pypi: align | Projects | Ecosyste.ms: Papers

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.1371/journal.pcbi.1006457

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
Cited by: 118
Author(s): Weilong Zhao, Xinwei Sher
Software Mentions: 10
Published: almost 6 years ago

10.1186/1472-6807-13-2

Designing and benchmarking the MULTICOM protein structure prediction system
Cited by: 25
Author(s): Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pgen.1004900

An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia
Cited by: 41
Author(s): Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima Sinha, Daniel H. Chitwood
Software Mentions: 7
Published: almost 10 years ago

10.3390/microorganisms9071540

Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth
Cited by: 4
Author(s): Ņikita Zrelovs, Andris Dišlers, Andris Kazāks
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2105-15-167

PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Cited by: 4
Author(s): Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pgen.1006648

Adaptation of A-to-I RNA editing in Drosophila
Cited by: 56
Author(s): Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lü
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2019.00216

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis
Cited by: 78
Author(s): Anna Lundmark, Yue Hu, Mikael Huss, Gunnar Johannsen, Anders F. Andersson, Tülay Yucel‐Lindberg
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giaa088

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
Cited by: 16
Author(s): Eugenie C Yen, Shane McCarthy, Juan A. Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I. Meier, Ian A. Warren, Johanna Mappes, Richard Durbin, Chris D. Jiggins
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-14-156

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti1021
Cited by: 142
Author(s): Jan-Philip Schlüter, Jan Reinkensmeier, Melanie J. Barnett, Claus Lang, Elizaveta Krol, Robert Giegerich, Sharon R. Long, Anke Becker
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-021-07558-6

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)
Cited by: 5
Author(s): Huai‐Jun Xue, Yiwei Niu, Kari A. Segraves, Rui Nie, Ya Jing Hao, Li Li Zhang, Xin Cheng, Xuewen Zhang, Wen Zhu Li, Run Sheng Chen, Xing Yang
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.67578

Sec17/Sec18 can support membrane fusion without help from completion of SNARE zippering
Cited by: 18
Author(s): Hongki Song, Thomas Torng, Amy Orr, Axel T. Brunger, William Wickner
Software Mentions: 4
Published: over 3 years ago

10.3390/nu11061390

Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women
Cited by: 14
Author(s): Anna Ojo-Okunola, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Sugnet Gardner-Lubbe, Dan J. Stein, Heather J. Zar, Mark P. Nicol, Elloise du Toit
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007219

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Cited by: 11
Author(s): Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
Software Mentions: 4
Published: almost 5 years ago

10.3390/microorganisms9081737

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli
Cited by: 8
Author(s): Karla Vasco, Brian Nohomovich, Pallavi Singh, Cristina Venegas-Vargas, Rebekah E. Mosci, S. R. Rust, Paul C. Bartlett, Bo Norby, Daniel L. Grooms, Lixin Zhang, Shannon D. Manning
Software Mentions: 4
Published: about 3 years ago

10.1038/srep31558

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Cited by: 32
Author(s): Camilla Beate Hill, Andrew Cassin, Gabriel Keeble‐Gagnère, Monika S. Doblin, Antony Bacic, Ute Roessner
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-019-40127-2

Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis
Cited by: 7
Author(s): Elisavet Kaitetzidou, Ioanna Katsiadaki, Jacques Lagnel, Efthimia Antonopoulou, Elena Sarropoulou
Software Mentions: 4
Published: over 5 years ago

10.1002/cmdc.201700754

3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery
Cited by: 15
Author(s): Albert J. Kooistra, Márton Vass, Ross McGuire, Rob Leurs, Iwan J. P. de Esch, Gert Vriend, Stefan Verhoeven, Chris de Graaf
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0085611

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
Cited by: 87
Author(s): Paola Piombino, Alessandro Genovese, Sabrina Esposito, Luigi Moio, Pier Paolo Cutolo, Angela Chambery, Valeria Severino, Elisabetta Moneta, Daniel P. Smith, Sarah M. Owens, Jack A. Gilbert, Danilo Ercolini
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-8-416

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information
Cited by: 54
Author(s): Daniel Barthel, Jonathan D. Hirst, Jacek Błażewicz, Edmund K. Burke, Natalio Krasnogor
Software Mentions: 3
Published: about 17 years ago

10.1002/mbo3.312

Evaluation of <scp>DNA</scp> extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
Cited by: 52
Author(s): Katharina Burbach, Jana Seifert, Dietmar H. Pieper, Amélia Camarinha‐Silva
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.3640

