Ecosyste.ms: Papers

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago

10.1186/gb-2013-14-2-r16

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Cited by: 104
Author(s): Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A. Tsonis, Thilo Borchardt, Thomas Braun
Software Mentions: 6
Published: over 11 years ago

10.1002/pro.3783

The Dundee Resource for Sequence Analysis and Structure Prediction
Cited by: 11
Author(s): Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Mateusz Warowny, Alexey Drozdetskiy, James B. Procter, Geoffrey J. Barton
Software Mentions: 5
Published: almost 5 years ago

10.1107/S2059798317000031

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode
Cited by: 18
Author(s): Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, Cameron Mura
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1009108

Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis
Cited by: 5
Author(s): Necati Esener, Alexandre Maciel-Guerra, Katharina Giebel, Daniel Lea, Martin J. Green, Andrew J. Bradley, Tania Dottorini
Software Mentions: 5
Published: over 3 years ago

10.1002/mas.21522

The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5
Cited by: 10
Author(s): Manor Askenazi, Hisham Ben Hamidane, Johannes Graumann
Software Mentions: 4
Published: almost 8 years ago

10.15252/msb.20156351

Fundamentals of protein interaction network mapping
Cited by: 211
Author(s): Jamie Snider, Max Kotlyar, Punit Saraon, Zhong Yao, Igor Jurišica, Igor Štagljar
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-12-83

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models
Cited by: 11
Author(s): Juliana Silva Bernardes, Alessandra Carbone, Gerson Zaverucha
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2210-9-4

residues implicated in the formation K+ and Na+ ion channels effector toxins
Cited by: 11
Author(s): Rima Soli, Belhassen Kaabi, Mourad Barhoumi, Mohamed Elayeb, Najet Srairi-Abid
Software Mentions: 4
Published: over 15 years ago

10.1186/1756-0500-3-312

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
Cited by: 4
Author(s): Yves Sucaet, Eve Syrkin Wurtele
Software Mentions: 4
Published: almost 14 years ago

10.1111/pbi.13579

Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species
Cited by: 22
Author(s): Peng Gao, Teagen D. Quilichini, Chun Zhai, Li Qin, Kirby T. Nilsen, Qiang Li, Andrew Sharpe, Leon V. Kochian, Jitao Zou, Anireddy S. N. Reddy, Yangdou Wei, Curtis Pozniak, N. A. Patterson, C. Stewart Gillmor, Raju Datla, Daoquan Xiang
Software Mentions: 4
Published: over 3 years ago

10.1093/database/bau131

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
Cited by: 49
Author(s): José Villaveces, Rafael C. Jiménez, Pablo Porras, Noemi del-Toro, Margaret Duesbury, Marine Dumousseau, Sandra Orchard, Hongyoon Choi, Peipei Ping, Nansu Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-27177-8

Assigning biological function using hidden signatures in cystine-stabilized peptide sequences
Cited by: 5
Author(s): S. M. Ashiqul Islam, Christopher Michel Kearney, Erich J. Baker
Software Mentions: 3
Published: over 6 years ago

10.1074/jbc.M114.621789

Complex Structure and Biochemical Characterization of the Staphylococcus aureus Cyclic Diadenylate Monophosphate (c-di-AMP)-binding Protein PstA, the Founding Member of a New Signal Transduction Protein Family
Cited by: 47
Author(s): Ivan Campeotto, Yong Everett Zhang, Miroslav Mladenov, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-015-0633-x

PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides
Cited by: 24
Author(s): S. M. Ashiqul Islam, Tanvir Sajed, Christopher Michel Kearney, Erich J. Baker
Software Mentions: 3
Published: about 9 years ago

10.1186/1472-6807-8-18

A multi-template combination algorithm for protein comparative modeling
Cited by: 86
Author(s): Jianlin Cheng
Software Mentions: 3
Published: over 16 years ago

10.1186/1472-6807-6-4

Identification of similar regions of protein structures using integrated sequence and structure analysis tools
Cited by: 20
Author(s): Brandon Peters, Charles W. Moad, Eunseog Youn, Kris Buffington, Randy Heiland, Sean D. Mooney
Software Mentions: 3
Published: over 18 years ago

10.1186/s12876-020-01288-x

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer
Cited by: 23
Author(s): Haifeng Lian, Aili Wang, Yuanyuan Shen, Qian Wang, Zijun Zhou, Ranran Zhang, Kun Li, Chengxia Liu, Huiying Jia
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0254555

