Search Results

PyCoMo: a python package for community metabolic model creation and analysis.

• Authors : Predl, Michael^1,2 (AUTHOR); Mießkes, Marianne^3,4 (AUTHOR); Rattei, Thomas^1,2 (AUTHOR)

Subjects: *METABOLIC models; *SYNTROPHISM; *BIOGASMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Apr2024, Vol. 40 Issue 4, p1-4. 4p.

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GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data.

• Authors : Odle, Eric¹ (AUTHOR) ; Kahng, Samuel^2,3 (AUTHOR); Riewluang, Siratee¹ (AUTHOR)

Subjects: *INFORMATION superhighway; *INTERNATIONAL agencies; *PYTHON programming languageMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Apr2024, Vol. 40 Issue 4, p1-4. 4p.

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CLAUDIO: automated structural analysis of cross-linking data.

• Authors : Röhl, Alexander^1,2 (AUTHOR); Netz, Eugen^1,2 (AUTHOR); Kohlbacher, Oliver^1,2,3 (AUTHOR)

Subjects: *DATA analysis; *PROTEIN structure; *SOFTWARE development toolsMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Apr2024, Vol. 40 Issue 4, p1-4. 4p.

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GPro: generative AI-empowered toolkit for promoter design.

• Authors : Wang, Haochen^1,2,3,4 (AUTHOR); Du, Qixiu^1,2,3,4 (AUTHOR); Wang, Ye^1,2,3,4 (AUTHOR)

Subjects: *GENERATIVE artificial intelligence; *SOURCE code; *RESEARCH personnelMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Mar2024, Vol. 40 Issue 3, p1-4. 4p.

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EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow.

• Authors : Yu, Yiyang¹ (AUTHOR); Muthukumar, Shivani² (AUTHOR); Koo, Peter K¹ (AUTHOR)

Subjects: *ARTIFICIAL neural networks; *DATA augmentation; *DEEP learningMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Mar2024, Vol. 40 Issue 3, p1-4. 4p.

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Bioframe: operations on genomic intervals in Pandas dataframes.

• Authors : Abdennur, Nezar^1,2 (AUTHOR) ; Fudenberg, Geoffrey³ (AUTHOR) ; Flyamer, Ilya M⁴ (AUTHOR)

Subjects: *INTERVAL analysis; *DATA structures; *COMPUTATIONAL biologyMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.

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VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs.

• Authors : Charron, Philippe¹ (AUTHOR) ; Kang, Mingsong¹ (AUTHOR)

Subjects: *SINGLE nucleotide polymorphisms; *SPECIES diversity; *BACTERIAL evolutionMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.

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vcfpp: a C++ API for rapid processing of the variant call format.

• Authors : Li, Zilong¹ (AUTHOR)

Subjects: *C++; *PROGRAMMING languages; *BIG dataMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.

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Scbean: a python library for single-cell multi-omics data analysis.

• Authors : Zhang, Haohui¹ (AUTHOR); Wang, Yuwei¹ (AUTHOR); Lian, Bin¹ (AUTHOR)

Subjects: *MULTIOMICS; *DATA analysis; *ENGINEERING modelsMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.

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GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function.

• Authors : Miller, Danielle¹ (AUTHOR); Arias, Ofir¹ (AUTHOR); Burstein, David¹ (AUTHOR)

Subjects: *MICROBIAL genes; *LANGUAGE models; *WEB-based user interfacesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2024, Vol. 40 Issue 2, p1-4. 4p.

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FLAMS: Find Lysine Acylations and other Modification Sites.

• Authors : Longin, Hannelore^1,2 (AUTHOR); Broeckaert, Nand^1,2 (AUTHOR); Langen, Maarten¹ (AUTHOR)

Subjects: *LYSINE; *POST-translational modification; *WEB servicesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jan2024, Vol. 40 Issue 1, p1-4. 4p.

