10.3389/fnut.2020.00150

High-Resolution Mass Spectrometer–Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle
Cited by: 17
Author(s): Alka Chopra, Syed Azmal Ali, Shveta Bathla, Preeti Rawat, Vikas Vohra, Sudarshan Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-020-00981-z

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
Cited by: 17
Author(s): Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Γεώργιος Μαρίνος, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens, Martin von Bergen
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-12-402

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Cited by: 2,222
Author(s): Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. Beatson
Software Mentions: 4
Published: over 14 years ago

10.1186/s12866-019-1500-0

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Cited by: 101
Author(s): Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey, Christian H. Ahrens
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1008452

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania
Cited by: 12
Author(s): Megan A. Sloan, Karen Brooks, Thomas D. Otto, Mandy Sanders, James A. Cotton, Petros Ligoxygakis
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-020-02744-2

Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions
Cited by: 6
Author(s): Xuan Wang, Fei Shen, Yuan Gao, Kun Wang, Ruiting Chen, Jun Luo, Lili Yang, Xi Zhang, Changwei Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Cong Peng, Zhenhai Han, Xinzhong Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s13072-021-00395-7

Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina
Cited by: 13
Author(s): Florian Carlier, M. Li, Laetitia Maroc, Robert Debuchy, Charbel Souaid, Daan Noordermeer, Pierre Grognet, Fabienne Malagnac
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0008237

Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms
Cited by: 20
Author(s): Jayden Logan, Mark S. Pearson, Srikanth S. Manda, Young Jun Choi, Matthew A. Field, Ramon M. Eichenberger, Jason Mulvenna, Shivashankar H. Nagaraj, Ricardo Toshio Fujiwara, Pedro Henrique Gazzinelli-Guimarães, Lilian Lacerda Bueno, Vitor Luís Tenório Mati, Jeffrey M. Bethony, Makedonka Mitreva, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0009719

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Cited by: 6
Author(s): Luisa Berná, Gonzalo Greif, Sebastián Pita, Paula Faral-Tello, Florencia Díaz-Viraqué, Rita de Cássia Moreira de Souza, Gustavo Adolfo Vallejo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-018-5157-0

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)
Cited by: 39
Author(s): Rui Hu, Jie Xiao, Tao Gu, Xiao‐Lan Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-020-06820-7

Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Cited by: 6
Author(s): Clemens L. Weiß, Marie-Theres Gansauge, Ayinuer Aximu‐Petri, Matthias Meyer, Hernán A. Burbano
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5444-4

The plastid and mitochondrial genomes of Eucalyptus grandis
Cited by: 31
Author(s): Desré Pinard, Alexander Andrew Myburg, Eshchar Mizrachi
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
Cited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-015-1825-5

Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates
Cited by: 124
Author(s): Nan Zhang, Dongqing Yang, Dandan Wang, Youzhi Miao, Jiahui Shao, Xuan Zhou, Zhihui Xu, Qing Li, Haichao Feng, Shuqing Liu, Qirong Shen, Ruifu Zhang
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-015-1233-x

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: over 13 years ago

10.1186/s12915-020-00802-7

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Cited by: 25
Author(s): Timothy Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren E. Hagen, Christine G. Elsik, Kevin R. Macaluso, Abdu F. Azad
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2502-z

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
Cited by: 71
Author(s): Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian Foley, Leonard A. Smith, Rafael Fernández, Miia Lindström, Hannu Korkeala, Paul Keim, Jeffrey T. Foster, Karen K. Hill
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: over 6 years ago

10.1111/jpy.13079

Foliose <i>Ulva</i> Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
Cited by: 20
Author(s): Antoine Fort, Marcus McHale, Kévin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
Software Mentions: 4
Published: about 5 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
Cited by: 14
Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: about 7 years ago

10.1186/s12951-021-00916-2

Silicon dioxide nanoparticles induced neurobehavioral impairments by disrupting microbiota–gut–brain axis
Cited by: 23
Author(s): Jun Diao, Yinyin Xia, Xuejun Jiang, Jingfu Qiu, Shuqun Cheng, Junhao Su, Xinhao Duan, Min Gao, Xia Qin, Jun Zhang, Jie Fan, Zhen Zou, Chengzhi Chen
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-13-202

Comparing thousands of circular genomes using the CGView Comparison Tool
Cited by: 234
Author(s): Jason R. Grant, Adriano S. Arantes, Paul Stothard
Software Mentions: 4
Published: over 13 years ago