Expression differences inAphidius ervi(Hymenoptera: Braconidae) females reared on different aphid host species
Cited by: 11
Author(s): Gabriel I. Ballesteros, Juergen Gadau, Fabrice Legeai, Angélica González-González, Blas Lavandero, Jean Simon, Christian C. Figueroa
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pbio.1000574

Evidence of Activity-Specific, Radial Organization of Mitotic Chromosomes in Drosophila
Cited by: 26
Author(s): Yuri G. Strukov, Tuba Halise Sural, Mitzi I. Kuroda, John W. Sedat
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pcbi.0020057

Predicting Shine–Dalgarno Sequence Locations Exposes Genome Annotation Errors
Cited by: 75
Author(s): Joshua Starmer, Anne-Marie Stomp, Mladen A. Vouk, Donald L. Bitzer
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0218149

RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold
Cited by: 3
Author(s): Clare E. West, Saulo H. P. de Oliveira, Charlotte Deane
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0167524

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels
Cited by: 1
Author(s): Kota Kasahara, Kengo Kinoshita
Software Mentions: 3
Published: almost 8 years ago

10.3390/genes11080876

Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population
Cited by: 8
Author(s): Fatma Al‐Jasmi, Ranjit Vijayan, Naganeeswaran Sudalaimuthuasari, Abdul‐Kader Souid, Noushad Karuvantevida, Raja S. AlMaskari, Hidaya Mohammed Abdul Kader, Biduth Kundu, Khaled M. Hazzouri, Khaled M. A. Amiri
Software Mentions: 3
Published: over 4 years ago

10.1155/2013/467852

Evaluating the Immunogenicity of Protein Drugs by ApplyingIn VitroMHC Binding Data and the Immune Epitope Database and Analysis Resource
Cited by: 48
Author(s): Sinu Paul, Ravi V. Kolla, John Sidney, Daniela Weiskopf, Ward Fleri, Young S. Kim, Bjoern Peters, Alessandro Sette
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12870-018-1594-9

Transciptome profiling at early infection of Elaeis guineensis by Ganoderma boninense provides novel insights on fungal transition from biotrophic to necrotrophic phase
Cited by: 27
Author(s): Mohammad Nazri Abdul Bahari, Nurshafika Mohd Sakeh, Siti Nor Akmar Abdullah, Redzyque Ramza Ramli, Saeid Kadkhodaei
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0020889

The Significance of the ProtDeform Score for Structure Prediction and Alignment
Cited by: 1
Author(s): Jairo Rocha, Ricardo Alberich
Software Mentions: 2
Published: over 13 years ago

10.12688/f1000research.10336.2

Validation of commercially available sphingosine kinase 2 antibodies for use in immunoblotting, immunoprecipitation and immunofluorescence
Cited by: 1
Author(s): Heidi A. Neubauer, Stuart M. Pitson
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-7-140

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences
Cited by: 34
Author(s): George E. Liu, Lakshmi K. Matukumalli, Tad S. Sonstegard, Larry L Shade, Curtis P. Van Tassell
Software Mentions: 2
Published: over 18 years ago

10.1128/mSystems.00076-18

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
Cited by: 168
Author(s): Gareth Trubl, Ho Bin Jang, Simon Roux, Joanne B. Emerson, Natalie Solonenko, Dean Vik, Lindsey Solden, Jared Ellenbogen, Alexander T. Runyon, Benjamin Bolduc, Ben J. Woodcroft, S. R. Saleska, Gene W. Tyson, Kelly Wrighton, Matthew B. Sullivan, V. I. Rich
Software Mentions: 2
Published: about 6 years ago

10.1002/mgg3.1479

Multimodal imaging and genetic characteristics of Chinese patients with USH2A ‐associated nonsyndromic retinitis pigmentosa
Cited by: 4
Author(s): Chong Chen, Qiao Sun, Meng Gu, Tianwei Qian, Da Luo, Kun Liu, Xun Xu, Shizhu Yu
Software Mentions: 2
Published: about 4 years ago

10.1186/s40168-017-0241-2

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees
Cited by: 316
Author(s): Bram Beckers, Michiel Op De Beeck, Nele Weyens, Wout Boerjan, Jaco Vangronsveld
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0184307

Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages
Cited by: 6
Author(s): Damian Magill, В. Н. Крылов, О. В. Шабурова, John W. McGrath, Christopher C. R. Allen, John P. Quinn, Leonid Kulakov
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1007411

