibeom Park, Jungsoo Gim, Ah Reum Kim, Kyou‐Sup Han, Hyosang Kim, Seung-Ha Oh, Taesung Park, Woong-Yang Park, Byung Yoon Choi
Software Mentions: 2
Published: almost 12 years ago

10.1002/acn3.51119

Using urine to diagnose large‐scale mtDNA deletions in adult patients
Cited by: 10
Author(s): Kristin Nielsen Varhaug, Gonzalo S. Nido, I.F.M. de Coo, Pirjo Isohanni, Anu Suomalainen, Charalampos Tzoulis, Per M. Knappskog, Laurence A. Bindoff
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.119.400073

Genome-Wide Association Study of Yield Component Traits in Intermediate Wheatgrass and Implications in Genomic Selection and Breeding
Cited by: 27
Author(s): Prabin Bajgain, Xiaofei Zhang, James A. Anderson
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2015.00882

Evolution, diversification, and expression of KNOX proteins in plants
Cited by: 37
Author(s): Jie Gao, Xue Yang, Wei Zhao, Tiange Lang, Tore Samuelsson
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0162573

Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster
Cited by: 4
Author(s): Jennifer Hackett, Xiaofei Wang, Brittny R. Smith, Stuart J. Macdonald
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-018-1618-7

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Cited by: 623
Author(s): Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Góes de Jesus, Bradley J. Main, Amanda L Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman, Kristian G. Andersen
Software Mentions: 2
Published: almost 6 years ago

10.1099/jgv.0.001474

Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus
Cited by: 12
Author(s): Sarah Keep, Michael S Oade, Filip Lidzbarski-Silvestre, Kirsten Bentley, Phoebe Stevenson-Leggett, Graham Freimanis, Chandana Tennakoon, Nicholas D. Sanderson, John A. Hammond, Richard C. Jones, Paul Britton, Erica Bickerton
Software Mentions: 2
Published: about 4 years ago

10.3390/microorganisms9071445

Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
Cited by: 1
Author(s): Dung Minh Ha-Tran, Trinh Thi My Nguyen, Shou-Chen Lo, Chieh-Chen Huang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-020-07362-8

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
Cited by: 5
Author(s): Stephan Weißbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Donald Evans, Joachim Bürger, Karin Everschor-Sitte, Helen May-Simera, Susanne Gerber
Software Mentions: 2
Published: almost 4 years ago

10.1099/mgen.0.000117

Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island
Cited by: 10
Author(s): Derek S. Sarovich, Stephanie N. J. Chapple, Erin P. Price, Mark Mayo, Matthew T. G. Holden, Sharon J. Peacock, Bart J. Currie
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1004319

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization
Cited by: 50
Author(s): Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica C. Mar, Chii M. Lin, Melvenia M. Martin, Michaël Ryan, Mirit I. Aladjem, Eric E. Bouhassira
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1006404

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species
Cited by: 66
Author(s): Markus S. Schröder, Kontxi Martinez de San Vicente, Tâmara Heloísa Rocha Prandini, Stephen Hammel, Desmond G. Higgins, Eduardo Bagagli, Kenneth H. Wolfe, Geraldine Butler
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1000960

GC-Biased Evolution Near Human Accelerated Regions
Cited by: 33
Author(s): Sol Katzman, Andrew D. Kern, Katherine S. Pollard, Sofie R. Salama, David Haussler
Software Mentions: 2
Published: over 14 years ago

10.3390/cancers10010021

IRF4 Mediates the Oncogenic Effects of STAT3 in Anaplastic Large Cell Lymphomas
Cited by: 26
Author(s): Cecilia Bandini, Aldi Pupuleku, Elisa Spaccarotella, Elisa Pellegrino, Rui Wang, Nicoletta Vitale, Carlotta Duval, Daniela Cantarella, Andrea Rinaldi, Paolo Provero, Ferdinando Di Cunto, Enzo Medico, Francesco Bertoni, Giorgio Inghirami, Roberto Piva
Software Mentions: 2
Published: almost 7 years ago

10.3390/cancers11121895

Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma
Cited by: 16
Author(s): H Winter, Pamela J. Kaisaki, Joe Harvey, Edoardo Giacopuzzi, Matteo P. Ferla, Melissa M Pentony, Samantha J. L. Knight, Ricky A. Sharma, Jenny C. Taylor, James McCullagh
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41396-019-0475-z

