pypi: mapper | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2021.660920

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages
Cited by: 28
Author(s): José Luis Maturana, Juan Pablo Cárdenas
Software Mentions: 8
Published: over 3 years ago

10.3389/fmolb.2020.598583

SARS-CoV-2 Proteins Exploit Host’s Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways
Cited by: 29
Author(s): A. A. Khan, Abul B.M.M.K. Islam
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0209231

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents
Cited by: 11
Author(s): Christopher Cheleuitte-Nieves, Christopher A. Gulvik, John R. McQuiston, Ben W. Humrighouse, Melissa Bell, Aaron Villarma, Vincent A. Fischetti, Lars F. Westblade, Neil S Lipman
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0258157

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
Cited by: 4
Author(s): Matthew S. Tucker, Celia O’Brien, Mark C. Jenkins, Benjamin M. Rosenthal
Software Mentions: 7
Published: about 3 years ago

10.3389/fmicb.2019.00618

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0181033

Transcriptomic and metabolomic profiles of Chinese citrus fly, Bactrocera minax (Diptera: Tephritidae), along with pupal development provide insight into diapause program
Cited by: 14
Author(s): Jia Wang, Hong-Tao Fan, Ke-Cai Xiong, Ying‐Hong Liu
Software Mentions: 6
Published: over 7 years ago

10.1038/s41597-019-0261-9

A 2D hyperspectral library of mineral reflectance, from 900 to 2500 nm
Cited by: 7
Author(s): Laurent Fasnacht, Marie-Louise Vogt, Philippe Renard, Philip Brunner
Software Mentions: 6
Published: about 5 years ago

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 9 years ago

10.1098/rsfs.2020.0007

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
Cited by: 71
Author(s): Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 8 years ago

10.3389/fimmu.2018.01868

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Cited by: 11
Author(s): Friederike Ebner, Mathias Kuhring, Aleksandar Radonić, Ankur Midha, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-018-4541-0

Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma
Cited by: 8
Author(s): Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold, David S. Portnoy
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms9091906

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota
Cited by: 9
Author(s): Romina Díaz, Alexis Torres-Miranda, Guillermo Orellana, Daniel Garrido
Software Mentions: 5
Published: about 3 years ago

10.1093/gigascience/giy052

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
Cited by: 3
Author(s): Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G. Burchard, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes, Fusheng Wang, Zhaohui S. Qin
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: about 9 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 11 years ago

10.3389/fmicb.2018.01061

Profiling of the Transcriptomic Responses of Clonostachys rosea Upon Treatment With Fusarium graminearum Secretome
Cited by: 26
Author(s): Zerihun A. Demissie, Simon J. Foote, Yifang Tan, Michèle C. Loewen
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1007915

Functional lability of RNA-dependent RNA polymerases in animals
Cited by: 27
Author(s): Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Héctor Escrivà, Hervé Seitz
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0121558

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data
Cited by: 36
Author(s): Minerva Singh, Damian Evans, Boun Suy Tan, Chan Samean Nin
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0247028

How similar is “similar,” or what is the best measure of soil spectral and physiochemical similarity?
Cited by: 2
Author(s): Rong Zeng, J P Zhang, Kaiyong Cai, Weichang Gao, Wenjie Pan, Chaoying Jiang, P Y Zhang, Bing Wu, C H Wang, Xing Jin, Daixun Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s41398-017-0075-5

Downregulation of the neuronal opioid gene expression concomitantly with neuronal decline in dorsolateral prefrontal cortex of human alcoholics
Cited by: 14
Author(s): Igor Bazov, Daniil Sarkisyan, О. Кононенко, Hiroyuki Watanabe, Victor M. Karpyak, Tatiana Yakovleva, Georgy Bakalkin
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-15-1039

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq
Cited by: 200
Author(s): Jeffrey E. Barrick, Geoffrey Colburn, Daniel E. Deatherage, Charles C. Traverse, Matthew D Strand, Jordan J Borges, David B. Knoester, Aaron Reba, Austin G. Meyer
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-017-3967-0

Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
Cited by: 15
Author(s): Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret Staton
Software Mentions: 4
Published: over 7 years ago