Detecting distant-homology protein structures by aligning deep neural-network based contact maps
Cited by: 42
Author(s): Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.709534

Genome-Wide Identification and Comparison of Cysteine Proteases in the Pollen Coat and Other Tissues in Maize
Cited by: 2
Author(s): Yanhua Li, Liangjie Niu, Xiaolin Wu, Claudia Faleri, Fuju Tai, Man Zhang, Hui Liu, Wei Wang, Giampiero Cai
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-8-238

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
Cited by: 477
Author(s): Morten Nielsen, Claus Lundegaard, Ole Lund
Software Mentions: 2
Published: over 17 years ago

10.1186/1472-6807-13-32

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Cited by: 8
Author(s): Manuel Rueda, Modesto Orozco, Maxim Totrov, Ruben Abagyan
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1000107

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
Cited by: 240
Author(s): Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
Software Mentions: 2
Published: over 16 years ago

10.7554/eLife.39705

Molecular function limits divergent protein evolution on planetary timescales
Cited by: 24
Author(s): Mariam M. Konaté, Germán Plata, Jimin Park, Dinara R. Usmanova, Harris H. Wang, Dennis Vitkup
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0168271

Identification of a Novel Homozygous Nonsense Mutation Confirms the Implication of GNAT1 in Rod-Cone Dystrophy
Cited by: 15
Author(s): Cécile Méjécase, Caroline Laurent-Coriat, Claudine Mayer, Olivier Poch, Saddek Mohand‐Saïd, Camille Prévot, Antonio Arnaiz‐Villena, Fiona Boyard, Christel Condroyer, Christelle Michiels, Steven G. Blanchard, Mélanie Letexier, Jean‐Paul Saraiva, José‐Alain Sahel, Isabelle Audo, Christina Zeitz
Software Mentions: 2
Published: almost 8 years ago

10.1073/pnas.2010644118

Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies
Cited by: 12
Author(s): Rajasree Kalagiri, Robyn L. Stanfield, Jill Meisenhelder, James J. La Clair, Stephen R. Fuhs, Ian A. Wilson, Tony Hunter
Software Mentions: 2
Published: over 3 years ago

10.1038/srep12501

Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding
Cited by: 52
Author(s): Linling He, Yuan Cheng, Leopold Kong, P. Azadnia, Erick Giang, Justin Kim, Malcolm R. Wood, Ian A. Wilson, Mansun Law, Jiang Zhu
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-019-3235-1

MADOKA: an ultra-fast approach for large-scale protein structure similarity searching
Cited by: 18
Author(s): Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu
Software Mentions: 2
Published: almost 5 years ago

10.1128/MRA.00697-20

Genome Sequences of SARS-CoV-2 Strains Detected in Hong Kong
Cited by: 5
Author(s): Chun Hang Au, Wai Sing Chan, Ho Yin Lam, Dona N. Ho, Simon Y. M. Lam, Jonpaul Sze-Tsing Zee, Tsun Leung Chan, S. K. Edmond
Software Mentions: 2
Published: over 4 years ago

10.1186/s13062-021-00291-w

Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites
Cited by: 9
Author(s): Birgit Eisenhaber, Swati Sinha, Chaitanya K. Jadalanki, Vladimir A. Shitov, Qiao Wen Tan, Fernanda L. Sirota, Frank Eisenhaber
Software Mentions: 2
Published: almost 4 years ago

10.3390/biom11091392

The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis
Cited by: 2
Author(s): Agustín Rico-Díaz, Aída Barreiro-Alonso, Cora Rey-Souto, Manuel Becerra, Mónica Lamas-Maceiras, M. Esperanza Cerdán, Ángel Vizoso-Vázquez
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2164-12-636

Employing machine learning for reliable miRNA target identification in plants
Cited by: 32
Author(s): Ashwani Jha, Ravi Shankar
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-019-3086-9

GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
Cited by: 29
Author(s): Nauman Ahmed, Jonathan Lévy, Siying Ren, Hamid Mushtaq, Koen Bertels, Zaid Al-Ars
Software Mentions: 2
Published: about 5 years ago

10.1002/mbo3.356

Spatial and temporal variability of bacterial communities within a combined sewer system
Cited by: 3
Author(s): Henriette Stokbro Jensen, Raju Sekar, Will Shepherd, A. Mark Osborn, Simon Tait, Catherine A. Biggs
Software Mentions: 2
Published: over 8 years ago

