pypi: 0 | Projects | Ecosyste.ms: Papers

10.7554/eLife.38012

Mammal communities are larger and more diverse in moderately developed areas
Cited by: 45
Author(s): Arielle W. Parsons, Tavis Forrester, Megan C Baker-Whatton, William J. McShea, Christopher T. Rota, Stephanie G. Schuttler, Joshua J. Millspaugh, Roland Kays
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0256471

Radiology- and gene-based risk stratification in small renal cell carcinoma: A preliminary study
Cited by: 0
Author(s): Takao Sugiyama, Yasuhiro Ushijima, Yuki Motomura, Katsumi Sakamoto, Masakazu Hirakawa, Akihiro Nishie, Koshi Mimori, Yasuo Yamashita, Takashi Tsutsumi, Kousei Ishigami
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-020-03565-8

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
Cited by: 22
Author(s): Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, M. A. Tangaro, Giovanni Chillemi, Graziano Pesole, Federico Zambelli
Software Mentions: 4
Published: over 4 years ago

10.1038/s42003-019-0606-0

Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites
Cited by: 49
Author(s): Maéva Angélique Techer, Rahul Rane, Miguel L. Grau, John M. K. Roberts, Shawn Sullivan, Ivan Liachko, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-020-02240-8

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer
Cited by: 51
Author(s): Miho Oka, Lai Xu, Toshihiro Suzuki, Toshiaki Yoshikawa, Hiromi Sanada, Hayato Uemura, Akiyasu C. Yoshizawa, Yutaka Suzuki, Tetsuya Nakatsura, Yasushi Ishihama, Ayako Suzuki, Masahide Seki
Software Mentions: 4
Published: almost 4 years ago

10.1002/ajpa.23763

The efficacy of whole human genome capture on ancient dental calculus and dentin
Cited by: 21
Author(s): Kirsten A. Ziesemer, Jazmín Ramos‐Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno L. P. Hoogland, Courtney A. Hofman, Domingo C. Salazar‐García, Bruno Fröhlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008900

A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata
Cited by: 25
Author(s): Paul J. Seear, Catherine L. Gregory, Darren Heavens, Roswitha Schmickl, Levi Yant, James D. Higgins
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-020-00740-7

Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues
Cited by: 24
Author(s): Jean-David Larouche, Assya Trofimov, Leslie Hesnard, Grégory Ehx, Qingchuan Zhao, Krystel Vincent, Chantal Durette, Patrick Gendron, Jean‐Philippe Laverdure, Éric Bonneil, Caroline Côté, Sébastien Lemieux, Pierre Thibault, Claude Perreault
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-018-5357-7

A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication
Cited by: 24
Author(s): Yanling Ma, Miao Liu, Jiri Stiller, Chunji Liu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13059-015-0735-9

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
Cited by: 39
Author(s): Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-017-07872-8

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale
Cited by: 28
Author(s): Chunmei He, Jaime A. Teixeira da Silva, Jian‐Wen Tan, Jianxia Zhang, Xiaoping Pan, Mingzhi Li, Jian‐Ping Luo, Jun Duan
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-15-563

Hemolymph proteome changes during worker brood development match the biological divergences between western honey bees (Apis mellifera) and eastern honey bees (Apis cerana)
Cited by: 28
Author(s): Feng Mao, Haitham Ramadan, Bin Han, Fang Yu, Jianke Li
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-021-07378-8

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Cited by: 19
Author(s): Dou Liu, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Hǎihóng Shāng, Hongbin Li, Gao Xiao
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep33782

The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae
Cited by: 22
Author(s): Jamal S. M. Sabir, Robert K. Jansen, Dhivya Arasappan, Virginie Calderon, Emmanuel Noutahi, Chunfang Zheng, Seongjun Park, Meshaal J. Sabir, Mohammed N. Baeshen, Nahid H. Hajrah, Mohammad A. Khiyami, Nabih A. Baeshen, Abdullah Y. Obaid, Abdulrahman L. Al-Malki, David Sankoff, Nadia El-Mabrouk, Tracey A. Ruhlman
Software Mentions: 3
Published: about 8 years ago