10.1016/j.mex.2019.100775

PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions
Cited by: 6
Author(s): Ahmad Zidan, Eman A. Saad, Nasser E. Ibrahim, Amal Mahmoud, Medhat H. Hashem, Alaa A. Hemeida
Software Mentions: 4
Published: almost 5 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms7120635

Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses
Cited by: 12
Author(s): Anoop Alex, Agostinho Antunes
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-017-3691-9

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
Cited by: 106
Author(s): Richard Kuo, Elizabeth Tseng, Lél Eöry, Ian R. Paton, Alan Archibald, David W. Burt
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1008870

Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death
Cited by: 10
Author(s): Irina Veith, Arianna Mencattini, Valentin Picant, Marco Serra, Marine Leclerc, Maria Colomba Comes, Fathia Mami‐Chouaib, Jacques Camonis, Stéphanie Descroix, Hamasseh Shirvani, Fatima Mechta‐Grigoriou, Gérard Zalcman, Maria Carla Parrini, Eugenio Martinelli
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers12020381

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models
Cited by: 16
Author(s): J. Tyson McDonald, R. Stainforth, Jack Miller, Thomas J. Cahill, Willian A. da Silveira, Komal S. Rathi, Gary Hardiman, Deanne Taylor, Sylvain V. Costes, Vinita Chauhan, Robert Meller, Afshin Beheshti
Software Mentions: 4
Published: almost 5 years ago

10.3390/s21041182

The New Hyperspectral Satellite PRISMA: Imagery for Forest Types Discrimination
Cited by: 56
Author(s): Elia Vangi, Giovanni D’Amico, Saverio Francini, Francesca Giannetti, Bruno Lasserre, Marco Marchetti, Gherardo Chirici
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2014.00031

Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone
Cited by: 28
Author(s): Laura Villanueva, Daan R. Speth, Theo van Alen, Alexander Hoischen, Mike S. M. Jetten
Software Mentions: 3
Published: almost 11 years ago

10.3390/microorganisms8010007

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum
Cited by: 20
Author(s): Korin Albert, Asha Rani, David A. Sela
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40246-020-00295-z

KVarPredDB: a database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses
Cited by: 3
Author(s): Yuyi Ying, Lu Lu, Santasree Banerjee, Lizhen Xu, Qiang Zhao, Hao Wu, Ruiqi Li, Xiao Xu, Hua Yu, Dante Neculai, Yongmei Xi, Fan Yang, Jiale Qin, Chen Li
Software Mentions: 3
Published: almost 4 years ago

10.3390/microorganisms9040757

Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters
Cited by: 11
Author(s): Qingmei Li, Yingli Zhou, Zhanfei Wei, Yong Wang
Software Mentions: 3
Published: over 3 years ago

10.1155/2018/6918797

Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer’s Disease
Cited by: 22
Author(s): Michalina Wężyk, Magdalena Spólnicka, Ewelina Pośpiech, Beata Pepłońska, Renata Zbieć-Piekarska, Jan Ilkowski, Maria Styczyńska, Anna Barczak, Marzena Zboch, Anna Filipek-Gliszczyńska, Magdalena Skrzypczak, Krzysztof Ginalski, Michał Kabza, Izabela Makałowska, Maria Barcikowska, Wojciech Branicki, Cezary Żekanowski
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0090240

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene
Cited by: 33
Author(s): Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul Seabury, Eric K. Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury
Software Mentions: 3
Published: over 10 years ago

10.3390/genes11030299

The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes
Cited by: 7
Author(s): Jakub Sawicki, Alina Bączkiewicz, Katarzyna Buczkowska, Piotr Górski, Katarzyna Krawczyk, Patryk Mizia, Kamil Myszczyński, Monika Ślipiko, Monika Szczecińska
Software Mentions: 3
Published: over 4 years ago

10.3389/fvets.2021.666512

Tandem Mass Tag-Based Quantitative Proteomic Analysis of Chicken Bursa of Fabricius Infected With Reticuloendotheliosis Virus
Cited by: 3
Author(s): Dahan Yang, Xiaoping Lv, Shujun Zhang, Shangen Zheng
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0214227