10.1002/mbo3.463

The first description of a hormone-sensitive lipase from a basidiomycete: Structural insights and biochemical characterization revealedBjerkandera adusta BaEstB 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

10.1186/s12936-018-2539-3

Population genetic structure of domain I of apical membrane antigen-1 in Plasmodium falciparum isolates from Hazara division of Pakistan
Cited by: 2
Author(s): Sahib Gul Afridi, Muhammad Irfan, Habib Ahmad, Muneeba Aslam, Mehwish Nawaz, Muhammad Ilyas, Asifullah Khan
Software Mentions: 1
Published: about 6 years ago

10.6026/97320630015131

Insights from the molecular docking analysis of phytohormone reveal brassinolide interaction with HSC70 from Pennisetum glaucum
Cited by: 7
Author(s): Gugulothu Baloji, Shobharani Pasham, Vinodha Mahankali, G. B. Mallikarjuna, Srinivas Ankanagari
Software Mentions: 1
Published: over 5 years ago

10.1111/mpp.13045

A haustorial‐expressed lytic polysaccharide monooxygenase from the cucurbit powdery mildew pathogen Podosphaera xanthii contributes to the suppression of chitin‐triggered immunity
Cited by: 20
Author(s): Álvaro Polonio, Dolores Fernández-Ortuño, Antonio de Vicente, Alejandro Pérez-Garcı́a
Software Mentions: 1
Published: over 3 years ago

10.3897/zookeys.549.6171

Phylogenetic placement of the unusual jumping spider Depreissia Lessert, and a new synapomorphy uniting Hisponinae and Salticinae (Araneae, Salticidae)
Cited by: 9
Author(s): Wayne P. Maddison, David R. Maddison, Junxia Zhang, Tamás Szűts
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-020-64039-8

Bidirectional competitive interactions between motor memory and declarative memory during interleaved learning
Cited by: 4
Author(s): Sungshin Kim
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2229-8-45

Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens
Cited by: 330
Author(s): Jonas Å. H. Danielson, Urban Johanson
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12870-020-02812-7

EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense
Cited by: 4
Author(s): Nurshafika Mohd Sakeh, Siti Nor Akmar Abdullah, Mohammad Nazri Abdul Bahari, Azzreena Mohamad Azzeme, Noor Azmi Shaharuddin, Abu Seman Idris
Software Mentions: 1
Published: almost 4 years ago

10.1186/s43141-021-00125-2

Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental
Cited by: 8
Author(s): Preeti Anand, Jay Prakash Pandey, Dev Mani Pandey
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-7-256

An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
Cited by: 13
Author(s): Henrik Nielsen, Rasmus Wernersson
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pone.0021564

PP13, Maternal ABO Blood Groups and the Risk Assessment of Pregnancy Complications
Cited by: 43
Author(s): Nándor Gábor Than, Roberto Romero, Hamutal Meiri, Offer Erez, Yi Xu, Federica Tarquini, L Barna, András Szilágyi, Ron Ackerman, Marei Sammar, Tibor Füle, Katalin Karászi, Ilona Kovalszky, Zhong Dong, Chong Jai Kim, Péter Závodszky, Zoltán Papp, Ron Gonen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0061033

CGAP-Align: A High Performance DNA Short Read Alignment Tool
Cited by: 6
Author(s): Yaoliang Chen, Ji Hyung Hong, Wanyun Cui, Jacques Zaneveld, Wei Wang, Richard A. Gibbs, Yanghua Xiao, Rui Chen
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-015-0693-y

Amplitude spectrum distance: measuring the global shape divergence of protein fragments
Cited by: 1
Author(s): Clovis Galiez, F Coste
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0049284

Applying Ligands Profiling Using Multiple Extended Electron Distribution Based Field Templates and Feature Trees Similarity Searching in the Discovery of New Generation of Urea-Based Antineoplastic Kinase Inhibitors
Cited by: 7
Author(s): Eman M.E. Dokla, Abeer E. Mahmoud, Mohamed S.A. Elsayed, Ahmed H. El‐Khatib, Michael Linscheid, Khaled A. M. Abouzid
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0161254

A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive
Cited by: 3
Author(s): Ren-Bin Zhou, Hui‐Meng Lu, Jie Liu, Jian-Yu Shi, Jing Zhu, Qi Lu, Da‐Chuan Yin
Software Mentions: 1
Published: about 8 years ago