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CellularPotts.jl: simulating multiscale cellular models in Julia.

• Authors : Gregg, Robert W^1,2,3 (AUTHOR) ; Benos, Panayiotis V^1,2,3 (AUTHOR)

Subjects: *MULTISCALE modeling; *PHENOMENOLOGICAL biology; *POTTS modelMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jan2024, Vol. 40 Issue 1, p1-3. 3p.

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Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing.

• Authors : Morrison, Jacob¹ (AUTHOR) ; Zhou, Wanding^2,3 (AUTHOR); Johnson, Benjamin K¹ (AUTHOR)

Subjects: *WHOLE genome sequencing; *NUCLEOTIDE sequencing; *POLYMERASE chain reactionMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Dec2023, Vol. 39 Issue 12, p1-4. 4p.

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Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.

• Authors : Larsson, Ludvig¹ (AUTHOR); Franzén, Lovisa^1,2 (AUTHOR); Ståhl, Patrik L¹ (AUTHOR)

Subjects: *DATA visualization; *WEB-based user interfaces; *GENE expressionMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Oct2023, Vol. 39 Issue 10, p1-4. 4p.

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phippery: a software suite for PhIP-Seq data analysis.

• Authors : Galloway, Jared G¹ (AUTHOR); Sung, Kevin¹ (AUTHOR); Minot, Samuel S² (AUTHOR)

Subjects: *MULTIDIMENSIONAL scaling; *INTEGRATED software; *COMPUTER softwareMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Oct2023, Vol. 39 Issue 10, p1-2. 2p.

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BondGraphs.jl: composable energy-based modelling in systems biology.

• Authors : Forrest, Joshua^1,2,3 (AUTHOR); Rajagopal, Vijay^3,4,5 (AUTHOR); Stumpf, Michael P H^1,2,6,7 (AUTHOR)

Subjects: *BOND graphs; *SOURCE code; *SYSTEMS biologyPLOVDIV (Bulgaria)MASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Oct2023, Vol. 39 Issue 10, p1-4. 4p.

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In Memoriam Emmanuel Farhi.

Subjects: *INTERNATIONAL finance; *INTERNATIONAL competition; *INTERMEDIATION (Finance)MASSACHUSETTS Institute of Technology

• Source: Review of Economic Studies. Nov2021, Vol. 88 Issue 6, p2567-2569. 3p. 1 Color Photograph.

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Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.

• Authors : He, Xin¹ (AUTHOR); Huang, Xianhui¹ (AUTHOR); Long, Yuexuan¹ (AUTHOR)

Subjects: *GENOMICS; *GENOMES; *GENE expressionMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Sep2023, Vol. 39 Issue 9, p1-4. 4p.

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PyDESeq2: a python package for bulk RNA-seq differential expression analysis.

• Authors : Muzellec, Boris¹ (AUTHOR) ; Teleńczuk, Maria¹ (AUTHOR); Cabeli, Vincent¹ (AUTHOR)

Subjects: *RNA sequencing; *PYTHON programming language; *SOURCE codeMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Sep2023, Vol. 39 Issue 9, p1-3. 3p.

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Tracking and curating putative SARS-CoV-2 recombinants with RIVET.

• Authors : Smith, Kyle¹ (AUTHOR); Ye, Cheng² (AUTHOR); Turakhia, Yatish² (AUTHOR)

Subjects: *SARS-CoV-2; *RIVETS & riveting; *DATABASESMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Sep2023, Vol. 39 Issue 9, p1-3. 3p.

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DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data.

• Authors : Feng, Zhenhuan^1,2 (AUTHOR); Fang, Peiyang³ (AUTHOR); Zheng, Hui^1,2,4 (AUTHOR)

Subjects: *PROTEOMICS; *QUANTITATIVE research; *MASS spectrometryMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Aug2023, Vol. 39 Issue 8, p1-4. 4p.

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crosshap: R package for local haplotype visualization for trait association analysis.

