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Design considerations for workflow management systems use in production genomics research and the clinic.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-99288-8
By:
- Ahmed, Azza E.;
- Allen, Joshua M.;
- Bhat, Tajesvi;
- Burra, Prakruthi;
- Fliege, Christina E.;
- Hart, Steven N.;
- Heldenbrand, Jacob R.;
- Hudson, Matthew E.;
- Istanto, Dave Deandre;
- Kalmbach, Michael T.;
- Kapraun, Gregory D.;
- Kendig, Katherine I.;
- Kendzior, Matthew Charles;
- Klee, Eric W.;
- Mattson, Nate;
- Ross, Christian A.;
- Sharif, Sami M.;
- Venkatakrishnan, Ramshankar;
- Fadlelmola, Faisal M.;
- Mainzer, Liudmila S.
Publication type:
Article
Transcriptomic and Immunohistochemical Profiling of SLC6A14 in Pancreatic Ductal Adenocarcinoma.
Published in:
BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/593572
By:
- Penheiter, Alan R.;
- Erdogan, Sibel;
- Murphy, Stephen J.;
- Hart, Steven N.;
- Felipe Lima, Joema;
- Rakhshan Rohakhtar, Fariborz;
- O’Brien, Daniel R.;
- Bamlet, William R.;
- Wuertz, Ryan E.;
- Smyrk, Thomas C.;
- Couch, Fergus J.;
- Vasmatzis, George;
- Bender, Claire E.;
- Carlson, Stephanie K.
Publication type:
Article
TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.
Published in:
Nucleic Acids Research, 2015, v. 43, n. 14, p. 6945, doi. 10.1093/nar/gkv111
By:
- Chien, Jeremy;
- Sicotte, Hugues;
- Jian-Bing Fan;
- Humphray, Sean;
- Cunningham, Julie M.;
- Kalli, Kimberly R.;
- Oberg, Ann L.;
- Hart, Steven N.;
- Ying Li;
- Davila, Jaime I.;
- Baheti, Saurabh;
- Chen Wang;
- Dietmann, Sabine;
- Atkinson, Elizabeth J.;
- Asmann, Yan W.;
- Bell, Debra A.;
- Takayo Ota;
- Tarabishy, Yaman;
- Rui Kuang;
- Bibikova, Marina
Publication type:
Article
Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-27987-5
By:
- Cosgrove, Nicola;
- Varešlija, Damir;
- Keelan, Stephen;
- Elangovan, Ashuvinee;
- Atkinson, Jennifer M.;
- Cocchiglia, Sinéad;
- Bane, Fiona T.;
- Singh, Vikrant;
- Furney, Simon;
- Hu, Chunling;
- Carter, Jodi M.;
- Hart, Steven N.;
- Yadav, Siddhartha;
- Goetz, Matthew P.;
- Hill, Arnold D. K.;
- Oesterreich, Steffi;
- Lee, Adrian V.;
- Couch, Fergus J.;
- Young, Leonie S.
Publication type:
Article
From Days to Hours: Reporting Clinically Actionable Variants from Whole Genome Sequencing.
Published in:
PLoS ONE, 2014, v. 9, n. 2, p. 1, doi. 10.1371/journal.pone.0086803
By:
- Middha, Sumit;
- Baheti, Saurabh;
- Hart, Steven N.;
- Kocher, Jean-Pierre A.
Publication type:
Article
SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
Published in:
PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0083356
By:
- Hart, Steven N.;
- Sarangi, Vivekananda;
- Moore, Raymond;
- Baheti, Saurabh;
- Bhavsar, Jaysheel D.;
- Couch, Fergus J.;
- Kocher, Jean-Pierre A.
Publication type:
Article
Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML.
Published in:
NPJ Breast Cancer, 2020, v. 6, n. 1, p. 1, doi. 10.1038/s41523-020-0159-x
By:
- Hart, Steven N.;
- Polley, Eric C.;
- Shimelis, Hermella;
- Yadav, Siddhartha;
- Couch, Fergus J.
Publication type:
Article
The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk.
Published in:
NPJ Breast Cancer, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41523-017-0024-8
By:
- Slavin, Thomas P.;
- Maxwell, Kara N.;
- Lilyquist, Jenna;
- Vijai, Joseph;
- Neuhausen, Susan L.;
- Hart, Steven N.;
- Ravichandran, Vignesh;
- Thomas, Tinu;
- Maria, Ann;
- Villano, Danylo;
- Schrader, Kasmintan A.;
- Moore, Raymond;
- Hu, Chunling;
- Wubbenhorst, Bradley;
- Wenz, Brandon M.;
- D'Andrea, Kurt;
- Robson, Mark E.;
- Peterlongo, Paolo;
- Bonanni, Bernardo;
- Ford, James M.