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 8 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms22010347

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
Cited by: 8
Author(s): Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-14-918

POMO - Plotting Omics analysis results for Multiple Organisms
Cited by: 3
Author(s): Jake Lin, Richard Kreisberg, Aleksi Kallio, Andrew T. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, Reija Autio
Software Mentions: 4
Published: almost 13 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1005954

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
Cited by: 102
Author(s): Shubha Vij, Heiner Kuhl, Irina M. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, K. Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James Drake, Matthew Boitano, Richard J. Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, G. Gopikrishna, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
Software Mentions: 4
Published: over 9 years ago

10.1093/bioinformatics/btw116

Goldilocks: a tool for identifying genomic regions that are ‘just right’
Cited by: 2
Author(s): Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms22041811

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes
Cited by: 15
Author(s): Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-14-675

Efficient and accurate whole genome assembly and methylome profiling of E. coli
Cited by: 40
Author(s): Jason Powers, Victor Weigman, Jenny Shu, John Pufky, Donald Cox, Patrick Hurban
Software Mentions: 4
Published: almost 13 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: almost 5 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 8 years ago

10.3390/cancers12123738

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients
Cited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: almost 5 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 5 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 12 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: almost 8 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0146916

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
Cited by: 15
Author(s): Sophie Weiss, Thomas J. Mansell, Pooneh Mortazavi, Rob Knight, Ryan T. Gill
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2019.01400

Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: almost 8 years ago

10.1093/gigascience/gix015

Enhancing knowledge discovery from cancer genomics data with Galaxy
Cited by: 7
Author(s): Marco A. Albuquerque, Bruno M. Grande, Elie Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal, Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0255822

Evaluation of the severity of nonalcoholic fatty liver disease through analysis of serum exosomal miRNA expression
Cited by: 5
Author(s): Jeong‐An Gim, Soo Min Bang, Young‐Sun Lee, Sun Young Yim, Young Kul Jung, Hayeon Kim, Baek-hui Kim, Ji Hoon Kim, Yeon Seok Seo, Hyung Joon Yim, Jong Eun Yeon, Soon Ho Um, Kwan Soo Byun
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: about 9 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: about 10 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-018-1392-6

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions
Cited by: 99
Author(s): Paul Bailey, Christian Schudoma, William J. Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew J. Moscou, Ksenia V. Krasileva
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.61562

Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans
Cited by: 40
Author(s): Alice V. Easton, Shenghan Gao, Scott P Lawton, Sasisekhar Bennuru, Asis Khan, Eric Dahlstrom, Rita G. Oliveira, Stella Kepha, Stephen F. Porcella, Joanne P. Webster, Roy M. Anderson, Michael E. Grigg, Richard E. Davis, Jianbin Wang, Thomas B. Nutman
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.29391

Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites
Cited by: 25
Author(s): Fabien Sindikubwabo, Shibin Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y. Botté, Artur Scherf, Mohamed-Ali Hakimi
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: almost 12 years ago

10.7717/peerj.3162

The genomic sequence of<i>Exiguobacterium chiriqhucha</i>str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-020-02138-5

Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
Cited by: 40
Author(s): Scott A. Lujan, Matthew J. Longley, Margaret H. Humble, Christopher A. Lavender, Adam Burkholder, Emma L. Blakely, Charlotte L. Alston, Gráinne Gorman, D.M. Turnbull, Robert McFarland, Robert W. Taylor, Thomas A. Kunkel, William C. Copeland
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 7 years ago

10.1186/s13073-021-00889-9

Single-cell sequencing of the small and AT-skewed genome of malaria parasites
Cited by: 4
Author(s): Shiwei Liu, Adam C Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell, Jennifer L. Guler
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.11351

Multivariate analysis of electrophysiological diversity of Xenopus visual neurons during development and plasticity
Cited by: 21
Author(s): Christopher M. Ciarleglio, Arseny S. Khakhalin, Angelia F Wang, Alexander C Constantino, Sarah P Yip, Carlos D. Aizenman
Software Mentions: 4
Published: about 10 years ago

10.1128/mSystems.00692-19

The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation
Cited by: 39
Author(s): Shouke Zhang, Jinping Shu, Huai‐Jun Xue, Wei Zhang, Yabo Zhang, Yaning Liu, Linxin Fang, Yangdong Wang, Haojie Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s40246-018-0170-6

Forward and reverse mutations in stages of cancer development
Cited by: 11
Author(s): Taobo Hu, Yogesh Kumar, Shazia Iram, Si Duan, Yang Li, Lei Chen, Jinfei Chen, Rong Yin, Ava Kwong, Gilberto Ka Kit Leung, Wai Kin Mat, Zhenggang Wu, Xi Long, Colin Chan, Si Chen, Peggy Lee, Siu Kin Ng, Timothy Y. C. Ho, Jianfeng Yang, Xueliang Ding, Suk Ying Tsang, Xinrui Zhou, Danhua Zhang, Enbo Zhou, Lin Xu, Wai-sang Poon, Hongyang Wang, Hong Xue
Software Mentions: 4
Published: over 7 years ago

10.3390/ijerph16203966

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China
Cited by: 16
Author(s): Lei Zhang, Yu Cheng, Guang Gao, Jiahu Jiang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: over 12 years ago

10.1128/mBio.01650-17

<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown Rust
Cited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: almost 8 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giz012

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Cited by: 138
Author(s): Marivi Colle, Courtney P. Leisner, Ching Man Wai, Shujun Ou, Kevin A. Bird, Jie Wang, Jennifer H. Wisecaver, Alan E. Yocca, Elizabeth I. Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo Qing Song, Kevin L. Childs, Anthony L. Schilmiller, Nicholi Vorsa, C. Robin Buell, Robert VanBuren, Ning Jiang, Patrick P. Edger
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2021.736411

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Cited by: 2
Author(s): Dong Han, Qiaojuan Yan, Jun Li, Zhengqiang Jiang, Shanchao Yang
Software Mentions: 4
Published: about 4 years ago

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic <i>Escherichia coli</i> Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-57546-1

Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001
Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1000832

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Cited by: 238
Author(s): Michael J. Clark, Nils Homer, Brian D. O’Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson
Software Mentions: 4
Published: almost 16 years ago

10.1093/infdis/jiz318

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach
Cited by: 13
Author(s): Sarah Mollerup, Maria E. Asplund, Jens Friis-Nielsen, Kristín Rós Kjartansdóttir, Helena Fridholm, Thomas Arn Hansen, José Alejandro Romero Herrera, Christopher J. Barnes, Randi Holm Jensen, Stine Raith Richter, Ida Broman Nielsen, Carlotta Pietroni, David E. Alquezar‐Planas, Alba Rey‐Iglesia, Pernille V. S. Olsen, Ewa Rajpert De Meyts, Line Groth‐Pedersen, Christian von Buchwald, David Hebbelstrup Jensen, Robert Gniadecki, Estrid Høgdall, Jill Levin Langhoff, Imre Pete, Ildikó Vereczkey, Zsolt Baranyai, Karen Dybkær, Hans Erik Johnsen, Torben Steiniche, Peter Hokland, Jacob Rosenberg, Ulrik Baandrup, Thomas Sicheritz-Pontén, Eske Willerslev, Søren Brunak, Ole Lund, Tobias Mourier, Lasse Vinner, Jose M. G. Izarzugaza, Lars Peter Nielsen, Anders J. Hansen
Software Mentions: 4
Published: over 6 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-22237-5

Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Cited by: 13
Author(s): Álvaro Chiner‐Oms, Fernando Gónzález-Candelas, Iñaki Comas
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-17484-x

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals
Cited by: 109
Author(s): Christian Cr Voolstra, Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean‐François Flot, Sylvie Tambutté, Denis Allemand, Manuel Aranda
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-17203-6

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0027121

Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage
Cited by: 27
Author(s): Patrick J. Biggs, Paul Fearnhead, Grant S. Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian L. Cookson, Philip E. Carter, Nigel P. French
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0231867

Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis
Cited by: 4
Author(s): Yue Wang, Donovan Bailey, Shikai Yin, Xin Dong
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-20862-8

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0095347

Identification of Gene Expression Changes from Colitis to CRC in the Mouse CAC Model
Cited by: 14
Author(s): Xin Li, Yuyan Gao, Ming Yang, Qi Zhao, Guangyu Wang, Yan Yang, Yue Yang, Hui Liu, Yanqiao Zhang
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0131673

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse
Cited by: 43
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0242194

Identification of potential target genes and crucial pathways in small cell lung cancer based on bioinformatic strategy and human samples
Cited by: 6
Author(s): Xiuwen Chen, Li Wang, Xiaomin Su, Senyuan Luo, Xianbin Tang, Yugang Huang
Software Mentions: 3
Published: about 5 years ago