The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction
Cited by: 3
Author(s): Teng Ruei Chen, Chia Hua Lo, Sheng Hung Juan, Wei Cheng Lo
Software Mentions: 3
Published: about 3 years ago

10.3390/biom8040111

Ceramide Synthase 6: Comparative Analysis, Phylogeny and Evolution
Cited by: 8
Author(s): Roger S. Holmes, Keri Barron, Natalia I. Krupenko
Software Mentions: 2
Published: almost 6 years ago

10.15252/embj.201899543

<scp>FAM</scp> 35A associates with <scp>REV</scp> 7 and modulates <scp>DNA</scp> damage responses of normal and <scp>BRCA</scp> 1‐defective cells
Cited by: 67
Author(s): Junya Tomida, Kei-ichi Takata, Sarita Bhetawal, Maria D. Person, Hsueh-Ping Chao, Dean G. Tang, Richard D. Wood
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-7-462

Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis
Cited by: 7
Author(s): Aijazuddin Syed, Chris Upton
Software Mentions: 2
Published: almost 18 years ago

10.1186/s12864-020-06978-0

ACEP: improving antimicrobial peptides recognition through automatic feature fusion and amino acid embedding
Cited by: 23
Author(s): Hongtuo Fu, Zicheng Cao, Mingyuan Li, Shunfang Wang
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-6-177

Comparative analysis of programmed cell death pathways in filamentous fungi
Cited by: 98
Author(s): Natalie D. Fedorova, Jonathan H. Badger, Geoff Robson, Jennifer Wortman, William C. Nierman
Software Mentions: 2
Published: almost 19 years ago

10.2196/mededu.5950

A Critical Analysis of Anesthesiology Podcasts: Identifying Determinants of Success
Cited by: 17
Author(s): Devin Singh, Fahad Alam, Clyde Matava
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-14-S3-S2

Collective judgment predicts disease-associated single nucleotide variants
Cited by: 189
Author(s): Emidio Capriotti, Russ B. Altman, Yana Bromberg
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2148-7-71

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species
Cited by: 59
Author(s): Radhey S. Gupta, Emily Lorenzini
Software Mentions: 2
Published: over 17 years ago

10.3390/medicina55050195

Preliminary Work Towards Finding Proteins as Potential Vaccine Candidates for Vibrio cholerae Pakistani Isolates through Reverse Vaccinology
Cited by: 3
Author(s): Samia Zeb, Amjad Ali, Sardar Muhammad Gulfam, Habib Bokhari
Software Mentions: 2
Published: over 5 years ago

10.1111/jopy.12380

Becoming who you are: An integrative review of self‐determination theory and personality systems interactions theory
Cited by: 64
Author(s): Sander L. Koole, Caroline Schlinkert, Tobias Maldei, Nicola Baumann
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0206143

Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7
Cited by: 7
Author(s): Masoud Lotfan, Suman Choudhary, Munna Lal Yadav, Sudarshan Kumar, Surender Singh, Shveta Bathla, Preeti Rawat, Jai K. Kaushik, Ashok Kumar Mohanty
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-37647-8

Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins
Cited by: 31
Author(s): Michael J. Mansfield, Travis G. Wentz, Sicai Zhang, Elliot Jeon Lee, Min Dong, Shashi Sharma, Andrew C. Doxey
Software Mentions: 2
Published: over 5 years ago

10.1002/mbo3.463

The first description of a hormone-sensitive lipase from a basidiomycete: Structural insights and biochemical characterization revealed<i>Bjerkandera adusta Ba</i>EstB as a novel esterase
Cited by: 10
Author(s): María del Rayo Sánchez-Carbente, Ramón Alberto Batista-García, Ayixón Sánchez-Reyes, Angela Escudero-Garcia, Catalina Morales-Herrera, Laura I. Cuervo-Soto, Leidys French-Pacheco, Arline Fernández-Silva, Carlos Amero, Edmundo Castillo, Jorge Luis Folch-Mallol
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1000054

Predicting Co-Complexed Protein Pairs from Heterogeneous Data
Cited by: 71
Author(s): Jian Qiu, William Stafford Noble
Software Mentions: 2
Published: over 16 years ago