Publication type:
Article
An integrative model for the comprehensive classification of BRCA1 and BRCA2 variants of uncertain clinical significance.
Published in:
NPJ Genomic Medicine, 2022, v. 7, n. 1, p. 1, doi. 10.1038/s41525-022-00302-3
By:
- Iversen Jr., Edwin S.;
- Lipton, Gary;
- Hart, Steven N.;
- Lee, Kun Y.;
- Hu, Chunling;
- Polley, Eric C.;
- Pesaran, Tina;
- Yussuf, Amal;
- LaDuca, Holly;
- Chao, Elizabeth;
- Karam, Rachid;
- Goldgar, David E.;
- Couch, Fergus J.;
- Monteiro, Alvaro N. A.
Publication type:
Article
Microarray analysis of the in vivo sequence preferences of a minor groove binding drug.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-32
By:
- Eckdahl, Todd T.;
- Brown, Adam D.;
- Hart, Steven N.;
- Malloy, Kelly J.;
- Shott, Martha;
- Yiu, Gloria;
- Mays Hoopes, Laura L.;
- Heyer, Laurie J.
Publication type:
Article
Cybersecurity and Information Assurance for the Clinical Laboratory.
Published in:
Journal of Applied Laboratory Medicine, 2023, v. 8, n. 1, p. 145, doi. 10.1093/jalm/jfac119
By:
- Patel, Ankush U;
- Williams, Christopher L;
- Hart, Steven N;
- Garcia, Christopher A;
- Durant, Thomas J S;
- Cornish, Toby C;
- McClintock, David S
Publication type:
Article
Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy.
Published in:
Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00736
By:
- Kendig, Katherine I.;
- Baheti, Saurabh;
- Bockol, Matthew A.;
- Drucker, Travis M.;
- Hart, Steven N.;
- Heldenbrand, Jacob R.;
- Hernaez, Mikel;
- Hudson, Matthew E.;
- Kalmbach, Michael T.;
- Klee, Eric W.;
- Mattson, Nathan R.;
- Ross, Christian A.;
- Taschuk, Morgan;
- Wieben, Eric D.;
- Wiepert, Mathieu;
- Wildman, Derek E.;
- Mainzer, Liudmila S.
Publication type:
Article
Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4.
Published in:
2019
By:
- Heldenbrand, Jacob R.;
- Baheti, Saurabh;
- Bockol, Matthew A.;
- Drucker, Travis M.;
- Hart, Steven N.;
- Hudson, Matthew E.;
- Iyer, Ravishankar K.;
- Kalmbach, Michael T.;
- Kendig, Katherine I.;
- Klee, Eric W.;
- Mattson, Nathan R.;
- Wieben, Eric D.;
- Wiepert, Mathieu;
- Wildman, Derek E.;
- Mainzer, Liudmila S.
Publication type:
Correction Notice
Recommendations for performance optimizations when using GATK3.8 and GATK4.
Published in:
BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-3169-7
By:
- Heldenbrand, Jacob R;
- Baheti, Saurabh;
- Bockol, Matthew A;
- Drucker, Travis M;
- Hart, Steven N;
- Hudson, Matthew E;
- Iyer, Ravishankar K;
- Kalmbach, Michael T;
- Kendig, Katherine I;
- Klee, Eric W;
- Mattson, Nathan R;
- Wieben, Eric D;
- Wiepert, Mathieu;
- Wildman, Derek E;
- Mainzer, Liudmila S
Publication type:
Article
Bioinformatics for Clinical Next Generation Sequencing.
Published in:
Clinical Chemistry, 2015, v. 61, n. 1, p. 124, doi. 10.1373/clinchem.2014.224360
By:
- Oliver, Gavin R.;
- Hart, Steven N.;
- Klee, Eric W.
Publication type:
Article
Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes.
Published in:
Briefings in Bioinformatics, 2016, v. 17, n. 4, p. 672, doi. 10.1093/bib/bbv075
By:
- Hart, Steven N.;
- Maxwell, Kara N.;
- Thomas, Tinu;
- Ravichandran, Vignesh;
- Wubberhorst, Bradley;
- Klein, Robert J.;
- Schrader, Kasmintan;
- Szabo, Csilla;
- Weitzel, Jeffrey N.;
- Neuhausen, Susan L.;
- Nathanson, Katherine;
- Offit, Kenneth;
- Couch, Fergus J.;
- Vijai, Joseph
Publication type:
Article
VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.
Published in:
Briefings in Bioinformatics, 2016, v. 17, n. 2, p. 346, doi. 10.1093/bib/bbv051
By:
- Hart, Steven N.;
- Duffy, Patrick;
- Quest, Daniel J.;
- Hossain, Asif;
- Meiners, Mike A.;
- Kocher, Jean-Pierre
Publication type:
Article
Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma.
