Ecosyste.ms: Papers

10.1186/s12862-017-0995-y

The colonization and divergence patterns of Brandt’s vole (Lasiopodomys brandtii) populations reveal evidence of genetic surfing
Cited by: 11
Author(s): Ke Li, Michael H. Kohn, Songmei Zhang, Xiaofeng Wan, Dazhao Shi, Deng Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s13007-021-00730-9

A label-free, fast and high-specificity technique for plant cell wall imaging and composition analysis
Cited by: 7
Author(s): Huimin Xu, Yuanyuan Zhao, Yuanzhen Suo, Yayu Guo, Yi Man, Yanping Jing, Xin-Qiang He, Jinxing Lin
Software Mentions: 2
Published: over 3 years ago

10.1128/MRA.00336-21

Draft Genome Sequence of Pandrug-Resistant Pseudomonas aeruginosa SPA03, Isolated from a Patient with Benign Prostatic Hyperplasia
Cited by: 1
Author(s): Pachi Pulusu Chanakya, Balaram Khamari, Manmath Lama, Arun Sai Kumar Peketi, Prakash Kumar, Valakunja Nagaraja, Eswarappa Pradeep Bulagonda
Software Mentions: 2
Published: over 3 years ago

10.1186/s12014-020-09290-x

Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources
Cited by: 25
Author(s): Sara R. Savage, Bing Zhang
Software Mentions: 2
Published: over 4 years ago

10.3390/cells9020355

Impaired Nuclear Export of the Ribonucleoprotein Complex and Virus-Induced Cytotoxicity Combine to Restrict Propagation of the A/Duck/Malaysia/02/2001 (H9N2) Virus in Human Airway Cells
Cited by: 2
Author(s): Sriram Kumar, David Yeo, Nisha Muralidharan, Soak Kuan Lai, Cathlyn Tong, Boon Huan Tan, Richard J. Sugrue
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.ppat.1008871

Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis
Cited by: 15
Author(s): Amit Luthra, Jairo M. Montezuma-Rusca, Carson J. La Vake, Morgan LeDoyt, Kristina N. Delgado, Timothy C. Davenport, Mary Fiel-Gan, Melissa J. Caimano, Justin D. Radolf, Kelly L. Hawley
Software Mentions: 2
Published: about 4 years ago

10.1186/s12896-017-0393-y

Adaptation of the GoldenBraid modular cloning system and creation of a toolkit for the expression of heterologous proteins in yeast mitochondria
Cited by: 32
Author(s): Ana Pérez-González, R. Kniewel, Marcel Veldhuizen, Harshit Verma, Mónica Navarro-Rodríguez, Luis M. Rubio, Elena Caro
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pbio.3000373

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform
Cited by: 43
Author(s): Erin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenář, Madlen Stephani, Richard Imre, Elisabeth Roitinger, Richard K. Hughes, Khaoula Belhaj, Karl Mechtler, Frank L.H. Menke, Tolga O. Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin Dagdas
Software Mentions: 2
Published: over 5 years ago

10.3390/cells1041029

A Novel Type III Endosome Transmembrane Protein, TEMP
Cited by: 1
Author(s): Rajith Aturaliya, Markus C. Kerr, Rohan D. Teasdale
Software Mentions: 2
Published: about 12 years ago

10.1038/s42003-020-01184-w

Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibition
Cited by: 8
Author(s): Jinxin Xu, Xiaowen Tang, Yiguang Zhu, Zhijun Yu, Kai Su, Yulong Zhang, Dong Yu, Weiming Zhu, Changsheng Zhang, Ruibo Wu, Jinsong Liu
Software Mentions: 2
Published: over 4 years ago

10.1099/mic.0.041491-0

ccrAB Ent serine recombinase genes are widely distributed in the Enterococcus faecium and Enterococcus casseliflavus species groups and are expressed in E. faecium
Cited by: 9
Author(s): Eva katrin Bjørkeng, Girum Tadesse Tessema, Eirik W. Lundblad, Patrick Butaye, Rob J. L. Willems, Johanna U. Ericson Sollid, Arnfinn Sundsfjord, Kristin Hegstad
Software Mentions: 2
Published: almost 14 years ago