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated
Cited by: 40
Author(s): Devani Romero Picazo, Tal Dagan, Rebecca Ansorge, Jillian M. Petersen, Nicole Dubilier, Anne Kupczok
Software Mentions: 2
Published: over 5 years ago

10.1002/humu.22490

Robust Diagnostic Genetic Testing Using Solution Capture Enrichment and a Novel Variant‐Filtering Interface
Cited by: 35
Author(s): Christopher M. Watson, Laura A. Crinnion, Joanne Morgan, Sally M. Harrison, Christine P. Diggle, Julian Adlard, Helen Lindsay, Nick Camm, Ruth Charlton, Eamonn Sheridan, David T. Bonthron, Graham R. Taylor, Ian Carr
Software Mentions: 2
Published: over 10 years ago

10.1093/hmg/ddv272

Homozygous loss-of-function variants in European cosmopolitan and isolate populations
Cited by: 25
Author(s): Vera B. Kaiser, Victoria Svinti, James Prendergast, You-Ying Chau, Archie Campbell, Inga Patarčić, Inês Barroso, Peter K. Joshi, Nicholas D. Hastie, Ana Miljković, Martin S. Taylor, Generation Scotland, Uk K, Stefan Enroth, Yasin Memari, Anja Kolb-Kokocinski, Alan F. Wright, Ulf Gyllensten, Richard Durbin, Igor Rudan, Harry Campbell, Ozren Polašek, Åsa Johansson, Sascha Sauer, David J. Porteous, Ross M. Fraser, Camilla Drake, Véronique Vitart, Caroline Hayward, Colin A. Semple, James F. Wilson
Software Mentions: 2
Published: over 9 years ago

10.1038/s41419-021-03810-9

Pericentromeric Satellite III transcripts induce etoposide resistance
Cited by: 6
Author(s): Julian Kanne, Michelle Hussong, Jörg Isensee, Álvaro Muñoz‐López, Jan Wolffgramm, Felix Heß, Christina Grimm, Sergey Bessonov, Lydia Meder, Jie Wang, Hans Christian Reinhardt, Margarete Odenthal, Tim Hucho, Reinhard Büttner, Daniel Summerer, Michal R. Schweiger
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.119.400657

Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family
Cited by: 10
Author(s): Thu-Phuong Nguyen, Cornelia Mühlich, Setareh Mohammadin, Erik van den Bergh, Adrian E. Platts, Fabian B. Haas, Stefan A. Rensing, M. Eric Schranz
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.01007-20

Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235
Cited by: 17
Author(s): Sebastian Fischer, Sarah Dethlefsen, Jens Klockgether, Burkhard Tümmler
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1004549

Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture
Cited by: 48
Author(s): Martin Ar, Helio A. Costa, Tuuli Lappalainen, Brenna M. Henn, Jeffrey M. Kidd, Muh Ching Yee, Fabian Grubert, Howard M. Cann, M Snyder, Stephen B. Montgomery, Carlos D. Bustamante
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-015-0832-9

Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization
Cited by: 48
Author(s): Т. Н. Кузнецова, Shuang-Yin Wang, Nagesha A.S. Rao, Amit Mandoli, Joost H.A. Martens, Nils Rother, Aafke Aartse, Laszlo Groh, Eva M. Janssen-Megens, Guoliang Li, Yijun Ruan, Colin Logie, Hendrik G. Stunnenberg
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1004527

Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes
Cited by: 50
Author(s): Yuheng Huang, Stephen I. Wright, Aneil F. Agrawal
Software Mentions: 2
Published: over 10 years ago

10.1186/s13756-019-0653-9

First report of Klebsiella quasipneumoniae harboring blaKPC-2 in Saudi Arabia
Cited by: 13
Author(s): Sharif Hala, Chakkiath Paul Antony, Mohammed M. Alshehri, Abdulhakeem Althaqafi, Asim Alsaedi, Areej Mufti, Mai Kaaki, Baraa AlhajHussein, Hosam M. Zowawi, Abdulfattah Al-Amri, Arnab Pain
Software Mentions: 2
Published: almost 5 years ago

10.1128/mBio.01339-17

Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum
Cited by: 99
Author(s): Victoria E. Sepúlveda, Roberto Márquez, David A. Turissini, William E. Goldman, Daniel R. Matute
Software Mentions: 2
Published: almost 7 years ago