Published in:
Carcinogenesis, 2014, v. 35, n. 4, p. 822, doi. 10.1093/carcin/bgt485
By:
- Eckel-Passow, Jeanette E.;
- Serie, Daniel J.;
- Bot, Brian M.;
- Joseph, Richard W.;
- Hart, Steven N.;
- Cheville, John C.;
- Parker, Alexander S.
Publication type:
Article
Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer.
Published in:
2018
By:
- Hu, Chunling;
- Hart, Steven N.;
- Polley, Eric C.;
- Gnanaolivu, Rohan;
- Shimelis, Hermela;
- Lee, Kun Y.;
- Lilyquist, Jenna;
- Na, Jie;
- Moore, Raymond;
- Antwi, Samuel O.;
- Bamlet, William R.;
- Chaffee, Kari G.;
- DiCarlo, John;
- Wu, Zhong;
- Samara, Raed;
- Kasi, Pashtoon M.;
- McWilliams, Robert R.;
- Petersen, Gloria M.;
- Couch, Fergus J.
Publication type:
journal article
Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy.
Published in:
PLoS ONE, 2015, v. 10, n. 12, p. 1, doi. 10.1371/journal.pone.0145176
By:
- Kohli, Manish;
- Wang, Liguo;
- Xie, Fang;
- Sicotte, Hugues;
- Yin, Ping;
- Dehm, Scott M.;
- Hart, Steven N.;
- Vedell, Peter T.;
- Barman, Poulami;
- Qin, Rui;
- Mahoney, Douglas W.;
- Carlson, Rachel E.;
- Eckel-Passow, Jeanette E.;
- Atwell, Thomas D.;
- Eiken, Patrick W.;
- McMenomy, Brendan P.;
- Wieben, Eric D.;
- Jha, Gautam;
- Jimenez, Rafael E.;
- Weinshilboum, Richard
Publication type:
Article
Assessment of Allelic Variation Among Massasauga Rattlesnake Populations via Microsatellite Analysis.
Published in:
Transactions of the Missouri Academy of Science, 2008, v. 42, p. 30, doi. 10.30956/0544-540X-42.2008.30
By:
- Hart, Steven N.;
- Durbian, Francis E.;
- Dillman, Casey B.;
- Eckdahl, Todd T.
Publication type:
Article
Novel patient-derived xenograft mouse model for pancreatic acinar cell carcinoma demonstrates single agent activity of oxaliplatin.
Published in:
2016
By:
- Hall, Jason C.;
- Marlow, Laura A.;
- Mathias, Adam C.;
- Dawson, Louis K.;
- Durham, William F.;
- Meshaw, Kenneth A.;
- Mullin, Robert J.;
- Synnott, Aidan J.;
- Small, Daniel L.;
- Krishna, Murli;
- von Hoff, Daniel;
- Schüler, Julia;
- Hart, Steven N.;
- Couch, Fergus J.;
- Colon-Otero, Gerardo;
- Copland, John A.
Publication type:
journal article
Whole‐exome sequencing of non‐BRCA1/BRCA2 mutation carrier cases at high‐risk for hereditary breast/ovarian cancer.
Published in:
Human Mutation, 2021, v. 42, n. 3, p. 290, doi. 10.1002/humu.24158
By:
- Felicio, Paula S.;
- Grasel, Rebeca S.;
- Campacci, Natalia;
- Paula, Andre E.;
- Galvão, Henrique C. R.;
- Torrezan, Giovana T.;
- Sabato, Cristina S.;
- Fernandes, Gabriela C.;
- Souza, Cristiano P.;
- Michelli, Rodrigo D.;
- Andrade, Carlos E.;
- Barros, Bruna Durães De Figueiredo;
- Matsushita, Marcus M.;
- Revil, Timothée;
- Ragoussis, Jiannis;
- Couch, Fergus J.;
- Hart, Steven N.;
- Reis, Rui M.;
- Melendez, Matias E.;
- Tonin, Patricia N.
Publication type:
Article
Mutation prevalence tables for hereditary cancer derived from multigene panel testing.
Published in:
Human Mutation, 2020, v. 41, n. 8, p. e1, doi. 10.1002/humu.24053
By:
- Hart, Steven N.;
- Polley, Eric C.;
- Yussuf, Amal;
- Yadav, Siddhartha;
- Goldgar, David E.;
- Hu, Chunling;
- LaDuca, Holly;
- Smith, Laura P.;
- Fujimoto, June;
- Li, Shuwei;
- Couch, Fergus J.;
- Dolinsky, Jill S.
Publication type:
Article
Susceptibility gene mutations in germline and tumors of patients with HER2-negative advanced breast cancer.