10.1186/1741-7007-10-84

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers
Cited by: 90
Author(s): Nathalie Pavy, Betty Pelgas, Jérôme Laroche, Philippe Rigault, Nathalie Isabel, Jean Bousquet
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pcbi.1002412

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire
Cited by: 74
Author(s): Jorg J.A. Calis, Rob J. de Boer, Can Keşmir
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1000387

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors
Cited by: 239
Author(s): Li Xie, Jerry Li, Lei Xie, Philip E. Bourne
Software Mentions: 2
Published: over 15 years ago

10.1038/s41421-021-00259-0

Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis
Cited by: 11
Author(s): Sensen Zhang, Baolei Yuan, Jordy Homing Lam, Jun Zhou, Xuan Zhou, Gerardo Ramos‐Mandujano, Xin‐Xia Tian, Yang Liu, Han Ren, Li Yu, Xin Gao, Maojun Yang
Software Mentions: 2
Published: over 3 years ago

10.3390/cells8040298

miR-1306 Mediates the Feedback Regulation of the TGF-β/SMAD Signaling Pathway in Granulosa Cells
Cited by: 22
Author(s): Liu Yang, Xiaohong Du, Lu Liu, Qiuyu Cao, Zengxiang Pan, Qifa Li
Software Mentions: 2
Published: over 5 years ago

10.1111/eva.12128

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon ( <i>Oncorhynchus tshawytscha</i> )
Cited by: 180
Author(s): Wesley A. Larson, Lisa W. Seeb, Meredith V. Everett, Ryan K. Waples, William D. Templin, James E. Seeb
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0072670

A Minimal Set of Tissue-Specific Hypomethylated CpGs Constitute Epigenetic Signatures of Developmental Programming
Cited by: 20
Author(s): Alejandro Colaneri, Tianyuan Wang, Vijayakanth Pagadala, Jaya Kittur, Nickolas G. Staffa, Shyamal D. Peddada, Elvira Isganaitis, Mary Elizabeth Patti, Lutz Birnbaumer
Software Mentions: 2
Published: about 11 years ago

10.1186/s12862-015-0405-2

Morphological and ecological divergence of Lilium and Nomocharis within the Hengduan Mountains and Qinghai-Tibetan Plateau may result from habitat specialization and hybridization
Cited by: 31
Author(s): Yongxing Gao, AJ Harris, Xing‐Jin He
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-018-19491-y

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides
Cited by: 68
Author(s): Asma Ehsan, Khalid Mahmood, Yaser Daanial Khan, Sher Afzal Khan, Kuo‐Chen Chou
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12934-020-01500-3

Improved production of germacrene A, a direct precursor of ß-elemene, in engineered Saccharomyces cerevisiae by expressing a cyanobacterial germacrene A synthase
Cited by: 18
Author(s): Weixin Zhang, Junqi Guo, Zheng Wang, Yanwei Li, Xiangfeng Meng, Yu Shen, Weifeng Liu
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12915-021-01039-8

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors
Cited by: 30
Author(s): Yoshihisa Hirakawa, Masuo Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, M. Taira, Kazushi Kinbara, Toshiya Senda
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0020085

OrthoList: A Compendium of C. elegans Genes with Human Orthologs
Cited by: 375
Author(s): Daniel D. Shaye, Iva Greenwald
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0247841

Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis
Cited by: 20
Author(s): Gabriel Rodrigues Coutinho Pereira, Bárbara de Azevedo Abrahim Vieira, Joelma Freire De Mesquita
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2202-8-95

Gene expression profiling in a mouse model of infantile neuronal ceroid lipofuscinosis reveals upregulation of immediate early genes and mediators of the inflammatory response
Cited by: 28
Author(s): Xingwen Qiao, Jui Yun Lu, Sandra L. Hofmann
Software Mentions: 2
Published: about 17 years ago

10.1038/s41598-020-72889-5

A structure-based computational workflow to predict liability and binding modes of small molecules to hERG
Cited by: 14
Author(s): Subha Kalyaanamoorthy, Shawn M. Lamothe, Xiaoqing Hou, Tae Chul Moon, Harley T. Kurata, Michael Houghton, Khaled Barakat
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0238784

Expression characteristics and regulatory mechanism of Apela gene in liver of chicken (Gallus gallus)
Cited by: 4
Author(s): Wenbo Tan, Hua Zheng, Dandan Wang, Fangyuan Tian, Hong Li, Xiaojun Liu
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-8-97

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Cited by: 42
Author(s): Huaiqiu Zhu, Gangqing Hu, Yifan Yang, Jin Wang, Zhen‐Su She
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1003554

Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4
Cited by: 50
Author(s): Harinder Manku, Carl D. Langefeld, Sandra G. Guerra, Talat H. Malik, Marta E. Alarcón‐Riquelme, Juan Manuel Anaya, Sang Cheol Bae, Susan A. Boackle, Elizabeth E. Brown, Lindsey A. Criswell, Barry I. Freedman, Patrick M. Gaffney, Peter Gregersen, Joel M. Guthridge, Sang Hoon Han, John B. Harley, Chaim O. Jacob, Judith A. James, Diane L. Kamen, Kenneth M. Kaufman, Jennifer A. Kelly, Javier Martín, Joan T. Merrill, Kathy L. Moser, Timothy B. Niewold, So Yeon Park, Bernardo A. Pons-Estel, Amr H. Sawalha, R. Hal Scofield, Nan Shen, Anne M. Stevens, Celi Sun, Gary S. Gilkeson, Jeff Edberg, Robert P. Kimberly, Swapan K. Nath, Betty P. Tsao, Tim J. Vyse
Software Mentions: 2
Published: over 11 years ago

10.3390/ma14123274

Synthesis, Spectroscopic, and Theoretical Study of Copper and Cobalt Complexes with Dacarbazine
Cited by: 6
Author(s): Grzegorz Świderski, Ryszard Łaźny, Michał Sienkiewicz, Monika Kalinowska, Renata Świsłocka, Ali Osman Acar, Aleksandra Golonko, Marzena Matejczyk, W. Lewandowski
Software Mentions: 2
Published: over 3 years ago

10.18632/aging.103262

Resveratrol promotes osteogenesis and alleviates osteoporosis by inhibiting p53
Cited by: 28
Author(s): Tao Yu, Zaiyan Wang, Xiaomeng You, Haichao Zhou, Wenbao He, Bing Li, Xia Jiang, Hongying Zhu, Youguang Zhao, Guangrong Yu, Yuan Xiong, Yunfeng Yang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0206689

The biological functions of target genes in pan-cancers and cell lines were predicted by miR-375 microarray data from GEO database and bioinformatics
Cited by: 4
Author(s): Jiang‐Hui Zeng, Xuzhi Liang, Huihua Lan, Xu Zhu, Xiu-Yun Liang
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0046084

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency
Cited by: 87
Author(s): Grant Thiltgen, Richard A. Goldstein
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1009594

A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice
Cited by: 3
Author(s): Giang Ngan Khong, Nhu Thi Le, Ngọc Mai Phạm Thị, Hélène Adam, Carole Gauron, Hoa Quang Le, Dung Tien Pham, Kelly Colonges, Xuan Hoi Pham, Vinh Nang, Michel Lebrun, Stéfan Jouannic
Software Mentions: 2
Published: over 3 years ago

10.1186/s12936-019-2770-6

HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance
Cited by: 10
Author(s): Feng‐Ling Si, Liang Qiao, Qianjun He, Yong Zhou, Zhen‐Tian Yan, Bin Chen
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-10-117

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins
Cited by: 65
Author(s): Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig, Dirk Walther
Software Mentions: 2
Published: over 15 years ago

10.1038/s41420-021-00413-3

The oncogene Mct-1 promotes progression of hepatocellular carcinoma via enhancement of Yap-mediated cell proliferation
Cited by: 1
Author(s): Wenjie Yang, Yicheng Ni, Shuguang Yang, Jicheng Yang, Xiaopei Yang, Feng Cheng, Xuehao Wang, Feng Zhang, Jianhua Rao
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pntd.0004861

MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors
Cited by: 45
Author(s): Carolina Firacative, Chandler C. Roe, Richard Malík, Kennio Ferreira‐Paim, Patricia Escandón, Jane E. Sykes, Laura Rocío Castañón-Olivares, Cudberto Contreras-Peres, Blanca Samayoa, Tania C. Sorrell, Elizabeth Castañeda, Shawn R. Lockhart, David M. Engelthaler, Wieland Meyer
Software Mentions: 2
Published: over 8 years ago

10.1186/1475-2875-13-313

Immunization against a merozoite sheddase promotes multiple invasion of red blood cells and attenuates Plasmodium infection in mice
Cited by: 3
Author(s): Ryan C. Smith, Daisy D. Colón-López, Jürgen Bosch
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0030483

TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules
Cited by: 91
Author(s): Lianming Zhang, Yiqing Chen, Hau-San Wong, Shuigeng Zhou, Hiroshi Mamitsuka, Shanfeng Zhu
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0052516

Comparative Analysis of Methods for Identifying Recurrent Copy Number Alterations in Cancer
Cited by: 11
Author(s): Xiguo Yuan, Junying Zhang, Shengli Zhang, Guoqiang Yu, Yue Wang
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-016-0917-9

Web-TCGA: an online platform for integrated analysis of molecular cancer data sets
Cited by: 135
Author(s): Mario C. Deng, Johannes Brägelmann, Joachim L. Schultze, Sven Perner
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12870-020-2329-2

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance
Cited by: 30
Author(s): Jie Sun, Xingjiang Xiong, Xiaoli Zhang, Hongjie Feng, Qian Zhu, Yanjun Li
Software Mentions: 2
Published: over 4 years ago

10.3390/life10120347

Bird Eye View of Protein Subcellular Localization Prediction
Cited by: 13
Author(s): Ravindra Kumar, Sandeep Kumar Dhanda
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12870-020-02651-6

Comprehensive analysis of the Ppatg3 mutant reveals that autophagy plays important roles in gametophore senescence in Physcomitrella patens
Cited by: 6
Author(s): Zexi Chen, Wenbo Wang, Xiaojun Pu, Xueyi Dong, Bei Gao, Ping Li, Yulin Jia, Aizhong Liu, Li Liu
Software Mentions: 2
Published: about 4 years ago

10.1128/mBio.01050-17

Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes
Cited by: 12
Author(s): Yushen Du, Tianhao Zhang, Lei Dai, Xiaojuan Zheng, Aleksandr M. Gorin, John Oishi, Ting-Ting Wu, Janice Yoshizawa, Xinmin Li, Otto O. Yang, Otoniel Martı́nez-Maza, Roger Detels, Ren Sun
Software Mentions: 2
Published: almost 7 years ago

10.1002/cam4.3902

Identification of inhibitory immune checkpoints and relevant regulatory pathways in breast cancer stem cells
Cited by: 6
Author(s): Huancong Shi, Yisi Yang
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-5-85

Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs
Cited by: 16
Author(s): Anna Henricson, Erik L. L. Sonnhammer, David L. Baillie, Ana Vaz Gomes
Software Mentions: 2
Published: about 20 years ago

10.1371/journal.pone.0238179

Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L
Cited by: 12
Author(s): Xin-Tong Zhou, Longfei Jia, Mouzheng Duan, Xue Chen, Cailin Qiao, Jinqi Ma, Chao Zhang, Fuyu Jing, Shengsen Zhang, Bo Yang, Liyuan Zhang, Jiana Li
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0107353

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation
Cited by: 70
Author(s): Niklas Berliner, Joan Teyra, Recep Çolak, Sebastian Garcia Lopez, Philip M. Kim
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0252213

Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L.
Cited by: 6
Author(s): Lili Nian, Xuelu Liu, Yingbo Yang, Xiaolin Zhu, Xianfeng Yi, Fasih Ullah Haider
Software Mentions: 2
Published: over 3 years ago

10.1186/s12870-016-0882-5

Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean
Cited by: 34
Author(s): Jing Wu, Lanfen Wang, Shumin Wang
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0250018

Agricultural co-operatives participating in supply chain integration in China: A qualitative comparative analysis
Cited by: 10
Author(s): Jiacheng Zhang, Jianli Luo, Li Jia
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0006202

Regulation of the Drosophila Enhancer of split and invected-engrailed Gene Complexes by Sister Chromatid Cohesion Proteins
Cited by: 100
Author(s): Cheri A. Schaaf, Ziva Misulovin, Gurmukh Sahota, Akbar M. Siddiqui, Yuri B. Schwartz, Tatyana G. Kahn, Vincenzo Pirrotta, Maria Gause, Dale Dorsett
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-7-12

Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies
Cited by: 13
Author(s): Zihua Hu, Gail R. Willsky
Software Mentions: 2
Published: almost 19 years ago

10.1186/s13046-021-02096-1

RNA m6A demethylase FTO-mediated epigenetic up-regulation of LINC00022 promotes tumorigenesis in esophageal squamous cell carcinoma
Cited by: 65
Author(s): Yuanbo Cui, Chunyan Zhang, Shanshan Ma, Zhe Li, Wenjie Wang, Ya Li, Yingchao Ma, Jiarui Fang, Yaping Wang, Wei Cao, Fangxia Guan
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0104651

Genome Analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: A Rhizobacterium That Improves Plant Growth and Stress Management
Cited by: 79
Author(s): Adnan Niazi, Shahid Manzoor, Shashidar Asari, Sarosh Bejai, Johan Meijer, Erik Bongcam‐Rudloff
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0234694

RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management
Cited by: 6
Author(s): Bryson M. F. Sjodin, Robyn L. Irvine, Michael A. Russello
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0099408

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes
Cited by: 16
Author(s): Laura J. Kingsley, Markus A. Lill
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0010126

Discovery of Selective Inhibitors Against EBNA1 via High Throughput In Silico Virtual Screening
Cited by: 58
Author(s): Ning Li, Scott B. Thompson, D. Schultz, Weiliang Zhu, Hualiang Jiang, Cheng Luo, Paul M. Lieberman
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0195971

Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms
Cited by: 33
Author(s): Morteza Seifi, Michael A. Walter
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0200155

Comparative transcriptome analysis provides global insight into gene expression differences between two orchid cultivars
Cited by: 8
Author(s): Jian Yu, Haiyan Song, Jianlin He, Qiang Wang, Jia Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-S4-S6

Feature-based multiple models improve classification of mutation-induced stability changes
Cited by: 13
Author(s): Lukas Folkman, Bela Stantić, Abdul Sattar
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0122294

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites
Cited by: 17
Author(s): Sriparna Datta, Soumik Mukhopadhyay
Software Mentions: 2
Published: over 9 years ago

10.1186/1759-4499-3-3

OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS
Cited by: 1
Author(s): Siu Wai Leung, Xue Ping Quan, Paolo Besana, Qian Li, Mark O. Collins, Dietlind L. Gerloff, David Robertson
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0017459

The Contribution of Coevolving Residues to the Stability of KDO8P Synthase
Cited by: 15
Author(s): Sharon H. Ackerman, Domenico L. Gatti
Software Mentions: 2
Published: over 13 years ago

10.3934/microbiol.2019.4.308

Degradation of poly aromatic fractions of crude oil and detection of catabolic genes in hydrocarbon-degrading bacteria isolated from Agbabu bitumen sediments in Ondo State
Cited by: 21
Author(s): Temitayo O. Olowomofe, J. O. Oluyege, B. I. Aderiye, O. A. Oluwole
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0005905

Genetic and Proteomic Evidence for Roles of Drosophila SUMO in Cell Cycle Control, Ras Signaling, and Early Pattern Formation
Cited by: 119
Author(s): Minghua Nie, Yongming Xie, Joseph A. Loo, Albert J. Courey
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0165374

Antennal Transcriptome and Differential Expression Analysis of Five Chemosensory Gene Families from the Asian Honeybee Apis cerana cerana
Cited by: 19
Author(s): Huiting Zhao, Yali Du, Pengfei Gao, Shujie Wang, Pan JianFang, Yusuo Jiang
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.33442

Decoding the centromeric nucleosome through CENP-N
Cited by: 98
Author(s): Satyakrishna Pentakota, Keda Zhou, Charlotte M. Smith, Stefano Maffini, Arsen Petrovic, Garry Morgan, John R. Weir, Ingrid R. Vetter, Andrea Musacchio, Karolin Luger
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-018-2482-x

Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum
Cited by: 25
Author(s): Manisha Pritam, Garima Singh, Suchit Swaroop, Akhilesh Kumar Singh, Satarudra Prakash Singh
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0029758

