 Software
"Software" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus,
MeSH (Medical Subject Headings). Descriptors are arranged in a hierarchical structure,
which enables searching at various levels of specificity.
Sequential operating instructions for a particular problem or function to be run on a digital computer.
| Descriptor ID |
D012984
|
| MeSH Number(s) |
L01.224.900
|
| Concept/Terms |
Software- Software
- Computer Software
- Software, Computer
- Computer Programs
- Computer Program
- Program, Computer
- Programs, Computer
Software Tools- Software Tools
- Software Tool
- Tool, Software
- Tools, Software
|
Below are MeSH descriptors whose meaning is more general than "Software".
Below are MeSH descriptors whose meaning is more specific than "Software".
This graph shows the total number of publications written about "Software" by people in UAMS Profiles by year, and whether "Software" was a major or minor topic of these publications.
To see the data from this visualization as text, click here.
| Year | Major Topic | Minor Topic | Total |
|---|
| 2025 | 2 | 4 | 6 | | 2024 | 1 | 3 | 4 | | 2023 | 3 | 4 | 7 | | 2022 | 1 | 2 | 3 | | 2021 | 2 | 5 | 7 | | 2020 | 8 | 6 | 14 | | 2019 | 4 | 2 | 6 | | 2018 | 6 | 5 | 11 | | 2017 | 6 | 2 | 8 | | 2016 | 5 | 6 | 11 | | 2015 | 3 | 5 | 8 | | 2014 | 7 | 9 | 16 | | 2013 | 6 | 9 | 15 | | 2012 | 5 | 3 | 8 | | 2011 | 2 | 5 | 7 | | 2010 | 5 | 4 | 9 | | 2009 | 2 | 4 | 6 | | 2008 | 4 | 7 | 11 | | 2007 | 5 | 6 | 11 | | 2006 | 0 | 2 | 2 | | 2005 | 0 | 2 | 2 | | 2004 | 1 | 4 | 5 | | 2003 | 0 | 2 | 2 | | 2002 | 1 | 1 | 2 | | 2001 | 0 | 1 | 1 | | 2000 | 1 | 0 | 1 | | 1998 | 0 | 2 | 2 | | 1996 | 0 | 1 | 1 | | 1995 | 1 | 1 | 2 | | 1992 | 0 | 3 | 3 | | 1990 | 0 | 1 | 1 |
To return to the timeline, click here.
Below are the most recent publications written about "Software" by people in Profiles over the past ten years.
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Lu D, Kalantar KL, Glascock AL, Chu VT, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform. Genome Med. 2025 May 06; 17(1):46.
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Kong R, Spreng RN, Xue A, Betzel RF, Cohen JR, Damoiseaux JS, De Brigard F, Eickhoff SB, Fornito A, Gratton C, Gordon EM, Holmes AJ, Laird AR, Larson-Prior L, Nickerson LD, Pinho AL, Razi A, Sadaghiani S, Shine JM, Yendiki A, Yeo BTT, Uddin LQ. A network correspondence toolbox for quantitative evaluation of novel neuroimaging results. Nat Commun. 2025 Mar 25; 16(1):2930.
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Wang T, Tam J, Chum T, Tai C, Marshall DC, Buckstein M, Liu J, Green S, Stewart RD, Liu T, Chao M. Evaluation of AI-based auto-contouring tools in radiotherapy: A single-institution study. J Appl Clin Med Phys. 2025 Apr; 26(4):e14620.
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Garc?a-Lezana T, Bobowicz M, Frid S, Rutherford M, Recuero M, Riklund K, Cabrelles A, Rygusik M, Fromont L, Francischello R, Neri E, Capella S, Navarro A, Prior F, Bona J, Nicolas P, Starmans MPA, Lekadir K, Rambla J. New implementation of data standards for AI in oncology: Experience from the EuCanImage project. Gigascience. 2025 Jan 06; 14.
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Du X, Dobrowolski A, Brochhausen M, Garrett TJ, Hogan WR, Lemas DJ. Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. J Am Soc Mass Spectrom. 2025 Feb 05; 36(2):433-438.