A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia
Cited by: 31
Author(s): Nischay Mishra, Shamsudeen F. Fagbo, Abdulaziz N. Alagaili, Adam Nitido, Simon H. Williams, James Ng, Bohyun Lee, Abdulkareem Durosinlorun, Joel A. Garcia, Komal Jain, Vishal Kapoor, Jonathan H. Epstein, Thomas Briese, Ziad A. Memish, Kevin J. Olival, W. Ian Lipkin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3045-z

An analytical workflow for accurate variant discovery in highly divergent regions
Cited by: 16
Author(s): Shulan Tian, Huihuang Yan, Claudia Neuhauser, Susan L. Slager
Software Mentions: 3
Published: about 8 years ago

10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pntd.0009327

Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Cited by: 7
Author(s): Nathalia Ballesteros, Marina Muñoz, Luz Helena Patiño, Carolina Hernández, Felipe González-Casabianca, Iván Carroll, Mauricio Santos-Vega, Jaime Cascante, Andrés Ángel, Alejandro Feged-Rivadeneira, Mónica Palma-Cuero, Carolina Flórez, Sergio Gómez, Adriana van de Guchte, Zenab Khan, Jayeeta Dutta, Ajay Obla, Hala Alshammary, Ana S. González-Reiche, Matthew M. Hernandez, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel, Alberto Paníz-Mondolfi, Juan David Ramírez
Software Mentions: 3
Published: over 3 years ago

10.1038/srep27043

Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line
Cited by: 33
Author(s): Mireia Borràs-Fresneda, Joan Francesc Barquinero, Maria Gomolka, Sabine Hornhardt, Ute Rößler, Gemma Armengol, Leonardo Barrios
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-018-4982-5

Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo
Cited by: 91
Author(s): Carmen Almiñana, Guillaume Tsikis, Valérie Labas, Rustem Uzbekov, Juliano Coelho da Silveira, Stefan Bauersachs, Pascal Mermillod
Software Mentions: 3
Published: over 6 years ago

10.3390/s17030578

Assessing the Spectral Properties of Sunlit and Shaded Components in Rice Canopies with Near-Ground Imaging Spectroscopy Data
Cited by: 21
Author(s): Kai Zhou, Xinqiang Deng, Xia Yao, Yongchao Tian, Weixing Cao, Yan Zhu, Susan L. Ustin, Tao Cheng
Software Mentions: 3
Published: over 7 years ago

10.1186/1754-6834-7-66

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
Cited by: 55
Author(s): Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, Erik Böer, Toni Gabaldón, José Almeida Cruz, Emmanuel Talla, Christian Marck, André Goffeau, Valérie Barbe, Philippe Baret, Keith Baronian, Sebastian Beier, Claudine Bleykasten, R. Bode, Serge Casarégola, Laurence Despons, Cécile Fairhead, Martin Giersberg, Przemysław Piotr Gierski, Urs Hähnel, Anja Hartmann, Dagmara Jankowska, Claire Jubin, Paul P. Jung, Ingrid Lafontaine, Véronique Leh-Louis, Marc Lemaire, Marina Marcet‐Houben, Martin Mascher, Guillaume Morel, Guy‐Franck Richard, Jan Riechen, Christine Sacerdot, Anasua Sarkar, Guilhem Savel, Joseph Schacherer, David James Sherman, Nils Stein, Marie Laure Straub, Agnès Thierry, Anke Trautwein-Schult, Benoît Vacherie, Éric Westhof, Sebastian Worch, Bernard Dujon, Jean Luc Souciet, Patrick Wincker, Uwe Scholz, Cécile Neuvéglise
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.14845

EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells
Cited by: 74
Author(s): Benjamin Krusche, Cristina Ottone, Melanie Clements, Ewan Johnstone, Katrin Goetsch, Lieven Huang, Silvia G Mota, Poonam Singh, Sanjay Khadayate, Azhaar Ashraf, Timothy Davies, Steven M. Pollard, Vincenzo De Paola, Federico Roncaroli, Jorge L. Martı́nez-Torrecuadrada, Paul Bertone, Simona Parrinello
Software Mentions: 3
Published: over 8 years ago

10.1186/s12865-021-00418-8

Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation
Cited by: 9
Author(s): Sarah Benjamin, Kelly L. Hawley, Paola Vera-Licona, Carson J. La Vake, Jorge Cervantes, Yijun Ruan, Justin D. Radolf, Juan C. Salazar
Software Mentions: 3
Published: over 3 years ago

10.1264/jsme2.ME16061

Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota
Cited by: 14
Author(s): Camilla Kristoffersen, Rasmus Bovbjerg Jensen, Ekaterina Avershina, D. Austbø, Anne‐Helene Tauson, Knut Rudi
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-018-2094-5

Fast and efficient short read mapping based on a succinct hash index
Cited by: 16
Author(s): Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07515-3

The myxozoan minicollagen gene repertoire was not simplified by the parasitic lifestyle: computational identification of a novel myxozoan minicollagen gene
Cited by: 3
Author(s): Jiří Kyslík, Anush Kosakyan, Serafim Nenarokov, Astrid S. Holzer, Ivan Fiala
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-13-493

Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina
Cited by: 193
Author(s): Serajul Islam, Samiul Haque, Mohammad Moinul Islam, Emdadul Mannan Emdad, Abdul Karimi Halim, Quazi Md. Mosaddeque Hossen, Zakir Hossain, Borhan Ahmed, Sifatur Rahim, Shibley Rahman, Monjurul Alam, Shaobin Hou, Xuehua Wan, Jennifer A. Saito, Maqsudul Alam
Software Mentions: 2
Published: about 12 years ago

10.1186/s12864-018-5121-z

Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain
Cited by: 16
Author(s): Maria-Antonia Zamora-Lagos, Simone Eckstein, Angela Langer, Athanasios Gazanis, Friedhelm Pfeiffer, Bianca Habermann, Ralf Heermann
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-16-S12-S14

An integrative approach for efficient analysis of whole genome bisulfite sequencing data
Cited by: 7
Author(s): Jong-Hun Lee, Sung‐Joon Park, Kenta Nakai
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-15-633

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
Cited by: 4
Author(s): Verónica Lloréns‐Rico, Luís Serrano, María Lluch‐Senar
Software Mentions: 2
Published: over 10 years ago

10.1186/1755-8794-1-41

A high confidence, manually validated human blood plasma protein reference set
Cited by: 140
Author(s): Susann Schenk, Gary J. Schoenhals, Gustavo Souza, Matthias Mann
Software Mentions: 2
Published: about 16 years ago

10.1264/jsme2.ME19148

Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells
Cited by: 3
Author(s): Rino Isshiki, Hirotsugu Fujitani, Satoshi Tsuneda
Software Mentions: 2
Published: almost 5 years ago

10.1074/mcp.M116.062331

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease
Cited by: 30
Author(s): Matthew P. Torres, Henry Dewhurst, Niveda Sundararaman
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0046415

Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura
Cited by: 21
Author(s): Nicola Palmieri, Viola Nolte, Anton Suvorov, Carolin Kosiol, Christian Schlötterer
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0233813

Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations
Cited by: 12
Author(s): William T. Molin, Eric Patterson, Christopher Saski
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0226491

Applying circuit theory and landscape linkage maps to reintroduction planning for California Condors
Cited by: 6
Author(s): Jesse G. Delia, Joseph Brandt, L. Joseph Burnett, Susan M. Haig, Jeff P. Hollenbeck, Steve Kirkland, Bruce G. Marcot, Arianna Punzalan, Christopher West, Tiana Williams-Claussen, Rachel Wolstenholme, R Ichard P. Young
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0134031

Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries
Cited by: 27
Author(s): Christopher Saski, Ranjana Bhattacharjee, Brian E. Scheffler, Robert Asiedu
Software Mentions: 2
Published: over 9 years ago

10.1002/dvdy.175

The shape of things to come: Topological data analysis and biology, from molecules to organisms
Cited by: 35
Author(s): Erik J. Amézquita, Michelle Quigley, Tim Ophelders, Elizabeth Munch, Daniel H. Chitwood
Software Mentions: 2
Published: over 4 years ago