• Authors : Marsh, Jacob I^1,2 (AUTHOR); Petereit, Jakob^1,2 (AUTHOR); Johnston, Brady A³ (AUTHOR)

Subjects: *HAPLOTYPES; *GENOME-wide association studies; *DATA visualizationMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Aug2023, Vol. 39 Issue 8, p1-4. 4p.

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AARDVARK: an automated reversion detector for variants affecting resistance kinetics.

• Authors : Moreno, Thaidy¹ (AUTHOR); Magana, Joaquin² (AUTHOR); Quigley, David A^1,3,4 (AUTHOR)

Subjects: *DNA mismatch repair; *DNA repair; *NUCLEOTIDE sequenceMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Aug2023, Vol. 39 Issue 8, p1-3. 3p.

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MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.

• Authors : Zeng, Yong¹ (AUTHOR) ; Ye, Wenbin¹ (AUTHOR); Stutheit-Zhao, Eric Y¹ (AUTHOR)

Subjects: *CELL-free DNA; *DATA quality; *QUALITY controlMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jul2023, Vol. 39 Issue 7, p1-3. 3p.

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McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

• Authors : Li, Lun¹ (AUTHOR); Xu, Bo¹ (AUTHOR); Tian, Dongmei¹ (AUTHOR)

Subjects: *INTERNET servers; *ALGORITHMS; HAPLOTYPESMASSACHUSETTS Institute of Technology

• Source: Briefings in Bioinformatics. May2023, Vol. 24 Issue 3, p1-9. 9p.

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Cellenium—a scalable and interactive visual analytics app for exploring multimodal single-cell data.

• Authors : Jahn, Carsten¹ (AUTHOR); Ibrahim, Mahmoud² (AUTHOR); Busch, Jannis¹ (AUTHOR)

Subjects: *VISUAL analytics; *WEB analytics; *WEB-based user interfacesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jun2023, Vol. 39 Issue 6, p1-3. 3p.

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GIL: a python package for designing custom indexing primers.

• Authors : Mateyko, Nicholas¹ (AUTHOR); Tariq, Omar¹ (AUTHOR); Chen, Xinyi E¹ (AUTHOR)

Subjects: *PACKAGING design; *CUSTOM design; *PYTHON programming languageMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jun2023, Vol. 39 Issue 6, p1-3. 3p.

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NanoPack2: population-scale evaluation of long-read sequencing data.

• Authors : Coster, Wouter De^1,2 (AUTHOR) ; Rademakers, Rosa^1,2 (AUTHOR)

Subjects: *COMPUTER software quality control; *SOFTWARE upgrades; *ELECTRONIC data processingMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. May2023, Vol. 39 Issue 5, p1-3. 3p.

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PyHMMER: a Python library binding to HMMER for efficient sequence analysis.

• Authors : Larralde, Martin¹ (AUTHOR) ; Zeller, Georg¹ (AUTHOR)

Subjects: *SEQUENCE analysis; *PYTHON programming language; *AMINO acid sequenceMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. May2023, Vol. 39 Issue 5, p1-3. 3p.

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nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

• Authors : Guizard, Sébastien¹ (AUTHOR) ; Miedzinska, Katarzyna¹ (AUTHOR); Smith, Jacqueline¹ (AUTHOR)

Subjects: *ANNOTATIONS; *NUCLEOTIDE sequencing; *GENESMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. May2023, Vol. 39 Issue 5, p1-2. 2p.

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streammd: fast low-memory duplicate marking using a Bloom filter.

• Authors : Leonard, Conrad¹ (AUTHOR)

Subjects: *SEQUENCE analysis; *C++MASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Apr2023, Vol. 39 Issue 4, p1-3. 3p.

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WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)—a web application for visualization of wastewater pathogen sequencing results.