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Ziegler J, Hechtman JF, Rana S, Ptashkin RN, Jayakumaran G, Middha S, Chavan SS, Vanderbilt C, DeLair D, Casanova J, Shia J, DeGroat N, Benayed R, Ladanyi M, Berger MF, Fuchs TJ, Brannon AR, Zehir A. A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing. Nat Commun. 2025 01 02; 16(1):136.
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Acheampong DA, Jenjaroenpun P, Wongsurawat T, Kurilung A, Pomyen Y, Kandel S, Kunadirek P, Chuaypen N, Kusonmano K, Nookaew I. CAIM: coverage-based analysis for identification of microbiome. Brief Bioinform. 2024 Jul 25; 25(5).
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O'Connell KA, Kopchick B, Carlson T, Belardo D, Byrum SD. Understanding proteome quantification in an interactive learning module on Google Cloud Platform. Brief Bioinform. 2024 Jul 23; 25(Supplement_1).
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McAfee L, Heath Z, Anderson W, Hozi M, Orr JW, Kang YA. The development of an automated microscope image tracking and analysis system. Biotechnol Prog. 2024 Nov-Dec; 40(6):e3490.
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Wagner MM, Hogan WR, Levander JD, Diller M. Towards Machine-FAIR: Representing software and datasets to facilitate reuse and scientific discovery by machines. J Biomed Inform. 2024 06; 154:104647.
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Lemas DJ, Du X, Rouhizadeh M, Lewis B, Frank S, Wright L, Spirache A, Gonzalez L, Cheves R, Magalh?es M, Zapata R, Reddy R, Xu K, Parker L, Harle C, Young B, Louis-Jaques A, Zhang B, Thompson L, Hogan WR, Modave F. Classifying early infant feeding status from clinical notes using natural language processing and machine learning. Sci Rep. 2024 04 03; 14(1):7831.
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Charrasse S, Racine V, Saint-Omer C, Poquillon T, Lionnard L, Ledru M, Gonindard C, Delaunois S, Kissa K, Frye RE, Pastore M, Reynes C, Frechet M, Chajra H, Aouacheria A. Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells. PLoS One. 2024; 19(3):e0301372.
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Chappell K, Byrum SD. Understanding PTM Cross Talk Through a Visualization Tool, PTMViz. Methods Mol Biol. 2024; 2836:57-65.
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Buatti JS, Kirby N, Stathakis S, Li R, Sivabhaskar S, de Oliveira M, Duke K, Kabat CN, Papanikolaou N, Paragios N. Standardizing and improving dose predictions for head and neck cancers using complete sets of OAR contours. Med Phys. 2024 Feb; 51(2):898-909.
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Ryan ML, Knod JL, Pandya SR. Creation of Three-dimensional Anatomic Models in Pediatric Surgical Patients Using Cross-sectional Imaging: A Demonstration of Low-cost Methods and Applications. J Pediatr Surg. 2024 Mar; 59(3):426-431.
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Du X, Dastmalchi F, Diller MA, Brochhausen M, Garrett TJ, Hogan WR, Lemas DJ. An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. J Am Soc Mass Spectrom. 2023 Dec 06; 34(12):2857-2863.
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Shafi O, Liu D, Thompson C, Margo T, Bennett T, Suresh S, Yu F. Defining Electronic Health Record Standards for Child Health: A State-of-the-Art Review. Appl Clin Inform. 2024 01; 15(1):55-63.
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Zayas CE, Whorton JM, Sexton KW, Mabry CD, Dowland SC, Brochhausen M. Development and validation of the early warning system scores ontology. J Biomed Semantics. 2023 09 20; 14(1):14.
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Eisenstein EL, Zozus MN, Garza MY, Lanham HJ, Adagarla B, Walden A, Benjamin DK, Zimmerman KO, Kumar KR. Assessing clinical site readiness for electronic health record (EHR)-to-electronic data capture (EDC) automated data collection. Contemp Clin Trials. 2023 05; 128:107144.
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics. 2023 02 06; 19(2):11.
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Bona JP, Utecht J, Bost S, Brochhausen M, Prior F. The PRISM semantic cohort builder: a novel tool to search and access clinical data in TCIA imaging collections. Phys Med Biol. 2022 12 23; 68(1).