10.1099/acmi.0.000034

Ocins database: a database of bug-busters from Bifidobacterium, Lactobacillus, and Enterococcus
Cited by: 5
Author(s): Shilja Choyam, Suresh Psn, Rahul Pandey, Kammara Rajagopal
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-8-398

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time
Cited by: 13
Author(s): Dorota Retelska, Emmanuel Beaudoing, Cédric Notredame, C. Victor Jongeneel, Philipp Bücher
Software Mentions: 1
Published: almost 18 years ago

10.1016/j.csbj.2017.01.011

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions
Cited by: 19
Author(s): Seyed Morteza Najibi, Mehdi Maadooliat, Lan Zhou, Jianhua Z. Huang, Xin Gao
Software Mentions: 1
Published: almost 8 years ago

10.1038/s12276-019-0371-7

TGF-β1/IL-11/MEK/ERK signaling mediates senescence-associated pulmonary fibrosis in a stress-induced premature senescence model of Bmi-1 deficiency
Cited by: 67
Author(s): Haiyun Chen, Hongjie Chen, Jinsong Liang, Xiaohong Gu, Jiahui Zhou, Chunfeng Xie, Xuemei Lv, Rong Wang, Qing Li, Zhiyuan Mao, Hai-Jian Sun, Guo‐Wei Zuo, Dengshun Miao, Jianliang Jin
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-15-S4-S2

The structural network of Interleukin-10 and its implications in inflammation and cancer
Cited by: 54
Author(s): Saliha Ece Acuner-Ozbabacan, Billur Hatice Engin, Emine Guven-Maiorov, Guray Kuzu, Serena Muratcioğlu, Alper Baspinar, Zhong Chen, Carter Van Waes, Attila Gürsoy, Özlem Keskin, Ruth Nussinov
Software Mentions: 1
Published: over 10 years ago

10.3389/fchem.2020.00081

A Pilot Study of All-Computational Drug Design Protocol–From Structure Prediction to Interaction Analysis
Cited by: 7
Author(s): Yifei Wu, Lei Lou, Zhong‐Ru Xie
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2019.01342

Biochemical Characterization of a Novel Monospecific Endo-β-1,4-Glucanase Belonging to GH Family 5 From a Rhizosphere Metagenomic Library
Cited by: 19
Author(s): Anna Wierzbicka-Woś, Ruth Henneberger, Ramón Alberto Batista-García, Liliana Martínez-Ávila, Stephen A. Jackson, Jonathan Kennedy, Alan D. W. Dobson
Software Mentions: 1
Published: over 5 years ago

10.3389/fninf.2020.00018

Beware (Surprisingly Common) Left-Right Flips in Your MRI Data: An Efficient and Robust Method to Check MRI Dataset Consistency Using AFNI
Cited by: 15
Author(s): Daniel Glen, Paul A. Taylor, Bradley R. Buchsbaum, Robert W. Cox, Richard C. Reynolds
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2019.01244

Novel Informatic Tools to Support Functional Annotation of the Durum Wheat Genome
Cited by: 5
Author(s): Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis Pozniak, Penny J. Tricker, Ute Baumann
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-13-292

Effective inter-residue contact definitions for accurate protein fold recognition
Cited by: 42
Author(s): Chao Yuan, Hao Chen, Daisuke Kihara
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13099-019-0317-6

Recombinant fusion protein of Heparin-Binding Hemagglutinin Adhesin and Fibronectin Attachment Protein (rHBHA-FAP) of Mycobacterium avium subsp. paratuberculosis elicits a strong gamma interferon response in peripheral blood mononuclear cell culture
Cited by: 5
Author(s): Vida Eraghi, Abdollah Derakhshandeh, Ahmad Hosseini, Masoud Haghkhah, Leonardo Antonio Sechi, Azar Motamedi Boroojeni
Software Mentions: 1
Published: over 5 years ago

10.1007/s10822-013-9640-z

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor
Cited by: 3
Author(s): Marcus Malo, Ronnie Persson, Peder Svensson, Kristina Luthman, Lars Brive
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1000634

Evolutionary Dynamics of Human Rotaviruses: Balancing Reassortment with Preferred Genome Constellations
Cited by: 174
Author(s): Sarah McDonald, Jelle Matthijnssens, John K. McAllen, Erin Hine, Larry Overton, Shiliang Wang, Philippe Lemey, Mark Zeller, Marc Van Ranst, David Spiro, John T. Patton
Software Mentions: 1
Published: about 15 years ago

Projects: pypi: align

Papers Mentioning align 80