10.3390/vaccines6010001

Structural Analysis and Epitope Prediction of MHC Class-1-Chain Related Protein-A for Cancer Vaccine Development
Cited by: 16
Author(s): Tayo Alex Adekiya, Raphael Taiwo Aruleba, Sbonelo Khanyile, Priscilla Masamba, Babatunji Emmanuel Oyinloye, Abidemi Paul Kappo
Software Mentions: 2
Published: over 6 years ago

10.1038/srep38860

Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem
Cited by: 42
Author(s): Hansaim Lim, Paul A. Gray, Lei Xie, Aleksandar Poleksić
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1007651

The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing
Cited by: 53
Author(s): Ethel Bayer-Santos, William Cenens, Bruno Y. Matsuyama, Gabriel Umaji Oka, Giancarlo Di Sessa, Izabel Del Valle Mininel, Tiago Lubiana, Chuck S. Farah
Software Mentions: 2
Published: about 5 years ago

10.1093/jamia/ocv001

Development of data representation standards by the human proteome organization proteomics standards initiative
Cited by: 54
Author(s): Eric W. Deutsch, Juan Pablo Albar, Pierre Alain Binz, Martin Eisenacher, Andrew R. Jones, Gerhard Mayer, Gilbert S. Omenn, Sandra Orchard, Juan Antonio Vizcaíno, Henning Hermjakob
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-5-157

Cited by: 33
Author(s): Andrew F. Neuwald, Jun S. Liu
Software Mentions: 2
Published: over 20 years ago

10.1002/pro.3779

ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins
Cited by: 74
Author(s): Adi Ben Chorin, Gal Masrati, Amit Kessel, Aya Narunsky, Josef Sprinzak, Shlomtzion Lahav, Haim Ashkenazy, Nir Ben‐Tal
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.plasmid.2017.03.002

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids
Cited by: 63
Author(s): Alex Orlek, Hang Phan, Anna E. Sheppard, Michel Doumith, Matthew J. Ellington, Tim E. A. Peto, Derrick W. Crook, A Sarah Walker, Neil Woodford, Muna F. Anjum, Nicole Stoesser
Software Mentions: 2
Published: over 7 years ago

10.1186/s40709-015-0032-5

Data integration in biological research: an overview
Cited by: 44
Author(s): Vasileios Lapatas, Michalis Stefanidakis, Rafael C. Jiménez, Allegra Via, Maria Victoria Schneider
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1001210

The Subtilisin-Like Protease AprV2 Is Required for Virulence and Uses a Novel Disulphide-Tethered Exosite to Bind Substrates
Cited by: 77
Author(s): Ruth M. Kennan, Wilson Wong, Om P. Dhungyel, Xiaoyan Han, D. Wong, Dane Parker, Carlos J. Rosado, Ruby H. P. Law, Sheena McGowan, Shane Reeve, Vita Levina, Glenn A. Powers, Robert N. Pike, Stephen P. Bottomley, A. Ian Smith, Ian Marsh, Richard J. Whittington, James C. Whisstock, Corrine Joy Porter, Julian I. Rood
Software Mentions: 2
Published: almost 14 years ago

10.15252/embj.2020106164

Cryo‐EM reveals the complex architecture of dynactin's shoulder region and pointed end
Cited by: 15
Author(s): C.K. Lau, Francis J. O’Reilly, S. Balaji, Samuel E Lacey, Juri Rappsilber, Andrew P. Carter
Software Mentions: 2
Published: over 3 years ago

10.1002/prot.25088

Potential DNA binding and nuclease functions of ComEC domains characterized<i>in silico</i>
Cited by: 22
Author(s): James Alexander Baker, Felix Šimkovic, Helen M.C. Taylor, Daniel J. Rigden
Software Mentions: 2
Published: about 8 years ago

10.3390/ijerph16010054

Exploring Behavior of People with Suicidal Ideation in a Chinese Online Suicidal Community
Cited by: 11
Author(s): Zheng Wang, Guang Yu, Xianyun Tian
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-020-07703-6

Assessment of various continual reassessment method models for dose-escalation phase 1 oncology clinical trials: using real clinical data and simulation studies
Cited by: 3
Author(s): Greg James, Stefan N. Symeonides, Jayne Marshall, J. Young, Glen Clack
Software Mentions: 2
Published: over 3 years ago

10.15252/embj.2020105127

Identification and characterization of diverse OTU deubiquitinases in bacteria
Cited by: 33
Author(s): Alexander F Schubert, Justine Nguyen, Tyler G. Franklin, Paul P. Geurink, Cameron G Roberts, Daniel J. Sanderson, Lauren N. Miller, Huib Ovaa, Kay Hofmann, Jonathan N. Pruneda, David Komander
Software Mentions: 2
Published: about 4 years ago