10.1098/rsos.170988

The York Gospels: a 1000-year biological palimpsest
Cited by: 60
Author(s): Matthew D. Teasdale, Sarah Fiddyment, Jiří Vnouček, Valeria Mattiangeli, Camilla Speller, Annelise Binois, Martin Carver, Catherine Dand, Timothy P. Newfield, Christopher C. Webb, Daniel G. Bradley, Matthew J. Collins
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-17000-1

Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis
Cited by: 25
Author(s): Shiv D. Kale, Tariq Ayubi, Dawoon Chung, Nuria Tubau-Juni, Andrew Leber, Ha X. Dang, Saikumar Karyala, Raquel Hontecillas, Christopher B. Lawrence, Robert A. Cramer, Josep Bassaganya‐Riera
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pmed.1002136

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine
Cited by: 25
Author(s): Gerald Goh, RM Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock‐Ah Im, Sung‐Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil L. Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton
Software Mentions: 3
Published: almost 8 years ago

10.1093/jxb/eru266

Experimental and bioinformatic characterization of a recombinant polygalacturonase-inhibitor protein from pearl millet and its interaction with fungal polygalacturonases
Cited by: 8
Author(s): S. Prabhu, Ratna Singh, Stephan Kolkenbrock, Neerakkal Sujeeth, Nour Eddine El Gueddari, Bruno M. Moerschbacher, K. Ramachandra Kini, Martin Wagenknecht
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pntd.0008439

Unravelling the proteomic signature of extracellular vesicles released by drug-resistant Leishmania infantum parasites
Cited by: 33
Author(s): Noélie Douanne, George Dong, Mélanie Douanne, Martin Olivier, Christopher Fernández-Prada
Software Mentions: 3
Published: over 4 years ago

10.1002/acm2.12425

Medical physics 3.0 versus 1.0: A case study in digital radiography quality control
Cited by: 2
Author(s): D Carver, Charles E. Willis, Paul J. Stauduhar, Thomas Nishino, John G. Wells, Ehsan Samei
Software Mentions: 3
Published: over 6 years ago

10.1038/srep24180

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years
Cited by: 21
Author(s): Xiaotao Jiang, Feng Guo, Tong Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-018-4900-x

Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)
Cited by: 24
Author(s): Zhiqiang Tian, Lina Sun, Yanyan Li, Linfa Quan, Huaijiang Zhang, Wentao Yan, Qiang Yue, Qiu GuiSheng
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1008216

Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease
Cited by: 52
Author(s): Justine Charon, Matthew J. Grigg, John Sebastian Eden, Kim A. Piera, Hafsa Rana, Timothy William, Karrie Rose, Miles P. Davenport, Nicholas M. Anstey, Edward C. Holmes
Software Mentions: 3
Published: almost 5 years ago

10.1093/gigascience/gix044

Comprehensive analysis of microorganisms accompanying human archaeological remains
Cited by: 15
Author(s): Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-10-S3-S13

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads
Cited by: 13
Author(s): Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong, Suhua Shi
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0080210

Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes
Cited by: 25
Author(s): Fabian Kurth, Kieran Rimmer, Lakshmanane Premkumar, Biswaranjan Mohanty, Wilko Duprez, Maria A. Halili, Stephen R. Shouldice, Begoña Heras, David P. Fairlie, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pntd.0000258

On the Extent and Origins of Genic Novelty in the Phylum Nematoda
Cited by: 69
Author(s): James D. Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-15-779

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments
Cited by: 59
Author(s): Imran Khan, Emanuel Maldonado, Vı́tor Vasconcelos, Stephen J. O’Brien, Warren E. Johnson, Agostinho Antunes
Software Mentions: 3
Published: about 10 years ago

10.1186/s12863-020-00945-0

Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis
Cited by: 5
Author(s): Zhaohui Cai, Qiongyu Guo, Zhichao Yao, Wenping Zheng, Junfei Xie, Shuai Bai, Hongyu Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-46094-y

Human Corneal Expression of SLC4A11, a Gene Mutated in Endothelial Corneal Dystrophies
Cited by: 23
Author(s): Deepti Malhotra, Sampath K. Loganathan, Anthony M. Chiu, Chris M. Lukowski, Joseph R. Casey
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-021-04155-y

DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information
Cited by: 13
Author(s): Xiaoyun Yang, Liyuan Zhao, Wei Fang, Jing Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-020-00758-x