Published in:
NPJ Breast Cancer, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41523-024-00667-x
By:
- Fasching, Peter A.;
- Hu, Chunling;
- Hart, Steven N.;
- Ruebner, Matthias;
- Polley, Eric C.;
- Gnanaolivu, Rohan D.;
- Hartkopf, Andreas D.;
- Huebner, Hanna;
- Janni, Wolfgang;
- Hadji, Peyman;
- Tesch, Hans;
- Uhrig, Sabrina;
- Ettl, Johannes;
- Lux, Michael P.;
- Lüftner, Diana;
- Wallwiener, Markus;
- Wurmthaler, Lena A.;
- Goossens, Chloë;
- Müller, Volkmar;
- Beckmann, Matthias W.
Publication type:
Article
Robust hierarchical density estimation and regression for re-stained histological whole slide image co-registration.
Published in:
PLoS ONE, 2019, v. 14, n. 7, p. 1, doi. 10.1371/journal.pone.0220074
By:
- Jiang, Jun;
- Larson, Nicholas B.;
- Prodduturi, Naresh;
- Flotte, Thomas J.;
- Hart, Steven N.
Publication type:
Article
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Published in:
Bioinformatics, 2014, v. 30, n. 18, p. 2678, doi. 10.1093/bioinformatics/btu363
By:
- Wang, Chen;
- Evans, Jared M.;
- Bhagwate, Aditya V.;
- Prodduturi, Naresh;
- Sarangi, Vivekananda;
- Middha, Mridu;
- Sicotte, Hugues;
- Vedell, Peter T.;
- Hart, Steven N.;
- Oliver, Gavin R.;
- Kocher, Jean-Pierre A.;
- Maurer, Matthew J.;
- Novak, Anne J.;
- Slager, Susan L.;
- Cerhan, James R.;
- Asmann, Yan W.
Publication type:
Article
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.
Published in:
Bioinformatics, 2014, v. 30, n. 13, p. 1920, doi. 10.1093/bioinformatics/btu137
By:
- Kocher, Jean-Pierre A.;
- Quest, Daniel J.;
- Duffy, Patrick;
- Meiners, Michael A.;
- Moore, Raymond M.;
- Rider, David;
- Hossain, Asif;
- Hart, Steven N.;
- Dinu, Valentin
Publication type:
Article
Racial and Ethnic Differences in Multigene Hereditary Cancer Panel Test Results for Women With Breast Cancer.
Published in:
2021
By:
- Yadav, Siddhartha;
- LaDuca, Holly;
- Polley, Eric C;
- Hu, Chunling;
- Niguidula, Nancy;
- Shimelis, Hermela;
- Lilyquist, Jenna;
- Na, Jie;
- Lee, Kun Y;
- Gutierrez, Stephanie;
- Yussuf, Amal;
- Hart, Steven N;
- Davis, Brigette Tippin;
- Chao, Elizabeth C;
- Pesaran, Tina;
- Goldgar, David E;
- Dolinsky, Jill S;
- Couch, Fergus J
Publication type:
journal article
Contribution of Germline Predisposition Gene Mutations to Breast Cancer Risk in African American Women.
Published in:
2020
By:
- Palmer, Julie R;
- Polley, Eric C;
- Hu, Chunling;
- John, Esther M;
- Haiman, Christopher;
- Hart, Steven N;
- Gaudet, Mia;
- Pal, Tuya;
- Anton-Culver, Hoda;
- Trentham-Dietz, Amy;
- Bernstein, Leslie;
- Ambrosone, Christine B;
- Bandera, Elisa V;
- Bertrand, Kimberly A;
- Bethea, Traci N;
- Gao, Chi;
- Gnanaolivu, Rohan D;
- Huang, Hongyan;
- Lee, Kun Y;
- LeMarchand, Loic
Publication type:
journal article
The Contribution of Germline Predisposition Gene Mutations to Clinical Subtypes of Invasive Breast Cancer From a Clinical Genetic Testing Cohort.
Published in:
2020
By:
- Hu, Chunling;
- Polley, Eric C;
- Yadav, Siddhartha;
- Lilyquist, Jenna;
- Shimelis, Hermela;
- Na, Jie;
- Hart, Steven N;
- Goldgar, David E;
- Shah, Swati;
- Pesaran, Tina;
- Dolinsky, Jill S;
- LaDuca, Holly;
- Couch, Fergus J
Publication type:
journal article
Risk of Different Cancers Among First-degree Relatives of Pancreatic Cancer Patients: Influence of Probands' Susceptibility Gene Mutation Status.
Published in:
2019
By:
- Antwi, Samuel O;
- Fagan, Sarah E;
- Chaffee, Kari G;
- Bamlet, William R;
- Hu, Chunling;
- Polley, Eric C;
- Hart, Steven N;
- Shimelis, Hermela;
- Lilyquist, Jenna;
- