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1. Full Text MetaSPAdes: A new versatile metagenomic assembler
by Nurk, Sergey and Meleshko, Dmitry and Korobeynikov, Anton and Pevzner, Pavel A
Genome Research, ISSN 1088-9051, 05/2017, Volume 27, Issue 5, pp. 824 - 834
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus... 
BIOCHEMISTRY & MOLECULAR BIOLOGY | ALGORITHMS | SHORT READS | CD-HIT | SINGLE-CELL | DE-NOVO ASSEMBLER | COMMUNITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | LONG READS | DIVERSITY | POLYMORPHIC GENOMES | SEQUENCING DATA | Genome, Bacterial | Software | Genomics - methods | Metagenome | Sequence Analysis, DNA - methods | Contig Mapping - methods | Research | Alternate generation | Biological diversity | Method
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2. Full Text DeepSol: a deep learning framework for sequence-based protein solubility prediction
by Khurana, Sameer and Rawi, Reda and Kunji, Khalid and Chuang, Gwo-Yu and Bensmail, Halima and Mall, Raghvendra
Bioinformatics, ISSN 1367-4803, 08/2018, Volume 34, Issue 15, pp. 2605 - 2613
Abstract Motivation Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | CD-HIT | Original Papers
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3. Full Text Temporary adhesion of the proseriate flatworm Minona ileanae
by Pjeta, R and Wunderer, J and Bertemes, P and Hofer, T and Salvenmoser, W and Lengerer, B and Coassin, S and Erhart, G and Beisel, C and Sobral, D and Kremser, L and Lindner, H and Curini-Galletti, M and Stelzer, CP and Hess, MW and Ladurner, P
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, ISSN 0962-8436, 10/2019, Volume 374, Issue 1784, p. 20190194
Flatworms can very rapidly attach to and detach from many substrates. In the presented work, we analysed the adhesive system of the marine proseriate flatworm... 
RED-SEA | Platyhelminthes | Planaria | PROTEIN | flatworms | BIOLOGY | bioadhesion | GENOME | GLAND | CD-HIT | 1001
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4. Full Text ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
by Ashkenazy, Haim and Abadi, Shiran and Martz, Eric and Chay, Ofer and Mayrose, Itay and Pupko, Tal and Ben-Tal, Nir
Nucleic acids research, ISSN 0305-1048, 07/2016, Volume 44, Issue 1, pp. W344 - W350
The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate... 
RATE-INFERENCE | TRANSFER-RNA FUNCTION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | PROTEIN DATA-BANK | MODEL | FUNCTIONALLY IMPORTANT RESIDUES | MITOCHONDRIAL-DNA | WEB SERVER | AMINO-ACID SUBSTITUTION | CD-HIT | User-Computer Interface | Saccharomyces cerevisiae - genetics | Humans | Phylogeny | RNA - genetics | Saccharomyces cerevisiae - metabolism | Computer Graphics | Plants - genetics | Base Sequence | Escherichia coli - metabolism | Conserved Sequence | Protein Domains | Nucleic Acid Conformation | Amino Acid Sequence | Protein Structure, Secondary | Models, Statistical | RNA - chemistry | Sequence Homology, Nucleic Acid | Biological Evolution | DNA - genetics | Proteins - genetics | Sequence Homology, Amino Acid | DNA - chemistry | Plants - metabolism | Sequence Alignment | Algorithms | Animals | Escherichia coli - genetics | Internet | Proteins - chemistry | Web Server issue
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5. Full Text Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
by McMurdie, Paul J and Holmes, Susan
PLoS ONE, ISSN 1932-6203, 04/2013, Volume 8, Issue 4, p. e61217
Background: The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from... 