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans
Cited by: 18
Author(s): Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt, Georg K. Gerber
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008552

Tracking human population structure through time from whole genome sequences
Cited by: 63
Author(s): Ke Wang, Iain Mathieson, Jared O’Connell, Stephan Schiffels
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-016-1118-6

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Cited by: 91
Author(s): Abhinav Nellore, Andrew E. Jaffe, Jean‐Philippe Fortin, José Alquicira-Hernández, Leonardo Collado‐Torres, Siruo Wang, Robert A. Phillips, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, Jeffrey T. Leek
Software Mentions: 3
Published: almost 8 years ago

10.1093/gigascience/gix017

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
Cited by: 49
Author(s): Geng Li, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng‐Chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Lei Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1006188

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins
Cited by: 6
Author(s): Linda Dib, Nicolas Salamin, David Gfeller
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-014-0468-1

The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment
Cited by: 81
Author(s): Seung Chul Shin, Do Hwan Ahn, Su Jin Kim, Chul Woo Pyo, Yongrok Choi, Mi-Kyeong Kim, Jung-Eun Lee, Jong Eun Lee, H. William Detrich, John H. Postlethwait, David Edwards, Sung Gu Lee, Hyun Park
Software Mentions: 3
Published: about 10 years ago

10.3390/genes6041315

Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction
Cited by: 8
Author(s): Sathishkumar Natarajan, Senthil Kumar Thamilarasan, Jong-In Park, Mi-Young Chung, Ill–Sup Nou
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12911-016-0325-0

Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing
Cited by: 7
Author(s): Wolfgang Kuchinke, Christian Krauth, René Bergmann, Töresin Karakoyun, Astrid Woollard, Irene Schluender, Benjamin Braasch, Martin Eckert, Christian Ohmann
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2016.01186

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: over 8 years ago

10.1098/rsta.2019.0056

Exascale applications: skin in the game
Cited by: 51
Author(s): Francis J. Alexander, Ann S. Almgren, John B. Bell, A. Bhattacharjee, Jacqueline Chen, P. Colella, David Daniel, Jack Deslippe, Lori Freitag Diachin, Erik W. Draeger, Anshu Dubey, Thom H. Dunning, Thomas M. Evans, Ian Foster, Marianne M. François, Timothy C. Germann, Mark S. Gordon, Salman Habib, Mahantesh Halappanavar, Steven P. Hamilton, William E. Hart, Zhenyu Huang, Aimee L. Hungerford, Daniel Kasen, Paul Kent, Tzanio Kolev, Douglas B. Kothe, A. S. Kronfeld, Ye Luo, Paul B. Mackenzie, David McCallen, O. E. Bronson Messer, Susan M. Mniszewski, Chris Oehmen, A. Perazzo, Danny Pérez, David F. Richards, William J. Rider, Robert N. Rieben, Kenneth J. Roche, A. Siegel, Michael Sprague, Carl I. Steefel, Rick Stevens, Madhava Syamlal, Mark A. Taylor, John A. Turner, Jean‐Luc Vay, Artur F Voter, Theresa L. Windus, Katherine Yelick
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-5-176

Cited by: 42
Author(s): Charu G. Kumar, Richard D. LeDuc, George Gong, Levan Roinishivili, Harris A. Lewin, Lei Liu
Software Mentions: 3
Published: almost 21 years ago

10.1371/journal.pcbi.1000156

PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
Cited by: 22
Author(s): Rahul Siddharthan
Software Mentions: 3
Published: about 16 years ago

10.3390/genes12050634

Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in Oryza sativa
Cited by: 5
Author(s): Zhengqing Yuan, Weixiong Long, Haifei Hu, Ting Liang, Xiaoyun Luo, Zhongli Hu, Rong Zhu, Xianting Wu
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-016-0989-x

MUFFINN: cancer gene discovery via network analysis of somatic mutation data
Cited by: 118
Author(s): Ara Cho, Jung Eun Shim, Eiru Kim, Fran Supek, Ben Lehner, Insuk Lee
Software Mentions: 3
Published: over 8 years ago