10.12688/f1000research.27676.2

In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b
Cited by: 6
Author(s): Shahram Mesdaghi, David Murphy, Filomeno Sánchez Rodríguez, José Javier Burgos-Mármol, Daniel J. Rigden
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0003589

FastBLAST: Homology Relationships for Millions of Proteins
Cited by: 14
Author(s): Morgan N. Price, Paramvir Dehal, Adam P. Arkin
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0099492

A 14.7 kDa Protein from Francisella tularensis subsp. novicida (Named FTN_1133), Involved in the Response to Oxidative Stress Induced by Organic Peroxides, Is Not Endowed with Thiol-Dependent Peroxidase Activity
Cited by: 7
Author(s): Diogo de Abreu Meireles, Thiago Gerônimo Pires Alegria, Simone Alves, Carla Rani Rocha Arantes, Luís Eduardo Soares Netto
Software Mentions: 2
Published: about 10 years ago

10.1111/mmi.13485

UAP56 is a conserved crucial component of a divergent mRNA export pathway in<i>Toxoplasma gondii</i>
Cited by: 22
Author(s): Mariana Serpeloni, Elena Jiménez-Ruiz, Newton Medeiros Vidal, Constanze Kroeber, Nicole Andenmatten, Leandro Lemgruber, Patrícia Alves Mörking, Gurman S. Pall, Markus Meissner, Andréa Rodrigues Ávila
Software Mentions: 2
Published: about 8 years ago

10.1186/s12889-017-4750-5

How is the Lives Saved Tool (LiST) used in the global health community? Results of a mixed-methods LiST user study
Cited by: 18
Author(s): Angela Stegmuller, Andrew Self, Kate Litvin, Timothy Roberton
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-13-153

Molecular evolution of dihydrouridine synthases
Cited by: 28
Author(s): J. Kasprzak, Anna Czerwoniec, Janusz M. Bujnicki
Software Mentions: 2
Published: about 12 years ago

10.1038/s42003-021-02543-x

Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding
Cited by: 8
Author(s): Sabeen Survery, Fredrik Hurtig, Syed Razaul Haq, Jens Eriksson, Lionel Guy, K. Johan Rosengren, Ann-Christin Lindås, N. Celestine
Software Mentions: 2
Published: about 3 years ago

10.1002/fsn3.2153

Spectroscopic and in silico investigation of the interaction between GH1 β‐glucosidase and ginsenoside Rb ₁
Cited by: 8
Author(s): Shuning Zhong, Yan Mi, Haifeng Zou, Ping Zhao, Haiqing Ye, Tiehua Zhang, Can Zhao
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0145857

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search
Cited by: 6
Author(s): Matija Korpar, Martin Šošić, Dino Blažeka, Mile Šikić
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-019-3232-4

Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method
Cited by: 8
Author(s): Yao Yao, Yaping Lv, Ling Li, Huimin Xu, Binbin Ji, Jing Chen, Chun Li, Bo Liao, Xuying Nan
Software Mentions: 2
Published: almost 5 years ago

10.1186/1745-6150-7-18

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
Cited by: 390
Author(s): Dapeng Zhang, Robson Francisco de Souza, Vivek Anantharaman, Lakshminarayan M. Iyer, L. Aravind
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2105-10-399

Considering scores between unrelated proteins in the search database improves profile comparison
Cited by: 1
Author(s): Ruslan I. Sadreyev, Yong Wang, Nick V. Grishin
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pcbi.1004705

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Cited by: 19
Author(s): Matthew Oberhardt, Raphy Zarecki, Lea Reshef, Fangfang Xia, Miquel Duran‐Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben‐Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin
Software Mentions: 2
Published: over 8 years ago

10.1186/1756-0381-1-12

A survey of visualization tools for biological network analysis
Cited by: 197
Author(s): Georgios A. Pavlopoulos, Anna-Lynn Wegener, Reinhard Schneider
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0191860

Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives
Cited by: 48
Author(s): Sunniva Katharina Thode, Ewelina Rojek, Michał Kozłowski, Rafi Ahmad, Peik Haugen
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2148-8-316

Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster
Cited by: 29
Author(s): Andrew C. Doxey, Michael Lynch, Kirsten M. Müller, Elizabeth M. Meiering, Brendan J. McConkey
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pcbi.1000132

Protein Complex Evolution Does Not Involve Extensive Network Rewiring
Cited by: 51
Author(s): Teunis J. P. van Dam, Berend Snel
Software Mentions: 2
Published: about 16 years ago

10.1016/j.bbapap.2013.02.017

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
Cited by: 40
Author(s): Gerhard Mayer, Andrew R. Jones, Pierre‐Alain Binz, Eric W. Deutsch, Sandra Orchard, Luisa Montecchi-Palazzi, Juan Antonio Vizcaíno, Henning Hermjakob, David Oveillero, Randall K. Julian, Christian Stephan, Helmut E. Meyer, Martin Eisenacher
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1007339

Multi-state design of flexible proteins predicts sequences optimal for conformational change
Cited by: 16
Author(s): Marion F. Sauer, Alexander M. Sevy, James E. Crowe, Jens Meiler
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0080737

PRICKLE1 Interaction with SYNAPSIN I Reveals a Role in Autism Spectrum Disorders
Cited by: 37
Author(s): Lily Paemka, Vinit B. Mahajan, Jessica M. Skeie, Levi P. Sowers, Salleh N. Ehaideb, Pedro González-Alegre, Toshikuni Sasaoka, Hirotaka Tao, Asuka Miyagi, Naoto Ueno, Keizo Takao, Tsuyoshi Miyakawa, Shu Wu, Benjamin W. Darbro, Polly J. Ferguson, Andrew A. Pieper, Jeremiah K. Britt, John A. Wemmie, Danielle S. Rudd, Thomas H. Wassink, Hatem El‐Shanti, Heather C Mefford, Gemma L. Carvill, J. Robert Manak, Alexander G. Bassuk
Software Mentions: 2
Published: almost 11 years ago

10.3389/fnins.2020.600423

Cortical Thickness in Migraine: A Coordinate-Based Meta-Analysis
Cited by: 10
Author(s): LiQin Sheng, HaiRong Ma, Yuanyuan Shi, Zhenyu Dai, JianGuo Zhong, Fei Chen, PingLei Pan
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-14-427

Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis
Cited by: 62
Author(s): Christian Frech, Nansheng Chen
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-0381-2-8

3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach
Cited by: 8
Author(s): Khader Shameer, Nagarajan Paramasivam, Gaurav Kumar, Ramanathan Sowdhamini
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2148-11-7

Comparative genomics of proteins involved in RNA nucleocytoplasmic export
Cited by: 31
Author(s): Mariana Serpeloni, Newton Medeiros Vidal, Samuel Goldenberg, Andréa Rodrigues Ávila, Federico G. Hoffmann
Software Mentions: 1
Published: over 13 years ago

10.1186/1472-6807-13-24

Quantification of the impact of PSI:Biology according to the annotations of the determined structures
Cited by: 1
Author(s): Paul DePietro, Elchin S. Julfayev, William A. McLaughlin
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2148-9-60

Ancient diversification of eukaryotic MCM DNA replication proteins
Cited by: 75
Author(s): Yuan Liu, Thomas A. Richards, Stephen J. Aves
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-017-1686-9

Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance
Cited by: 21
Author(s): Tsuneo Oda, Kyungtaek Lim, Kentaro Tomii
Software Mentions: 1
Published: over 7 years ago

10.1186/1472-6807-6-8

A tale of two ferredoxins: sequence similarity and structural differences
Cited by: 27
Author(s): S. Sri Krishna, Ruslan I. Sadreyev, Nick V. Grishin
Software Mentions: 1
Published: over 18 years ago

10.1186/1472-6807-7-25

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs
Cited by: 95
Author(s): Ke Chen, Lukasz Kurgan, Jishou Ruan
Software Mentions: 1
Published: over 17 years ago

10.1186/1472-6807-9-54

The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain
Cited by: 8
Author(s): Martial Marbouty, Cyril Saguez, Franck Chauvat
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2148-7-29

Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins
Cited by: 189
Author(s): Vassiliki Lila Koumandou, Joel B. Dacks, Richard M. R. Coulson, Mark C. Field
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-8-356

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
Cited by: 32
Author(s): Jos Boekhorst, Berend Snel
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2458-13-S2-S6