BIOINFORMATICS | METAGENOMICS | SERVER | MULTIDISCIPLINARY SCIENCES | SEQUENCE | DIVERSITY | COMMUNITIES | CD-HIT | RESOURCE | TOOLS | Multivariate Analysis | Data Interpretation, Statistical | Humans | Software | Phylogeny | Metagenome | Principal Component Analysis | Sequence Analysis, DNA | Public software | Nucleotide sequencing | Web sites | DNA sequencing | Microbial activity | Taxonomy | Ordination | Multivariate analysis | Gene sequencing | Microorganisms | Packages | Censuses | Computer graphics | Phylogenetics | Genetics | Bioinformatics | Deoxyribonucleic acid--DNA | Hypothesis testing | Medical research | Statistical analysis | Filtration | Data processing | Ecology | Source code | Clustering | Computer programs | Freeware | Census | Production methods | Methods | Deoxyribonucleic acid | DNA
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6. Full Text High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
by Jones, David T and Kandathil, Shaun M
Bioinformatics, ISSN 1367-4803, 10/2018, Volume 34, Issue 19, pp. 3308 - 3315
Abstract Motivation In addition to substitution frequency data from protein sequence alignments, many state-of-the-art methods for contact prediction rely on... 
DIRECT-COUPLING ANALYSIS | RESIDUE CONTACTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | CD-HIT | Original Papers
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7. Full Text WebMGA: A customizable web server for fast metagenomic sequence analysis
by Wu, Sitao and Zhu, Zhengwei and Fu, Liming and Niu, Beifang and Li, Weizhong
BMC Genomics, ISSN 1471-2164, 09/2011, Volume 12, Issue 1, pp. 444 - 444
Background: The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing... 
OCEAN SAMPLING EXPEDITION | MICROBIAL COMMUNITIES | ALIGNMENT | DNA FRAGMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GUT MICROBIOME | GENETICS & HEREDITY | PHYLOGENETIC CLASSIFICATION | RIBOSOMAL-RNA DATABASE | LARGE PROTEIN DATABASES | CD-HIT | RESOURCE | Metagenomics | Computational Biology - methods | Software | Internet | Sequence Analysis, DNA - methods | Cluster Analysis | Usage | Information management | Research | Nucleotide sequence | Analysis | Internet server software | Genomics | Algorithms | Research & development--R&D | Taxonomy | Quality control | Packaging | Cameras | Internet service providers | Web browsers | Programming languages | Methods | Data bases
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8. Full Text Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter
by Žifčáková, Lucia and Větrovský, Tomáš and Howe, Adina and Baldrian, Petr
Environmental Microbiology, ISSN 1462-2912, 01/2016, Volume 18, Issue 1, pp. 288 - 301
Summary Understanding the ecology of coniferous forests is very important because these environments represent globally largest carbon sinks.... 
DE-BRUIJN GRAPHS | SEQUENCES | EXTRACELLULAR ENZYME-ACTIVITIES | LITTER | FUNGAL COMMUNITIES | BOREAL FOREST | MICROBIOLOGY | BACTERIAL | RIBOSOMAL-RNA | IDENTIFICATION | CD-HIT | Forests | Fungi - classification | Soil Microbiology | RNA, Messenger - genetics | Pinaceae - microbiology | Gene Expression Profiling | Archaea - classification | Bacteria - genetics | Fungi - genetics | RNA, Messenger - biosynthesis | Microbiota - genetics | Ecosystem | Mycorrhizae | Bacteria - classification | Soil | Trees - microbiology | Archaea - genetics | Seasons | Transcription, Genetic - genetics | Photosynthesis | Enzymes | Coniferous forests | RNA | Ecosystems | Analysis | Genomics | Soil microbiology | Forest soils | Fungi | Summer
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9. Full Text Reference assembly and gene expression analysis of Apostichopus japonicus larval development
by Boyko, Alexey V and Girich, Alexander S and Eliseikina, Marina G and Maslennikov, Sergey I and Dolmatov, Igor Yu
Scientific Reports, ISSN 2045-2322, 12/2019, Volume 9, Issue 1, pp. 1131 - 11
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages-blastula, gastrula, auricularia, pentactula-on an... 