10.3390/pathogens9010026

Phylogenomic Analysis of Two Co-Circulating Canine Distemper Virus Lineages in Colombia
Cited by: 6
Author(s): July Duque-Valencia, Francisco J. Díaz, Julián Ruíz-Sáenz
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2020.02078

Delineating the Immuno-Dominant Antigenic Vaccine Peptides Against gacS-Sensor Kinase in Acinetobacter baumannii: An in silico Investigational Approach
Cited by: 10
Author(s): A. S. Smiline Girija
Software Mentions: 3
Published: about 4 years ago

10.3390/pathogens9110872

Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions
Cited by: 8
Author(s): Julie K. Weckworth, Brian W. Davis, Melody Roelke‐Parker, Rebecca P. Wilkes, Craig Packer, Ernest Eblate, Michael K. Schwartz, L. Scott Mills
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.4573

Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers
Cited by: 1
Author(s): Adam P. A. Cardilini, Craig D. H. Sherman, William B. Sherwin, Lee A. Rollins
Software Mentions: 3
Published: over 6 years ago

10.3390/v7031454

Interaction Research on the Antiviral Molecule Dufulin Targeting on Southern Rice Black Streaked Dwarf Virus P9-1 Nonstructural Protein
Cited by: 23
Author(s): Zhenchao Wang, Xiangyang Li, Wenli Wang, Weiying Zhang, Yu Lu, Deyu Hu, Baoan Song
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2016.01342

Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios
Cited by: 55
Author(s): Samantha M. Gromek, Andrea M. Suria, Matthew S. Fullmer, Jillian L. Garcia, J. Peter Gogarten, Spencer V. Nyholm, Marcy J. Balunas
Software Mentions: 3
Published: about 8 years ago

10.1016/j.omtn.2020.06.004

Prediction of m5C Modifications in RNA Sequences by Combining Multiple Sequence Features
Cited by: 31
Author(s): Lijun Dou, Xiaoling Li, Hui Ding, Lei Xu, Hong‐Bing Xiang
Software Mentions: 3
Published: about 4 years ago

10.3390/vaccines2030515

Peptide Vaccine: Progress and Challenges
Cited by: 479
Author(s): Weidang Li, Medha Joshi, Smita Singhania, Kyle H. Ramsey, Ashlesh K. Murthy
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2018.00912

Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows
Cited by: 38
Author(s): Thomas Partridge, Annalisa Nicastri, Anna E. Kliszczak, L M Yindom, Benedikt M. Kessler, Nicola Ternette, Persephone Borrow
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-017-3711-9

Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Cited by: 22
Author(s): Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 3
Published: about 7 years ago

10.1186/1743-422X-8-285

Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway
Cited by: 38
Author(s): Benjamin Terrier, Laurence Josset, Julien Textoris, Virginie Marcel, Gaëlle Cartet, Olivier Ferraris, Catherine Nguyen, Bruno Lina, Jean‐Jacques Diaz, Jean-Christophe Bourdon, Manuel Rosa‐Calatrava
Software Mentions: 3
Published: over 13 years ago

10.3390/molecules20069977

DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations
Cited by: 39
Author(s): Alberto Cuzzolin, Mattia Sturlese, Ivana Malvacio, Antonella Ciancetta, Stefano Moro
Software Mentions: 3
Published: over 9 years ago

10.3390/molecules26030645

Volatile Organic Compounds, Bacterial Airway Microbiome, Spirometry and Exercise Performance of Patients after Surgical Repair of Congenital Diaphragmatic Hernia
Cited by: 0
Author(s): Gert Warncke, Georg Singer, Jana Windhaber, Lukas Schabl, Elena Friehs, Wolfram Miekisch, Peter Gierschner, Ingeborg Klymiuk, Ernst Eber, Katarina Zeder, Andreas Pfleger, Beate Obermüller, Holger Till, Christoph Castellani
Software Mentions: 3
Published: almost 4 years ago

10.1074/mcp.RA119.001791

Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search
Cited by: 35
Author(s): Qingbo Shu, Mengjie Li, Lian Shu, Zhiwu An, Jifeng Wang, Hao Lv, Ming Yang, Tao Cai, Tony Hu, Yan Fu, Fuquan Yang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12885-021-08320-7

Genomic features of rapid versus late relapse in triple negative breast cancer
Cited by: 9
Author(s): Yiqing Zhang, Sarah Asad, Zachary Weber, David Tallman, William Nock, Meghan Wyse, Jerome F. Bey, Kristin L. Dean, Elizabeth Adams, Sinclair Stockard, Jasneet Singh, Eric P. Winer, Nancy U. Lin, Yi‐Zhou Jiang, Ding Ma, Peng Wang, Leming Shi, Wei Huang, Mathew Cherian, Maryam B. Lustberg, Bhuvaneswari Ramaswamy, Sagar Sardesai, Jeffrey VanDeusen, Nicole Williams, Robert Wesolowski, Samilia Obeng‐Gyasi, Gina M. Sizemore, Claire F. Verschraegen, Daniel G. Stover
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.721030

Pan-Cancer Analysis of PARP1 Alterations as Biomarkers in the Prediction of Immunotherapeutic Effects and the Association of Its Expression Levels and Immunotherapy Signatures
Cited by: 29
Author(s): Xinke Zhang, Yingying Wang, Abdulrahim Gari, Chunhua Qu, Jiewei Chen
Software Mentions: 3
Published: about 3 years ago

10.1186/s12885-020-07456-2

Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma
Cited by: 5
Author(s): Wenshuai Liu, Hanxing Tong, Chenlu Zhang, Rongyuan Zhuang, He Guo, Chen Lv, Hua Yang, Qiaowei Lin, Xi Guo, Zhiming Wang, Yan Wang, Feng Shen, Shengzhou Wang, Chun Dai, Guan Wang, Jun Li, Weiqi Lu, Yong Zhang, Yuhong Zhou
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-019-5429-3

Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection
Cited by: 11
Author(s): Chen Huang, Dongliang Leng, Shixue Sun, Xiaohua Douglas Zhang
Software Mentions: 3
Published: almost 6 years ago

10.3390/molecules23071635

Investigation of Hydro-Lipophilic Properties of N-Alkoxyphenylhydroxynaphthalenecarboxamides †
Cited by: 11
Author(s): Iva Kapustíková, Andrzej Bąk, Tomáš Goněc, Jiří Kos, Violetta Kozik, Josef Jampílek
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.737598

Editorial: Predicting High-Risk Individuals for Common Diseases Using Multi-Omics and Epidemiological Data
Cited by: 1
Author(s): Debajyoti Chowdhury, Xin Zhou, Bailiang Li, Yuanwei Zhang, William K. Cheung, Aiping Lü, Lu Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.01015

Targeting Mutated Plus Germline Epitopes Confers Pre-clinical Efficacy of an Instantly Formulated Cancer Nano-Vaccine
Cited by: 34
Author(s): Mona O. Mohsen, Monique Vogel, Carsten Riether, Julius Müller, Silvia Salatino, Nicola Ternette, Ariane Gomes, Gustavo Cabral-Miranda, Aadil El-Turabi, Christiane Ruedl, Thomas M. Kündig, Said Dermime, Alexander Knuth, Daniel E. Speiser, Martin F. Bachmann
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2014.00031

Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: almost 11 years ago

10.3389/fendo.2021.698511

Mutational Landscape of the Proglucagon-Derived Peptides
Cited by: 7
Author(s): Peter Lindquist, Jakob Sture Madsen, Hans Bräuner‐Osborne, Mette M. Rosenkilde, Alexander S. Hauser
Software Mentions: 3
Published: over 3 years ago

10.1186/s12885-019-6180-5

Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition
Cited by: 35
Author(s): Alexandra Kalmár, Zsófia Brigitta Nagy, Orsolya Galamb, István Csabai, András Bodor, Barnabás Wichmann, Gábor Valcz, Barbara Kinga Barták, Zsolt Tulassay, Péter Igaz, Béla Molnár
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07576-4

Long non-coding RNA pairs to assist in diagnosing sepsis
Cited by: 18
Author(s): Xubin Zheng, Kwong‐Sak Leung, Man‐Hon Wong, Lixin Cheng
Software Mentions: 3
Published: over 3 years ago

10.3390/medsci7060074

In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts
Cited by: 0
Author(s): P. Sneha, Urmi Shah, S. Balaji
Software Mentions: 3
Published: over 5 years ago