Equity monitoring for social marketing: use of wealth quintiles and the concentration index for decision making in HIV prevention, family planning, and malaria programs
Cited by: 14
Author(s): Nirali M. Chakraborty, Rebecca Firestone, Nicole M. Bellows
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-7-103

Analysis of septins across kingdoms reveals orthology and new motifs
Cited by: 245
Author(s): Fangfang Pan, Russell L. Malmberg, Michelle Momany
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2458-13-S2-S3

Modeling health impact of global health programs implemented by Population Services International
Cited by: 5
Author(s): Hongmei Yang, Susan Duvall, Amy Ratcliffe, David Jeffries, Warren Stevens
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-4-26

Cited by: 10
Author(s): Sachiko Matsutani
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2105-7-124

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
Cited by: 84
Author(s): Jiangning Song, Kevin Burrage, Yawen Zheng, Thomas Huber
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2458-13-S2-S2

Putting health metrics into practice: using the disability-adjusted life year for strategic decision making
Cited by: 9
Author(s): Kim Longfield, Brian K. Smith, Rob Gray, Lek Ngamkitpaiboon, Nadja A. Vielot
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1005038

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence
Cited by: 29
Author(s): Juliana Silva Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2458-13-S2-S4

Applying the disability-adjusted life year to track health impact of social franchise programs in low- and middle-income countries
Cited by: 3
Author(s): Dominic Montagu, Lek Ngamkitpaiboon, Susan Duvall, Amy Ratcliffe
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1001029

Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases
Cited by: 54
Author(s): Robert J. Fieldhouse, Zachari Turgeon, Dawn White, A. Rod Merrill
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2474-15-299

Prediction of poor outcomes six months following total knee arthroplasty in patients awaiting surgery
Cited by: 43
Author(s): Eugen Lungu, François Desmeules, Clermont E. Dionne, Étienne L. Belzile, Pascal‐André Vendittoli
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-7-57

FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Cited by: 195
Author(s): Yanan Yu, Mya Breitbart, Pat McNairnie, Forest Rohwer
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-6-185

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
Cited by: 31
Author(s): Mindaugas Margelevičius, Česlovas Venclovas
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2105-11-204

Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins
Cited by: 16
Author(s): Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert, Michael Schroeder
Software Mentions: 1
Published: over 14 years ago

10.1107/S1744309110013242

New variants of known folds: do they bring new biology?
Cited by: 3
Author(s): Eugene V. Koonin
Software Mentions: 1
Published: about 14 years ago

10.3390/v9110331

Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review
Cited by: 59
Author(s): Graziele Pereira Oliveira, Rodrigo Araújo Lima Rodrigues, Maurício Lima, Betânia Paiva Drumond, Jônatas Santos Abrahão
Software Mentions: 1
Published: almost 7 years ago

10.3390/plants8120587

An Exploration of Common Greenhouse Gas Emissions by the Cyanobiont of the Azolla–Nostoc Symbiosis and Clues as to Nod Factors in Cyanobacteria
Cited by: 6
Author(s): D. Gunawardana
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12891-020-03707-2

Accurate implant fit and leg alignment after cruciate-retaining patient-specific total knee arthroplasty
Cited by: 8
Author(s): Joerg Arnholdt, Yama Kamawal, Konstantin Horas, Boris Michael Holzapfel, Fabian Gilbert, Axel Ripp, Maximilian Rudert, Andre F. Steinert
Software Mentions: 1
Published: almost 4 years ago

10.1093/ve/vez021

Novel hepatitis D-like agents in vertebrates and invertebrates
Cited by: 60
Author(s): Wei-Shan Chang, John H.‐O. Pettersson, Callum Le Lay, Mǎng Shī, Nathan Lo, Michelle Wille, John‐Sebastian Eden, Edward C. Holmes
Software Mentions: 1
Published: about 5 years ago

10.1186/s12985-018-0974-y

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis
Cited by: 59
Author(s): Natalya Yutin, Disa Bäckström, Thijs J. G. Ettema, Mart Krupovìč, Eugene V. Koonin
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2180-5-9

Cited by: 109
Author(s): Mark J. Pallen, Scott A. Beatson, Christopher M. Bailey
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2105-10-S15-S8

Protein subcellular localization prediction of eukaryotes using a knowledge-based approach
Cited by: 33
Author(s): Hsin-Nan Lin, Ching Tai Chen, Ting Yi Sung, Shinn-Ying Ho, Wen Lian Hsu
Software Mentions: 1
Published: almost 15 years ago