10.1038/s41426-018-0210-2

Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage
Cited by: 9
Author(s): Naadir Ganief, Jessica Sjouerman, Claudia Albeldas, Kehilwe C. Nakedi, Clemens Hermann, Bridget Calder, Jonathan M. Blackburn, Nelson C. Soares
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2018.02282

Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation
Cited by: 52
Author(s): Sebastian Rausch, Ankur Midha, Mathias Kuhring, Nicole Affinass, Aleksandar Radonić, Anja A. Kühl, André Bleich, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2021.723479

Multivariate Analysis in Microbiome Description: Correlation of Human Gut Protein Degraders, Metabolites, and Predicted Metabolic Functions
Cited by: 7
Author(s): Stefano Raimondi, Rosalba Calvini, Francesco Candeliere, Alan Leonardi, Alessandro Ulrici, Maddalena Rossi, Alberto Amaretti
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2020.01681

Identification of Genes Required for Resistance to Peptidomimetic Antibiotics by Transposon Sequencing
Cited by: 9
Author(s): Alessandra Vitale, Gabriella Pessi, Matthias Urfer, Hans H. Locher, Katja Zerbe, Daniel Obrecht, John A. Robinson, Leo Eberl
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2020.625507

Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana
Cited by: 11
Author(s): Muhammad Mu′izzuddin Zulkapli, Nur Syatila Ab Ghani, Tiew Yik Ting, Wan Mohd Aizat, Hoe-Han Goh
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41438-019-0191-x

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
Cited by: 37
Author(s): Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Hazem Hassan, Bihong Feng, Nathan K Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
Software Mentions: 2
Published: about 5 years ago

10.1172/jci.insight.139043

Epigenetic silencing of CD4 expression in nonpathogenic SIV infection in African green monkeys
Cited by: 8
Author(s): Joseph C. Mudd, Stephen Lai, Sanjana Shah, Andrew R. Rahmberg, Jacob K. Flynn, Carly E. Starke, Molly Perkins, Amy Ransier, Samuel Darko, Daniel C. Douek, Vanessa M. Hirsch, Mark J. Cameron, Jason M. Brenchley
Software Mentions: 2
Published: about 4 years ago

10.1117/1.JBO.25.6.066005

Gastric cancer diagnosis using hyperspectral imaging with principal component analysis and spectral angle mapper
Cited by: 20
Author(s): Ningliang Liu, Yaxiong Guo, Houmin Jiang, Wei Yi
Software Mentions: 2
Published: over 4 years ago

10.1186/s13321-018-0308-5

Improved understanding of aqueous solubility modeling through topological data analysis
Cited by: 16
Author(s): Mariam Pirashvili, Lee Steinberg, Francisco Belchi Guillamon, Mahesan Niranjan, Jeremy G. Frey, Jacek Brodzki
Software Mentions: 2
Published: about 6 years ago

10.1128/JCM.02337-16

Copy Number Heterogeneity of JC Virus Standards
Cited by: 18
Author(s): Alexander L. Greninger, Allen C. Bateman, Ederlyn E. Atienza, Sharon Wendt, Negar Makhsous, Keith R. Jerome, Linda Cook
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-020-63252-9

GC-MS metabolomics reveals metabolic differences of the farmed Mandarin fish Siniperca chuatsi in recirculating ponds aquaculture system and pond
Cited by: 12
Author(s): Mingsong Xiao, Kelin Qian, Yuliang Wang, Fangyin Bao
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-72880-0

The genomes of a monogenic fly: views of primitive sex chromosomes
Cited by: 5
Author(s): Anne A. Andere, Meaghan L. Pimsler, Aaron M. Tarone, Christine Picard
Software Mentions: 2
Published: about 4 years ago

10.3390/s17051117

Characterization of Fine Metal Particles Derived from Shredded WEEE Using a Hyperspectral Image System: Preliminary Results
Cited by: 16
Author(s): Gabriele Candiani, Nicoletta Picone, L. Pompilio, Monica Pepe, Marcello Colledani
Software Mentions: 2
Published: over 7 years ago

