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101

SimOS: A Python Framework for Simulations of Optically Addressable Spins
Völker, Laura A. ; Abendroth, John M. ; Degen, Christian L. ; et al.

Quantum Physics Condensed Matter - Mesos... Physics - Chemical Physi... Physics - Computational... Physics - Physics Educat...
Report
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102

ICELLNET v2: a versatile method for cell–cell communication analysis from human transcriptomic data.
Massenet-Regad, Lucile ; Soumelis, Vassili
Bioinformatics. Mar2024, Vol. 40 Issue 3, p1-4. 4p.

CELL communication TRANSCRIPTOMES BIOTIC communities CELL adhesion FAMILY communication TELECOMMUNICATION system... …
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103

FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.
Koutrouli, Mikaela ; Nastou, Katerina ; Líndez, Pau Piera ; et al.
Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-11. 11p.

PROTEIN-protein interact... SOURCE code FUNCTIONAL analysis RNA sequencing
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104

Software Documentation Management In Software Maintenance Phase- A Case Study of A Judicial Operating System in a Court
Yang Ren-Shuen ; Department of Information Science and Applications

Software maintenance Source code documentatio... Java Server Page(JSP) Judicial operating syste... droit
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105

DTCNS: A python toolbox for digital twin-oriented complex networked systems
Wen, Jiaqi ; Gabrys, Bogdan ; Musial, Katarzyna
In SoftwareX September 2024 27

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106

3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations
Beckmann, Irene ; Waldl, Maria ; Will, Sebastian ; et al.
RNA. 30(2):113-123

coarse-grained folding s... steric feasibility folding pathways RNA-RNA interaction RNA-RNA interaction fold... [SDV.BIBS]Life Sciences... …
Zeitschrift
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107

Models and evolution: An introduction to the special issue
Pierantonio, Alfonso ; Schätz, Bernhard
In The Journal of Systems & Software January 2016 111:270-271

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108

Semblans: automated assembly and processing of RNA-seq data.
Woodcock-Girard MD ; Bretz EC ; Robertson HM ; et al.
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

Transcriptome High-Throughput Nucleoti... Computational Biology me... Gene Expression Profilin... Software RNA-Seq methods …
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109

Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space.
Sukumaran J ; Meila M
Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

Computational Biology me... Information Theory Algorithms Genetic Speciation Phylogeny Software
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110

SurfR: Riding the wave of RNA-seq data with a comprehensive bioconductor package to identify surface protein-coding genes.
Maurizio A ; Tascini AS ; Morelli MJ
Publisher: Oxford University Press Country of Publication: England NLM ID: 9918282081306676 Publication Model: eCollection Cited Medium: Internet ISSN: 2635-0041 (Electronic) Linking ISSN: 26350041 NLM ISO Abbreviation: Bioinform Adv Subsets: PubMed not MEDLINE

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111

nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis.
Peltzer, Alexander ; Mohr, Christopher ; Stadermann, Kai B ; et al.
Bioinformatics. Jan2024, Vol. 40 Issue 1, p1-4. 4p.

AMAZON Web Services Inc. AMAZON.COM Inc. GENE expression SOFTWARE development too... SOURCE code QUALITY control …
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112

TransAnnot—a fast transcriptome annotation pipeline.
Zelenskaia, Mariia ; Arangasamy, Yazhini ; Mirdita, Milot ; et al.
Bioinformatics Advances. 2024, Vol. 4 Issue 1, p1-4. 4p.

AMINO acid sequence SOURCE code GENE ontology TRANSCRIPTOMES C++
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113

Meta-analysis of RNA interaction profiles of RNA-binding protein using the RBPInper tool.
Cogan, Joseph A ; Benova, Natalia ; Kuklinkova, Rene ; et al.
Bioinformatics Advances. 2024, Vol. 4 Issue 1, p1-7. 7p.

RNA-binding proteins MULTISENSOR data fusion SOURCE code GLUTAMINE STATISTICS
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114

MMV_Im2Im: an open-source microscopy machine vision toolbox for image-to-image transformation.
Sonneck, Justin ; Zhou, Yu ; Chen, Jianxu
GigaScience. 2024, Vol. 13 Issue 1, p1-20. 20p.

MACHINE learning COMPUTER vision IMAGE analysis DEEP learning RESEARCH personnel
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115

Reproducibility Starts at the Source: R, Python, and Julia Packages for Retrieving USGS Hydrologic Data.
Hodson, Timothy O. ; DeCicco, Laura A. ; Hariharan, Jayaram A. ; et al.
Water (20734441); Dec2023, Vol. 15 Issue 24, p4236, 10p

GEOLOGICAL Survey (U.S.) DATABASES PYTHONS PYTHON programming langu... INFORMATION retrieval WATER quality …
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116

Protein intrinsically disordered regions have a non-random, modular architecture.
McConnell, Brendan S ; Parker, Matthew W
Bioinformatics. Dec2023, Vol. 39 Issue 12, p1-8. 8p.

AMINO acid sequence PROTEINS GLOBULAR proteins SOURCE code PROTEIN domains AMINO acids …
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117

ROCCO: a robust method for detection of open chromatin via convex optimization.
Hamilton, Nolan H ; Furey, Terrence S
Bioinformatics. Dec2023, Vol. 39 Issue 12, p1-10. 10p.

CHROMATIN REGULATOR genes ROBUST statistics CONSTRAINED optimization SOURCE code PHENOTYPES
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118

YaHS: yet another Hi-C scaffolding tool.
Zhou, Chenxi ; McCarthy, Shane A ; Durbin, Richard ; et al.

E-Ressource
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120

string2string: A Modern Python Library for String-to-String Algorithms
Suzgun, Mirac ; Shieber, Stuart M. ; Jurafsky, Dan ; et al.

E-Ressource
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