READ ALIGNMENT | ASPIDOCHIROTA | SEA-CUCUMBER | REGENERATION | MULTIDISCIPLINARY SCIENCES | LARGE-SCALE | METAMORPHOSIS | GENERATION | IDENTIFICATION | TRANSCRIPTOME ANALYSIS | CD-HIT
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10. Full Text Unconventional N-H center dot center dot center dot N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures
by Deepak, RNVK and Sankararamakrishnan, R
BIOPHYSICAL JOURNAL, ISSN 0006-3495, 05/2016, Volume 110, Issue 9, pp. 1967 - 1979
Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically... 
CONTACTS | NMR DETECTION | TRANSMEMBRANE HELICES | BIOPHYSICS | PI INTERACTIONS | AB-INITIO | COMPLEXES | BASIS-SETS | ALPHA-HELICES | CD-HIT | INSIGHTS
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11. Full Text Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp.SRT127
by Nishimura, Y and Shiratori, T and Ishida, K and Hashimoto, T and Ohkuma, M and Inagaki, Y
SCIENTIFIC REPORTS, ISSN 2045-2322, 03/2019, Volume 9
Mitochondrial genomes exhibit diverse features among eukaryotes in the aspect of gene content, genome structure, and the mobile genetic elements such as... 
ORGANIZATION | RNA | DNA | MULTIDISCIPLINARY SCIENCES | SEQUENCE | LINEAR PLASMIDS | DIVERSITY | HELIOZOA | PLANT-MITOCHONDRIA | GROUP-I INTRON | CD-HIT
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12. Full Text Ultrafast clustering algorithms for metagenomic sequence analysis
by Li, Weizhong and Fu, Limin and Niu, Beifang and Wu, Sitao and Wooley, John
Briefings in Bioinformatics, ISSN 1467-5463, 11/2012, Volume 13, Issue 6, pp. 656 - 668
The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various... 
Metagenomics | OTU | Artificial duplicates | Next-generation sequencing | Clustering | Protein families | protein families | next-generation sequencing | BIOCHEMICAL RESEARCH METHODS | FAST PROGRAM | ESTIMATING SPECIES RICHNESS | SHORT READ ALIGNMENT | RARE BIOSPHERE | CD-HIT | OCEAN SAMPLING EXPEDITION | MICROBIAL COMMUNITIES | artificial duplicates | metagenomics | GUT MICROBIOME | MATHEMATICAL & COMPUTATIONAL BIOLOGY | clustering | LARGE PROTEIN DATABASES | WEB SERVER | Algorithms | Metagenome | Sequence Analysis, DNA | Cluster Analysis | Papers
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13. Full Text Antibody interface prediction with 3D Zernike descriptors and SVM
by Daberdaku, S and Ferrari, C
BIOINFORMATICS, ISSN 1367-4803, 06/2019, Volume 35, Issue 11, pp. 1870 - 1876
Motivation: Antibodies are a class of proteins capable of specifically recognizing and binding to a virtually infinite number of antigens. This binding... 
DESIGN | PROTEIN | DOCKING | BIOCHEMICAL RESEARCH METHODS | CHALLENGES | CD-HIT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | REGIONS | PROGRESS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | CANONICAL STRUCTURES | BINDING | NEXT-GENERATION
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14. Full Text Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
by Zhang, Zengming and Li, Yu and Lin, Biaoyang and Schroeder, Michael and Huang, Bingding
Bioinformatics, ISSN 1367-4803, 8/2011, Volume 27, Issue 15, pp. 2083 - 2088
Motivation: Protein-ligand binding sites are the active sites on protein surface that perform protein functions. Thus, the identification of those binding... 
SEQUENCES | BIOCHEMICAL RESEARCH METHODS | POCKETS | TOPOGRAPHY | CD-HIT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SITEHOUND | SERVER | MATHEMATICAL & COMPUTATIONAL BIOLOGY | TARGETS | DRUGGABILITY | COMPUTED ATLAS | CASTP | Protein Structure, Tertiary | Sequence Analysis, Protein - methods | Computational Biology - methods | Models, Molecular | Protein Interaction Mapping | Algorithms | Drug Design | Protein Binding | Ligands | Software | Internet | Proteins - chemistry | Binding Sites
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