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Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database (Oxford). 2022 10 08; 2022.
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Steiner SM, Slavych BK, Zraick RI. Assessment of Online Patient Education Material About Dysphagia. Dysphagia. 2023 06; 38(3):990-1000.
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Shekar P V, Vignesh Rangaswamy V, Subramanian M, Atreya AR, Yalagudri S, Chennapragada S, Saggu DK, Narasimhan C. High rate episodes in a dual chamber pacemaker: What is the mechanism? Pacing Clin Electrophysiol. 2022 Feb; 45(2):238-240.
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Robeson MS, O'Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol. 2021 11; 17(11):e1009581.
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West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun. 2021 08 09; 12(1):4886.
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Jarugula P, Scott S, Ivaturi V, Noack A, Moffett BS, Bhutta A, Gobburu JVS. Understanding the Role of Pharmacometrics-Based Clinical Decision Support Systems in Pediatric Patient Management: A Case Study Using Lyv Software. J Clin Pharmacol. 2021 06; 61 Suppl 1:S125-S132.
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Siebert JC, Saint-Cyr M, Borengasser SJ, Wagner BD, Lozupone CA, G?rg C. CANTARE: finding and visualizing network-based multi-omic predictive models. BMC Bioinformatics. 2021 Feb 19; 22(1):80.
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Wardell CP, Ashby C, Bauer MA. FiNGS: high quality somatic mutations using filters for next generation sequencing. BMC Bioinformatics. 2021 Feb 18; 22(1):77.
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Kulbeth HJ, Fukuda S, Brents LK. Automated quantification of opioid withdrawal in neonatal rat pups using Ethovision? XT software. Neurotoxicol Teratol. 2021 Mar-Apr; 84:106959.
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Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 2021 01 25; 49(2):e7.
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Yang X, Bian J, Hogan WR, Wu Y. Clinical concept extraction using transformers. J Am Med Inform Assoc. 2020 12 09; 27(12):1935-1942.
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Patel L, Shukla T, Huang X, Ussery DW, Wang S. Machine Learning Methods in Drug Discovery. Molecules. 2020 Nov 12; 25(22).
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Price NB, Chizinski CJ, Fontaine JJ, Pope KL, Rahe M, Rawlinson J. An open-sourced, web-based application to improve our ability to understand hunter and angler purchasing behavior from license data. PLoS One. 2020; 15(10):e0226397.
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Licon AL, Alexandrian A, Saenz D, Myers P, Rasmussen K, Stathakis S, Papanikolaou N, Kirby N. An open-source tool to visualize potential cone collisions while planning SRS cases. J Appl Clin Med Phys. 2020 Oct; 21(10):40-47.
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McCulloch J, Pawlowski J, Kirby N, Rasmussen K, Shi Z, Myers P, Stathakis S, Papanikolaou N, Saenz DL. Patient-specific dose quality assurance of single-isocenter multiple brain metastasis stereotactic radiosurgery using PTW Octavius 4D. J Appl Clin Med Phys. 2020 Sep; 21(9):107-115.
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Drew ED, Janes RW. PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. Nucleic Acids Res. 2020 07 02; 48(W1):W17-W24.
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Eisenstein EL, Garza MY, Rocca M, Gordon GS, Zozus M. eSource-Enabled vs. Traditional Clinical Trial Data Collection Methods: A Site-Level Economic Analysis. Stud Health Technol Inform. 2020 Jun 16; 270:961-965.
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Smith AK, Ropella GEP, McGill MR, Krishnan P, Dutta L, Kennedy RC, Jaeschke H, Hunt CA. Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms. PLoS Comput Biol. 2020 06; 16(6):e1007622.