Twist1 Directly Regulates Genes That Promote Cell Proliferation and Migration in Developing Heart Valves
Cited by: 40
Author(s): Mary P. Lee, Katherine E. Yutzey
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12918-017-0504-3

CPredictor3.0: detecting protein complexes from PPI networks with expression data and functional annotations
Cited by: 13
Author(s): Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms15069670

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
Cited by: 29
Author(s): Tugba G. Kucukkal, Ye Yang, Steve Chapman, Weiguo Cao, Emil Alexov
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0061556

Better Prognosis of Patients with Glioma Expressing FGF2-Dependent PDGFRA Irrespective of Morphological Diagnosis
Cited by: 11
Author(s): Dongfeng Chen, Annette Persson, Yingyu Sun, Leif G. Salford, David Gisselsson Nord, Elisabet Englund, Tao Jiang, Xiaolong Fan
Software Mentions: 2
Published: over 11 years ago

10.1186/s12917-015-0612-5

Development and validation of an indirect ELISA as a confirmatory test for surveillance of infectious bovine rhinotracheitis in vaccinated herds
Cited by: 14
Author(s): Luigi Bertolotti, Elvira Muratore, Chiara Nogarol, Claudio Caruso, Laura Lucchese, Margherita Profiti, Laura Anfossi, Loretta Masoero, S. Nardelli, Sergio Rosati
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms19124123

High Throughput Chemical Screening Reveals Multiple Regulatory Proteins on FOXA1 in Breast Cancer Cell Lines
Cited by: 7
Author(s): Shixiong Wang, Sachin Kumar Singh, Madhumohan R. Katika, Sandra López-Avilés, Antoni Hurtado
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms20235921

Structure of Staphylococcal Enterotoxin N: Implications for Binding Properties to Its Cellular Proteins
Cited by: 4
Author(s): Chi Zeng, Zhaoxin Liu, Zhenggang Han
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0112969

The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
Cited by: 24
Author(s): Seyed Hanif Mahboobi, Alex A. Javanpour, Mohammad R. K. Mofrad
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0126349

Comprehensive Analysis of a Vibrio parahaemolyticus Strain Extracellular Serine Protease VpSP37
Cited by: 16
Author(s): Monica Salamone, Aldo Nicosia, Carmelo Bennici, Paola Quatrini, Valentina Catania, S. Mazzola, Giulio Ghersi, Angela Cuttitta
Software Mentions: 2
Published: over 9 years ago

10.1016/j.bbamcr.2020.118675

The diversity of ACBD proteins – From lipid binding to protein modulators and organelle tethers
Cited by: 26
Author(s): Markus Islinger, Joseph L. Costello, Suzan Kors, Eric Soupène, Timothy P. Levine, Frans A. Kuypers, Michael Schrader
Software Mentions: 2
Published: over 4 years ago

10.1002/advs.201800420

Fluorination‐Enhanced Ambient Stability and Electronic Tolerance of Black Phosphorus Quantum Dots
Cited by: 65
Author(s): Xian Tang, Hong Chen, Joice Sophia Ponraj, Sathish Chander Dhanabalan, Qiang Xiao, Dianyuan Fan, Han Zhang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0138768

Berry Phenolic Compounds Increase Expression of Hepatocyte Nuclear Factor-1α (HNF-1α) in Caco-2 and Normal Colon Cells Due to High Affinities with Transcription and Dimerization Domains of HNF-1α
Cited by: 15
Author(s): Luis M. Real Hernandez, Jie Fan, Michelle H. Johnson, Elvira González de Mejía
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0214335

Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development
Cited by: 4
Author(s): Anuwat Kumpeangkeaw, Tan D, Lili Fu, Bingying Han, Xiaoyan Sun, Xiaowen Hu, Zehong Ding, Jiaming Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0226106

Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes
Cited by: 13
Author(s): Wen-Rong Wu, Adnane Nemri, Leila M. Blackman, Ann‐Maree Catanzariti, Jana Sperschneider, Gregory J. Lawrence, Peter N. Dodds, David A. Jones, Adrienne R. Hardham
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0145191

Warming and Elevated CO2 Interact to Drive Rapid Shifts in Marine Community Production
Cited by: 17
Author(s): Cascade J. B. Sorte, Matthew E. S. Bracken
Software Mentions: 2
Published: almost 9 years ago

10.3390/biom10040518

A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II
Cited by: 5
Author(s): Steffen Glöckner, A. Heine, G. Klebe
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2105-7-437

STAR: predicting recombination sites from amino acid sequence
Cited by: 6
Author(s): Denis C. Bauer, Mikael Bodén, Ricarda Thier, Elizabeth M. J. Gillam
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0205043

Can Drosophila melanogaster tell who’s who?
Cited by: 18
Author(s): Jonathan Schneider, Nihal Murali, Graham W. Taylor, Joel D. Levine
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms22115630

Prediction of Anticancer Peptides with High Efficacy and Low Toxicity by Hybrid Model Based on 3D Structure of Peptides
Cited by: 7
Author(s): Yuhong Zhao, Shijing Wang, Wenyi Fei, Yongdong Feng, Le Shen, Xinyu Yang, Min Wang, Min Wu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0042490

Gene Profile of Chemokines on Hepatic Stellate Cells of Schistosome-Infected Mice and Antifibrotic Roles of CXCL9/10 on Liver Non-Parenchymal Cells
Cited by: 26
Author(s): Yuejin Liang, Jie Luo, Qiao Lu, Ying Zhou, Hai Wei Wu, Dan Zheng, Yong ya Ren, Ke Sun, Yong Wang, Zhao Song Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0003686

Dysregulation of Mitochondrial Dynamics and the Muscle Transcriptome in ICU Patients Suffering from Sepsis Induced Multiple Organ Failure
Cited by: 138
Author(s): Katarina Fredriksson, Inga Tjäder, Pernille Keller, Nataša Petrovič, B. Ahlman, Camilla Schéele, Jan Wernerman, James A. Timmons, Olav Rooyackers
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0215723

In silico analysis of PFN1 related to amyotrophic lateral sclerosis
Cited by: 9
Author(s): Gabriel Rodrigues Coutinho Pereira, Giovanni Henrique Almeida Silva Tellini, Joelma Freire De Mesquita
Software Mentions: 2
Published: over 5 years ago

10.1186/s12984-017-0312-4

Adaptive hybrid robotic system for rehabilitation of reaching movement after a brain injury: a usability study
Cited by: 18
Author(s): Francisco Resquín, José González-Vargas, Jaime Ibáñez, F. Brunetti, I. Dimbwadyo, Laura Carrasco, Silas Franco dos Reis Alves, Carlos González-Alted, A. Gomez-Blanco, José L. Pons
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0004162

Molecular Time-Course and the Metabolic Basis of Entry into Dauer in Caenorhabditis elegans
Cited by: 57
Author(s): Pan Young Jeong, Min Seok Kwon, Hyoe Jin Joo, Young Ki Paik
Software Mentions: 2
Published: almost 16 years ago

10.1016/j.gpb.2017.03.004

Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis
Cited by: 1
Author(s): Zhining Sa, Jingqi Zhou, Yangyun Zou, Zhixi Su, Xun Gu
Software Mentions: 2
Published: over 7 years ago

10.3390/biom1010003

Comparative Studies of Vertebrate Beta Integrin Genes and Proteins: Ancient Genes in Vertebrate Evolution
Cited by: 8
Author(s): Roger S. Holmes, Ujjwal K. Rout
Software Mentions: 1
Published: about 13 years ago

10.3390/biomedicines9070727

Postnatal Expression Profile of MicroRNAs Associated with Cardiovascular Diseases in 3- to 11-Year-Old Preterm-Born Children
Cited by: 1
Author(s): Ilona Hromadníková, Ladislav Krofta, Jan Širc
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-017-3503-2

An integrated approach with new strategies for QSAR models and lead optimization
Cited by: 5
Author(s): Hui Hui Hsu, Yen Chao Hsu, Li Chang, Jinn-Moon Yang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0118227

Molecular Assessment of Mating Strategies in a Population of Atlantic Spotted Dolphins
Cited by: 4
Author(s): Michelle L. Green, Denise L. Herzing, John W. Baldwin
Software Mentions: 1
Published: almost 10 years ago