10.1128/mSphere.00402-18

The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci
Cited by: 7
Author(s): Audun Sivertsen, Jessin Janice, Torunn Pedersen, Theresa Wagner, Joachim Hegstad, Kristin Hegstad
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21041303

The Oviductal Extracellular Vesicles’ RNA Cargo Regulates the Bovine Embryonic Transcriptome
Cited by: 26
Author(s): Stefan Bauersachs, Pascal Mermillod, Carmen Almiñana
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.00433

Whole Genome Analysis of Lactobacillus plantarum Strains Isolated From Kimchi and Determination of Probiotic Properties to Treat Mucosal Infections by Candida albicans and Gardnerella vaginalis
Cited by: 34
Author(s): Bo Ram Beck, Gun-Seok Park, Yong Hyun Lee, Sunghoon Im, Do Yeun Jeong, Jihee Kang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-795

Tangram: a comprehensive toolbox for mobile element insertion detection
Cited by: 51
Author(s): Jiantao Wu, Wan Ping Lee, Alistair Ward, Jerilyn A. Walker, Miriam K. Konkel, Mark A. Batzer, Gábor Marth
Software Mentions: 1
Published: about 10 years ago

10.1017/S003118202100010X

Know your enemy – transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Lilian Pukk, Siim Kahar, Hanna Hartikainen, Riho Gross, Anti Vasemägi
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2020.555730

Identification and Analysis of the Tegument Protein and Excretory-Secretory Products of the Carcinogenic Liver Fluke Clonorchis sinensis
Cited by: 15
Author(s): Yong Shi, Kai Yu, Anli Liang, Yan Huang, Fang-qi Ou, Haiyan Wei, Xiaoling Wan, Yue Yang, Weiyu Zhang, Zhihua Jiang
Software Mentions: 1
Published: about 4 years ago

10.3390/v11111035

Mechanisms Mediating Nuclear Trafficking Involved in Viral Propagation by DNA Viruses
Cited by: 6
Author(s): Guohui Li, Xinyu Qi, Zhaoyang Hu, Qi Tang
Software Mentions: 1
Published: about 5 years ago

10.3390/molecules23050994

To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data
Cited by: 14
Author(s): Mohammed Zakariah, Shahanavaj Khan, Anis Ahmad Chaudhary, Christian Rolfo, Mohamed Maher Ben Ismail, Yousef Ajami Alotaibi
Software Mentions: 1
Published: over 6 years ago

10.3389/fped.2021.673957

Immune Dysregulation Mimicking Systemic Lupus Erythematosus in a Patient With Lysinuric Protein Intolerance: Case Report and Review of the Literature
Cited by: 9
Author(s): Josefina Longeri Contreras, Mabel Ladino, Katherine Aránguiz, Gonzalo Méndez, Zeynep Coban‐Akdemir, Bo Yuan, Richard A. Gibbs, Lindsay C. Burrage, James R. Lupski, Iván K. Chinn, Tiphanie P. Vogel, Jordan S. Orange, Cecilia Poli
Software Mentions: 1
Published: over 3 years ago

10.1098/rsob.120093

TheSaccharomyces cerevisiaeW303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt
Cited by: 85
Author(s): Markus Ralser, Heiner Kuhl, Markus Ralser, Martin Werber, Hans Lehrach, Michael Breitenbach, Bernd Timmermann
Software Mentions: 1
Published: over 12 years ago

10.1074/mcp.RA119.001611

Global Lysine Crotonylation and 2-Hydroxyisobutyrylation in Phenotypically Different Toxoplasma gondii Parasites
Cited by: 31
Author(s): David Yin, Ning Jiang, Yue Zhang, Dawei Wang, Xiaoyu Sang, Ying Feng, Rang Chen, Xinyi Wang, Na Yang, Qijun Chen
Software Mentions: 1
Published: about 5 years ago

10.1080/23802359.2018.1535861

The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens
Cited by: 0
Author(s): Hwa-Yong Lee, Suyun Moon, Chang-Duck Koo, Jong‐Wook Chung, Hojin Ryu
Software Mentions: 1
Published: almost 6 years ago