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Botvinik-Nezer R, Holzmeister F, Camerer CF, Dreber A, Huber J, Johannesson M, Kirchler M, Iwanir R, Mumford JA, Adcock RA, Avesani P, Baczkowski BM, Bajracharya A, Bakst L, Ball S, Barilari M, Bault N, Beaton D, Beitner J, Benoit RG, Berkers RMWJ, Bhanji JP, Biswal BB, Bobadilla-Suarez S, Bortolini T, Bottenhorn KL, Bowring A, Braem S, Brooks HR, Brudner EG, Calderon CB, Camilleri JA, Castrellon JJ, Cecchetti L, Cieslik EC, Cole ZJ, Collignon O, Cox RW, Cunningham WA, Czoschke S, Dadi K, Davis CP, Luca A, Delgado MR, Demetriou L, Dennison JB, Di X, Dickie EW, Dobryakova E, Donnat CL, Dukart J, Duncan NW, Durnez J, Eed A, Eickhoff SB, Erhart A, Fontanesi L, Fricke GM, Fu S, Galv?n A, Gau R, Genon S, Glatard T, Glerean E, Goeman JJ, Golowin SAE, Gonz?lez-Garc?a C, Gorgolewski KJ, Grady CL, Green MA, Guassi Moreira JF, Guest O, Hakimi S, Hamilton JP, Hancock R, Handjaras G, Harry BB, Hawco C, Herholz P, Herman G, Heunis S, Hoffstaedter F, Hogeveen J, Holmes S, Hu CP, Huettel SA, Hughes ME, Iacovella V, Iordan AD, Isager PM, Isik AI, Jahn A, Johnson MR, Johnstone T, Joseph MJE, Juliano AC, Kable JW, Kassinopoulos M, Koba C, Kong XZ, Koscik TR, Kucukboyaci NE, Kuhl BA, Kupek S, Laird AR, Lamm C, Langner R, Lauharatanahirun N, Lee H, Lee S, Leemans A, Leo A, Lesage E, Li F, Li MYC, Lim PC, Lintz EN, Liphardt SW, Losecaat Vermeer AB, Love BC, Mack ML, Malpica N, Marins T, Maumet C, McDonald K, McGuire JT, Melero H, M?ndez Leal AS, Meyer B, Meyer KN, Mihai G, Mitsis GD, Moll J, Nielson DM, Nilsonne G, Notter MP, Olivetti E, Onicas AI, Papale P, Patil KR, Peelle JE, P?rez A, Pischedda D, Poline JB, Prystauka Y, Ray S, Reuter-Lorenz PA, Reynolds RC, Ricciardi E, Rieck JR, Rodriguez-Thompson AM, Romyn A, Salo T, Samanez-Larkin GR, Sanz-Morales E, Schlichting ML, Schultz DH, Shen Q, Sheridan MA, Silvers JA, Skagerlund K, Smith A, Smith DV, Sokol-Hessner P, Steinkamp SR, Tashjian SM, Thirion B, Thorp JN, Tingh?g G, Tisdall L, Tompson SH, Toro-Serey C, Torre Tresols JJ, Tozzi L, Truong V, Turella L, van 't Veer AE, Verguts T, Vettel JM, Vijayarajah S, Vo K, Wall MB, Weeda WD, Weis S, White DJ, Wisniewski D, Xifra-Porxas A, Yearling EA, Yoon S, Yuan R, Yuen KSL, Zhang L, Zhang X, Zosky JE, Nichols TE, Poldrack RA, Schonberg T. Variability in the analysis of a single neuroimaging dataset by many teams. Nature. 2020 06; 582(7810):84-88.
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Storey AJ, Naceanceno KS, Lan RS, Washam CL, Orr LM, Mackintosh SG, Tackett AJ, Edmondson RD, Wang Z, Li HY, Frett B, Kendrick S, Byrum SD. ProteoViz: a tool for the analysis and interactive visualization of phosphoproteomics data. Mol Omics. 2020 08 01; 16(4):316-326.
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Ashby C, Rutherford M, Bauer MA, Peterson EA, Wang Y, Boyle EM, Wardell CP, Walker BA. TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use. BMC Bioinformatics. 2020 Apr 15; 21(1):144.
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Soong D, Stratford J, Avet-Loiseau H, Bahlis N, Davies F, Dispenzieri A, Sasser AK, Schecter JM, Qi M, Brown C, Jones W, Keats JJ, Auclair D, Chiu C, Powers J, Schaffer M. CNV Radar: an improved method for somatic copy number alteration characterization in oncology. BMC Bioinformatics. 2020 Mar 06; 21(1):98.