10.1099/mgen.0.000477

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Cited by: 68
Author(s): Mireia Coscollá, Sébastien Gagneux, Fabrizio Menardo, Chloé Loiseau, Paula Ruiz-Rodríguez, Sònia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sánchez-Busó, Florian Gehre, C. N’Dira Sanoussi, Martín Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham Alabi, Martin P. Grobusch, Robin Kobbe, Julian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Böttger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah-Manu, Daniela Brites
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-96778-7

Raspberry ketone diet supplement reduces attraction of sterile male Queensland fruit fly to cuelure by altering expression of chemoreceptor genes
Cited by: 2
Author(s): Mohammed Abul Monjur Khan, Nandan P. Deshpande, Lucas A. Shuttleworth, Terry Osborne, Damian Collins, Marc R. Wilkins, Geoff M. Gurr, Olivia L. Reynolds
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-021-94911-0

Evaluation of a high-throughput, cost-effective Illumina library preparation kit
Cited by: 4
Author(s): Eric S. Tvedte, Jane Michalski, Shaoji Cheng, Rayanna S. Patkus, Luke J. Tallon, Lisa Sadzewicz, Vincent M. Bruno, Joana C. Silva, David A. Rasko, Julie C. Dunning Hotopp
Software Mentions: 2
Published: over 3 years ago

10.1002/mgg3.395

Next generation sequencing panel based on single molecule molecular inversion probes for detecting genetic variants in children with hypopituitarism
Cited by: 11
Author(s): María Inés Pérez Millán, Sebastián Vishnopolska, Alexandre Z. Daly, Juan Pablo Vásquez Bustamante, Adriana Seilicovich, Ignacio Bergadá, Débora Braslavsky, Ana Keselman, Rosemary Lemons, Amanda H. Mortensen, Marcelo A. Martí, Sally A. Camper, Jacob O. Kitzman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-89683-6

Genome-wide insights into population structure and host specificity of Campylobacter jejuni
Cited by: 17
Author(s): Lennard Epping, Birgit Walther, Rosario M. Piro, Marie-Theres Knüver, Charlotte Huber, Andrea Thürmer, Antje Flieger, Angelika Fruth, Nicol Janecko, Lothar H. Wieler, Kerstin Stingl, Torsten Semmler
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-89195-3

Determination of a microRNA signature of protective kidney ischemic preconditioning originating from proximal tubules
Cited by: 5
Author(s): Usman Khalid, Robert H. Jenkins, Robert Andrews, Gilda Pino-Chávez, Benjamin C. Cossins, Rafael Chávez, Timothy Bowen, Donald Fraser
Software Mentions: 2
Published: over 3 years ago

10.1111/1755-0998.13293

Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
Cited by: 23
Author(s): Mads Radmer Jensen, Eva Egelyng Sigsgaard, Shenglin Liu, Andrea Manica, Steffen Bach, Michael Møller Hansen, Peter Rask Möller, Philip Francis Thomsen
Software Mentions: 2
Published: almost 4 years ago

10.1534/g3.119.400609

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)
Cited by: 9
Author(s): Jessie F. Salter, Oscar W. Johnson, Norman J. Stafford, William F. Herrin, Darren Schilling, Cody Cedotal, Robb T. Brumfield, Brant C. Faircloth
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-83507-3

Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach
Cited by: 4
Author(s): Sandhya Sharma, Anshika Tyagi, Harsha Srivastava, Gayatri Ramakrishna, Priya Sharma, Amitha Mithra Sevanthi, Amolkumar U. Solanke, Ramavtar Sharma, Nagendra Singh, T. R. Sharma, Kishor Gaikwad
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-83642-x

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
Cited by: 46
Author(s): Ki Wook Kim, Ira W. Deveson, Chi Nam Ignatius Pang, Malinna Yeang, Zin Naing, Thiruni Adikari, Jillian M. Hammond, Igor Stevanovski, Alicia G. Beukers, Andrey Verich, Simon Yin, David McFarlane, Marc R. Wilkins, Sacha Stelzer-Braid, Rowena A. Bull, Maria E. Craig, Sebastiaan J. van Hal, William D. Rawlinson
Software Mentions: 2
Published: almost 4 years ago

Projects: pypi: bwa

Papers Mentioning bwa 989