10.3390/microorganisms9010003

Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation
Cited by: 9
Author(s): Saskia Rughöft, Nico Jehmlich, Tony Gutiérrez, Sara Kleindienst
Software Mentions: 1
Published: almost 4 years ago

10.1128/mSphere.00656-19

Filamentation Is Associated with Reduced Pathogenicity of Multiple Non- albicans Candida Species
Cited by: 14
Author(s): Mohua Banerjee, Anna L. Lazzell, Jesús A. Romo, José L. Lopez-Ribot, David Kadosh
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.101282

The G-quadruplex DNA stabilizing drug pyridostatin promotes DNA damage and downregulates transcription of Brca1 in neurons
Cited by: 53
Author(s): Jose F. Moruno-Manchon, Edward C. Koellhoffer, Jayakrishnan Gopakumar, Shashank Hambarde, Nayun Kim, Louise D. McCullough, Andrey S. Tsvetkov
Software Mentions: 1
Published: about 7 years ago

10.1111/1751-7915.13773

Establishment of a Cuscuta campestris ‐mediated enrichment system for genomic and transcriptomic analyses of ‘ Candidatus Liberibacter asiaticus’
Cited by: 12
Author(s): Tao Li, Ling Zhang, Yunshuang Deng, Xiaoling Deng, Zheng Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-15-562

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
Cited by: 26
Author(s): Julia Metzger, Raúl Tonda, Sergi Beltrán, Lídia Águeda, Marta Gut, O. Distl
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.58542

Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates
Cited by: 17
Author(s): Samuel J. Modlin, Derek Conkle-Gutierrez, Calvin Kim, Scott N. Mitchell, Christopher A. Morrissey, Brian Weinrick, William R. Jacobs, Sarah M Ramirez-Busby, Sven Hoffner, Faramarz Valafar
Software Mentions: 1
Published: about 4 years ago

10.1186/s13326-016-0102-0

A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL
Cited by: 28
Author(s): Prudence Mutowo, A. Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax, John P. Overington
Software Mentions: 1
Published: about 8 years ago

10.3390/antiox10050756

Aqueous Blackcurrant Extract Improves Insulin Sensitivity and Secretion and Modulates the Gut Microbiome in Non-Obese Type 2 Diabetic Rats
Cited by: 18
Author(s): Hye‐Jeong Yang, Ting Zhang, Xuangao Wu, Minjung Kim, Young‐Ho Kim, Eun‐Suk Yang, Yeong‐Seok Yoon, Sunmin Park
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.45413

Junction Mapper is a novel computer vision tool to decipher cell–cell contact phenotypes
Cited by: 14
Author(s): Helena Brezovjakova, Chris Tomlinson, Noor Mohd Naim, Pamela Swiatlowska, Jennifer C. Erasmus, Stephan Huveneers, Julia Gorelik, Susann Bruche, Vania Braga
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.ppat.1006762

What matters in chronic Burkholderia cenocepacia infection in cystic fibrosis: Insights from comparative genomics
Cited by: 20
Author(s): Jaroslav Nunvář, Václav Čapek, Karel Fišer, Libor Fila, Pavel Dřevı́nek
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12284-021-00487-8

Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice
Cited by: 16
Author(s): Amitha Mithra Sevanthi, S. K. Sinha, Sureshkumar, Manju Rani, Manish Ranjan Saini, Sapna Kumari, Megha Kaushik, Chandra Prakash, Karnam Venkatesh, Gyanendra Singh, Trilochan Mohapatra, Pranab Kumar Mandal
Software Mentions: 1
Published: over 3 years ago

10.1186/1752-0509-6-73

Improving metabolic flux predictions using absolute gene expression data
Cited by: 126
Author(s): Dave Lee, Kieran Smallbone, Warwick B. Dunn, Ettore Murabito, Catherine Winder, Douglas B. Kell, Pedro Mendes, Neil Swainston
Software Mentions: 1
Published: over 12 years ago

Projects: pypi: mapper

Papers Mentioning mapper 122