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Zhang Y, Koru G. Understanding and detecting defects in healthcare administration data: Toward higher data quality to better support healthcare operations and decisions. J Am Med Inform Assoc. 2020 03 01; 27(3):386-395.
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Caputo M, Lyles JT, Salazar MS, Quave CL. LEGO MINDSTORMS Fraction Collector: A Low-Cost Tool for a Preparative High-Performance Liquid Chromatography System. Anal Chem. 2020 01 21; 92(2):1687-1690.
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Grigorian A, Fang P, Kirk T, Efendizade A, Jadidi J, Sighary M, Cohen-Addad DI. Learning from Gamers: Integrating Alternative Input Devices and AutoHotkey Scripts to Simplify Repetitive Tasks and Improve Workflow. Radiographics. 2020 Jan-Feb; 40(1):141-150.
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Cooke MB, O'Leary TP, Harris P, Ma R, Brown RE, Snyder JS. Pathfinder: open source software for analyzing spatial navigation search strategies. F1000Res. 2019; 8:1521.
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He X, Zhang R, Rizvi R, Vasilakes J, Yang X, Guo Y, He Z, Prosperi M, Huo J, Alpert J, Bian J. ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. BMC Med Inform Decis Mak. 2019 08 08; 19(Suppl 4):150.
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodr?guez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, V?zquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857.
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Drew ED, Janes RW. 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. Nucleic Acids Res. 2019 07 02; 47(W1):W477-W481.
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Bathla G, Limaye K, Policeni B, Klotz E, Juergens M, Derdeyn C. Achieving comparable perfusion results across vendors. The next step in standardizing stroke care: a technical report. J Neurointerv Surg. 2019 Dec; 11(12):1257-1260.
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Long DE, Villasante Tezanos AG, Wise JN, Kern PA, Bamman MM, Peterson CA, Dennis RA. A guide for using NIH Image J for single slice cross-sectional area and composition analysis of the thigh from computed tomography. PLoS One. 2019; 14(2):e0211629.
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Kabat CN, Defoor DL, Myers P, Kirby N, Rasmussen K, Saenz DL, Mavroidis P, Papanikolaou N, Stathakis S. Evaluation of the Elekta Agility MLC performance using high-resolution log files. Med Phys. 2019 Mar; 46(3):1397-1407.
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Kuo PH, Eshghi N, Tinaz S, Blumenfeld H, Louis ED, Zubal G. Optimization of Parameters for Quantitative Analysis of 123I-Ioflupane SPECT Images for Monitoring Progression of Parkinson Disease. J Nucl Med Technol. 2019 Mar; 47(1):70-74.
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Lossio-Ventura JA, Hogan W, Modave F, Guo Y, He Z, Yang X, Zhang H, Bian J. OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system. BMC Med Inform Decis Mak. 2018 07 23; 18(Suppl 2):55.
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Causey JL, Zhang J, Ma S, Jiang B, Qualls JA, Politte DG, Prior F, Zhang S, Huang X. Highly accurate model for prediction of lung nodule malignancy with CT scans. Sci Rep. 2018 06 18; 8(1):9286.
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McCarty JL, Golofit P, Tigges S, Skalski M. Digital Medical Illustration for the Radiologist. Radiographics. 2018 Jul-Aug; 38(4):1145-1157.
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Ramaker RC, Gordon ER, Cooper SJ. R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. Bioinformatics. 2018 05 15; 34(10):1789-1791.
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Younes F, Cosyn J, De Bruyckere T, Cleymaet R, Bouckaert E, Eghbali A. A randomized controlled study on the accuracy of free-handed, pilot-drill guided and fully guided implant surgery in partially edentulous patients. J Clin Periodontol. 2018 06; 45(6):721-732.
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Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X. DNAp: A Pipeline for DNA-seq Data Analysis. Sci Rep. 2018 05 01; 8(1):6793.
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Piccolo BD, Wankhade UD, Chintapalli SV, Bhattacharyya S, Chunqiao L, Shankar K. Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data. Bioinformatics. 2018 03 15; 34(6):1050-1052.