• Authors : Triska, Petr^1,2 (AUTHOR); Amman, Fabian^1,2 (AUTHOR); Endler, Lukas^1,2 (AUTHOR)

Subjects: *SARS-CoV-2; *ENVIRONMENTAL sampling; *WEB-based user interfacesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Apr2023, Vol. 39 Issue 4, p1-2. 2p.

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Chemical modification of Arthrobacter sarcosine oxidase by N-methylisothiazolinone reduces reactivity toward oxygen.

• Authors : Toyama, Fuka¹ (AUTHOR); Kimura, Hironori² (AUTHOR); Zhang, Yuqi¹ (AUTHOR)

Subjects: *ARTHROBACTER; *CHEMICAL properties; *SULFHYDRYL groupMASSACHUSETTS Institute of Technology

• Source: Bioscience, Biotechnology & Biochemistry. Jun2024, Vol. 88 Issue 6, p630-636. 7p.

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CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.

• Authors : Kurt, Semih¹ (AUTHOR) ; Chen, Mandi¹ (AUTHOR) ; Toosi, Hosein¹ (AUTHOR)

Subjects: *TRANSCRIPTOMES; *RNA sequencing; *DEEP learningMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. May2024, Vol. 40 Issue 5, p1-9. 9p.

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PATO: genome-wide prediction of lncRNA–DNA triple helices.

• Authors : Amatria-Barral, Iñaki¹ (AUTHOR) ; González-Domínguez, Jorge¹ (AUTHOR); Touriño, Juan¹ (AUTHOR)

Subjects: *LINCRNA; *PROCESS capability; *SOURCE codeMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Mar2023, Vol. 39 Issue 3, p1-3. 3p.

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genomepy: genes and genomes at your fingertips.

• Authors : Frölich, Siebren¹ (AUTHOR) ; van der Sande, Maarten¹ (AUTHOR); Schäfers, Tilman¹ (AUTHOR)

Subjects: *FUNCTIONAL genomics; *GENES; *REFERENCE sourcesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Mar2023, Vol. 39 Issue 3, p1-3. 3p.

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Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.

• Authors : L'Yi, Sehi¹ (AUTHOR); Keller, Mark S¹ (AUTHOR); Dandawate, Ariaki² (AUTHOR)

Subjects: *INTERNET servers; *SOFTWARE analytics; *VISUAL analyticsMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Feb2023, Vol. 39 Issue 2, p1-2. 2p.

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On the survival of a flawed theory of capital: mainstream economics and the Cambridge capital controversies.

• Authors : Nunes-Pereira, Francisco (AUTHOR) ; Moura, Mário Graça (AUTHOR)

Subjects: *HETERODOX economics; CONFORMITY; TECHNICAL institutesCAMBRIDGESHIRE (England)MASSACHUSETTS Institute of Technology ; UNIVERSITY of Cambridge

• Source: Cambridge Journal of Economics. Mar2024, Vol. 48 Issue 2, p169-186. 18p.

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SimService: a lightweight library for building simulation services in Python.

• Authors : Sego, T J¹ (AUTHOR)

Subjects: *PYTHON programming language; *SIMULATION software; *BIOLOGICAL modelsMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jan2024, Vol. 40 Issue 1, p1-5. 5p.

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pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells.

• Authors : Brown, Colin^1,2 (AUTHOR); Agarwal, Anuradha^1,3 (AUTHOR); Luque, Antoni^1,3,4,5 (AUTHOR)

Subjects: *SOURCE code; *PROTEINS; *CAPSIDSMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jan2024, Vol. 40 Issue 1, p1-5. 5p.

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Benchmarking and improving the performance of variant-calling pipelines with RecallME.

• Authors : Vozza, Gianluca^1,2 (AUTHOR); Bonetti, Emanuele^1,2 (AUTHOR); Tini, Giulia¹ (AUTHOR)

Subjects: *SINGLE nucleotide polymorphisms; *SOURCE code; *WEB-based user interfacesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Dec2023, Vol. 39 Issue 12, p1-6. 6p.