10.3389/fbioe.2019.00214

Computational Assessment of the Pharmacological Profiles of Degradation Products of Chitosan
Cited by: 27
Author(s): Diana Larisa Roman, Marin Roman, Claudia Som, Mélanie Schmutz, Edgar García Hernández, Peter Wick, Tommaso Casalini, Giuseppe Perale, Vasile Ostafe, Adriana Isvoran
Software Mentions: 3
Published: about 5 years ago

10.1016/j.molcel.2019.07.022

Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk
Cited by: 140
Author(s): James A. Letts, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, L.A. Sazanov
Software Mentions: 3
Published: about 5 years ago

10.1099/mgen.0.000175

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae
Cited by: 8
Author(s): Matthew A. Croxen, Tracy D. Lee, Robert Azana, Linda Hoang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-016-1389-7

New tools to analyze overlapping coding regions
Cited by: 1
Author(s): Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2020.574304

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing
Cited by: 11
Author(s): Ruixiang Xu, Zhen Wang, Yingjuan Su, Ting Wang
Software Mentions: 3
Published: about 4 years ago

10.1002/1878-0261.12757

Genome‐wide profiling of circulating tumor DNA depicts landscape of copy number alterations in pancreatic cancer with liver metastasis
Cited by: 11
Author(s): Wei Tao, Jian Zhang, Jin Li, Qi Chen, Xiaoqin Zhi, Wei Tao, Jingjiao Ma, Jiaqi Yang, Yiting Lou, Tao Ma, Xiang Li, Qi Zhang, Wei Chen, Risheng Que, Shunliang Gao, Xueli Bai, Tingbo Liang
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.722293

Precision N-Glycoproteomic Profiling of Murine Peritoneal Macrophages After Different Stimulations
Cited by: 2
Author(s): Lujie Yang, Tianqi Gong, Huali Shen, Jiangnan Pei, Lei Zhang, Quanqing Zhang, Yuanyu Huang, Zuojian Hu, Ziyue Pan, Pengyuan Yang, Gang Li, Hongxiu Yu
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.634617

CD96 Correlates With Immune Infiltration and Impacts Patient Prognosis: A Pan-Cancer Analysis
Cited by: 31
Author(s): Wenrui Ye, Cong Luo, Fangkun Liu, Zhixiong Liu, Fenghua Chen
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13068-020-1651-0

Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742
Cited by: 6
Author(s): Youzhi Miao, Xing Chen, Tuo Li, Han Zhu, Tang Si-yu, Dongyang Liu, Qirong Shen
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13068-017-0885-y

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
Cited by: 23
Author(s): Man Zhou, Peng Guo, Tao Wang, Limin Gao, Hang Yin, Cheng Cai, Jie Gu, Xin Lü
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0004839

Expression Analysis of the Theileria parva Subtelomere-Encoded Variable Secreted Protein Gene Family
Cited by: 39
Author(s): Jacqueline Schmuckli‐Maurer, Carlo Casanova, Stéfanie Schmied, Sarah Affentranger, Iana Parvanova, S. Kang'a, Vishvanath Nene, Frank Katzer, Declan J. McKeever, Joachim Müller, Richard P. Bishop, Arnab Pain, Dirk Dobbelaere
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0196346

Causal language and strength of inference in academic and media articles shared in social media (CLAIMS): A systematic review
Cited by: 63
Author(s): Noah Haber, Emily R. Smith, Ellen Moscoe, Kathryn Andrews, Robin Audy, Winnie Bell, Alana T. Brennan, Alexander Breskin, Jeremy C. Kane, Mahesh Karra, Elizabeth McClure, Elizabeth A. Suarez
Software Mentions: 3
Published: over 6 years ago

10.1155/2014/187105

Genome-Wide Uncovering of STAT3-Mediated miRNA Expression Profiles in Colorectal Cancer Cell Lines
Cited by: 18
Author(s): Jufeng Zhang, Xia Luo, Huiming Li, Ling Deng, Ying Wang
Software Mentions: 3
Published: almost 11 years ago

10.3390/biom10040509

The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II
Cited by: 7
Author(s): Steffen Glöckner, K. Ngo, Björn Wagner, A. Heine, G. Klebe
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0219452

Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure
Cited by: 17
Author(s): Petr Popov, Ilya V. Bizin, M. Michael Gromiha, A. Kulandaisamy, Dmitrij Frishman
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13143418

Phosphorylation of OGFOD1 by Cell Cycle-Dependent Kinase 7/9 Enhances the Transcriptional Activity of RNA Polymerase II in Breast Cancer Cells
Cited by: 1
Author(s): Han Teo Lee, Il Hwan Lee, Jaehwan Kim, Sang-Ho Lee, Sojung Kwak, Min Young Suh, In Kyeom Hwang, Bu Gyeong Kang, Sun Shin, Byung Il Lee, Sang Eun Lee, Jinmi Choi, Jae Seok Roe, Eun Jung Cho, Hong Duk Youn
Software Mentions: 3
Published: over 3 years ago

10.6026/97320630017424

Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference
Cited by: 0
Author(s): Noshin Nawar, Anik Paul, Hamida Nooreen Mahmood, Ismail Faisal, Ismail Hosen, Hossain Uddin Shekhar
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-13-346

Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations
Cited by: 11
Author(s): Hsin-Chou Yang, Peili Wang, Chien‐Wei Lin, Chien-Hsiun Chen, Chun-Houh Chen
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0248886

Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes
Cited by: 11
Author(s): Adrián Mosquera Orgueira, Roi Ferreiro Ferro, José Ángel Díaz Arias, Cristina Santos, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ággeles Bendaña López, Ayelén Melisa Blanco, Paula Melero Valentín, And Res Peleteiro Raindo, Marcos Pérez López, Manuel Mateo Pérez Encinas, Marta Sonia González Pérez, Marianela Rodríguez, José Luis Bello López
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-017-4147-y

An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta
Cited by: 30
Author(s): Xiaolong Cao, Haobo Jiang
Software Mentions: 3
Published: about 7 years ago

10.1155/2019/7376034

Identification of Potential Biomarkers and Survival Analysis for Head and Neck Squamous Cell Carcinoma Using Bioinformatics Strategy: A Study Based on TCGA and GEO Datasets
Cited by: 37
Author(s): Yujie Shen, Jinhui Liu, Liqing Zhang, Shikun Dong, Jiacheng Zhang, Yaqin Liu, Han Zhou, Wei Dong
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0079612

Comparative Transcriptome Analysis of Salivary Glands of Two Populations of Rice Brown Planthopper, Nilaparvata lugens, That Differ in Virulence
Cited by: 74
Author(s): Rui Ji, Haixin Yu, Qiang Fu, Hongdan Chen, Wenfeng Ye, Shaohui Li, Yonggen Lou
Software Mentions: 3
Published: about 11 years ago

10.1038/s42003-020-0827-2

Igf2bp3 maintains maternal RNA stability and ensures early embryo development in zebrafish
Cited by: 37
Author(s): Fan Ren, Qiaohong Lin, Gaorui Gong, Xian Du, Daojun Hong, Wenying Qin, Ran Miao, Yang Xiong, Rui Xiao, Xiaohui Li, Jian‐Fang Gui, Jie Mei
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-019-1953-1

Genome-wide identification, structure characterization, and expression pattern profiling of aquaporin gene family in cucumber
Cited by: 67
Author(s): Yong‐Guan Zhu, Lei Yang, Ning Liu, Jie Yang, Xi Zhou, Yuchen Xia, Yang He, Yan He, Haijun Gong, Dongfang Ma, Jia Yin
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-017-1835-1

Improving contig binning of metagenomic data using $$ {d}_2^S $$ oligonucleotide frequency dissimilarity
Cited by: 15
Author(s): Ying Wang, Kun Wang, Yang Lu, Fengzhu Sun
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-2736-9

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family
Cited by: 42
Author(s): Fengya Zheng, Haiyang Wu, Rongzhi Zhang, Shiming Li, Weiming He, Fuk‐Ling Wong, Genying Li, Shancen Zhao, Hon‐Ming Lam
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0249375

MiRNA-107 enhances the malignant progression of pancreatic cancer by targeting TGFBR3
Cited by: 11
Author(s): Tingke Tian, Qingmei Yang, Cuijuan Zhang, Xiaokun Li, Jiancheng Cheng
Software Mentions: 3
Published: over 3 years ago

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