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Bona JP, Ceusters W. Mismatches between major subhierarchies and semantic tags in SNOMED CT. J Biomed Inform. 2018 05; 81:1-15.
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Tuazon B, Narayanasamy G, Papanikolaou N, Kirby N, Mavroidis P, Stathakis S. Evaluation and comparison of second-check monitor unit calculation software with Pinnacle3 treatment planning system. Phys Med. 2018 Jan; 45:186-191.
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McConnell KA, Marston T, Zehren BE, Lirani A, Stanley DN, Bishop A, Crownover R, Eng T, Shi Z, Li Y, Baacke D, Kirby N, Rasmussen K, Papanikolaou N, Gutierrez AN. Dosimetric Evaluation of Pinnacle's Automated Treatment Planning Software to Manually Planned Treatments. Technol Cancer Res Treat. 2018 01 01; 17:1533033818780064.
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Wen Y, Murach KA, Vechetti IJ, Fry CS, Vickery C, Peterson CA, McCarthy JJ, Campbell KS. MyoVision: software for automated high-content analysis of skeletal muscle immunohistochemistry. J Appl Physiol (1985). 2018 01 01; 124(1):40-51.
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Dobretsov M, Petkau G, Hayar A, Petkau E. Clock Scan Protocol for Image Analysis: ImageJ Plugins. J Vis Exp. 2017 06 19; (124).
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Alonso A, Lasseigne BN, Williams K, Nielsen J, Ramaker RC, Hardigan AA, Johnston B, Roberts BS, Cooper SJ, Marsal S, Myers RM. aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments. Bioinformatics. 2017 Jun 01; 33(11):1727-1729.
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Scanlon DP, Bah A, Krzeminski M, Zhang W, Leduc-Pessah HL, Dong YN, Forman-Kay JD, Salter MW. An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors. Nat Commun. 2017 05 16; 8:15220.
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Pedersen TL, Nookaew I, Wayne Ussery D, M?nsson M. PanViz: interactive visualization of the structure of functionally annotated pangenomes. Bioinformatics. 2017 04 01; 33(7):1081-1082.
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Thankaswamy-Kosalai S, Sen P, Nookaew I. Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics. 2017 07; 109(3-4):186-191.
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Hogan WR, Hanna J, Hicks A, Amirova S, Bramblett B, Diller M, Enderez R, Modzelewski T, Vasconcelos M, Delcher C. Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request. J Biomed Semantics. 2017 Mar 03; 8(1):10.
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Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017 Jan 24; 18(1):61.
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Pandey T, Alapati S, Wadhwa V, Edupuganti MM, Gurram P, Lensing S, Jambhekar K. Evaluation of Myocardial Strain in Patients With Amyloidosis Using Cardiac Magnetic Resonance Feature Tracking. Curr Probl Diagn Radiol. 2017 Jul - Aug; 46(4):288-294.
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Zheng J, Erzurumluoglu AM, Elsworth BL, Kemp JP, Howe L, Haycock PC, Hemani G, Tansey K, Laurin C, Pourcain BS, Warrington NM, Finucane HK, Price AL, Bulik-Sullivan BK, Anttila V, Paternoster L, Gaunt TR, Evans DM, Neale BM. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics. 2017 01 15; 33(2):272-279.
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Mavridis L, Janes RW. PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates. Bioinformatics. 2017 01 01; 33(1):56-63.
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Whitmore L, Miles AJ, Mavridis L, Janes RW, Wallace BA. PCDDB: new developments at the Protein Circular Dichroism Data Bank. Nucleic Acids Res. 2017 01 04; 45(D1):D303-D307.
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Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millett N, DePasse J, Hanna J. The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. J Biomed Semantics. 2016 Aug 18; 7:50.
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Kirkwood ML, Guild JB, Arbique GM, Tsai S, Modrall JG, Anderson JA, Rectenwald J, Timaran C. New image-processing and noise-reduction software reduces radiation dose during complex endovascular procedures. J Vasc Surg. 2016 Nov; 64(5):1357-1365.
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Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016 11 01; 32(21):3345-3347.
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