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iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences.

• Authors : Arias, Pablo Millan¹ (AUTHOR) ; Hill, Kathleen A² (AUTHOR); Kari, Lila¹ (AUTHOR)

Subjects: *DEEP learning; *DNA sequencing; *INTERACTIVE learningMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Sep2023, Vol. 39 Issue 9, p1-5. 5p.

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Effects of Controlled Supramaximal High-Intensity Interval Training on Cardiorespiratory Fitness and Global Cognitive Function in Older Adults: The Umeå HIT Study—A Randomized Controlled Trial.

• Authors : Simonsson, Emma¹ (AUTHOR) ; Sandström, Sofi Levik² (AUTHOR); Hedlund, Mattias¹ (AUTHOR)

Subjects: *HIGH-intensity interval training; *CARDIOPULMONARY fitness; *OLDER peopleMASSACHUSETTS Institute of Technology

• Source: Journals of Gerontology Series A: Biological Sciences & Medical Sciences. Sep2023, Vol. 78 Issue 9, p1581-1590. 10p.

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LegNet: a best-in-class deep learning model for short DNA regulatory regions.

• Authors : Penzar, Dmitry^1,2,3 (AUTHOR) ; Nogina, Daria⁴ (AUTHOR); Noskova, Elizaveta⁴ (AUTHOR)

Subjects: *DEEP learning; *GENE expression; *REGULATOR genesMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Aug2023, Vol. 39 Issue 8, p1-9. 9p.

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A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data.

• Authors : Qi, Ren¹ (AUTHOR); Wu, Jin² (AUTHOR); Guo, Fei¹ (AUTHOR)

Subjects: SUPPORT vector machines; RNA sequencing; K-means clusteringMASSACHUSETTS Institute of Technology

• Source: Briefings in Bioinformatics. Jul2021, Vol. 22 Issue 4, p1-11. 11p.

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Finding motifs using DNA images derived from sparse representations.

• Authors : Chu, Shane K¹ (AUTHOR) ; Stormo, Gary D² (AUTHOR)

Subjects: *ARTIFICIAL neural networks; *COMPUTATIONAL biology; *SUPERVISED learningMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. Jun2023, Vol. 39 Issue 6, p1-10. 10p.

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Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data.

• Authors : Silva, Anjali^1,2 (AUTHOR); Qin, Xiaoke³ (AUTHOR); Rothstein, Steven J² (AUTHOR)

Subjects: *RNA sequencing; *GENE expression; *GENE regulatory networksMASSACHUSETTS Institute of Technology

• Source: Bioinformatics. May2023, Vol. 39 Issue 5, p1-8. 8p.

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S-ACF: a selective estimator for the autocorrelation function of irregularly sampled time series.

• Authors : Kreutzer, Lars T^1,2,3 (AUTHOR) ; Gillen, Edward^2,4 (AUTHOR); Briegal, Joshua T² (AUTHOR)

Subjects: *TIME series analysis; *GAUSSIAN processes; *STELLAR rotationMASSACHUSETTS Institute of Technology

• Source: Monthly Notices of the Royal Astronomical Society. Jul2023, Vol. 522 Issue 4, p5049-5061. 13p.

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Making the world from topological order.

• Authors : Ball, Philip¹ (AUTHOR)

Subjects: *NOBEL Prize in Physics; *QUBITS; *QUANTUM computingMASSACHUSETTS Institute of Technology

• Source: National Science Review. Mar2019, Vol. 6 Issue 2, p227-230. 4p.

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People and Places.

Subjects: *Life sciences; Career development; Endowment of researchCambridge (Mass.); Massachusetts; United StatesUnited States. Environmental Protection Agency ; Massachusetts Institute of Technology...

• Source: BioScience. May1977, Vol. 27 Issue 5, p371-375. 5p.

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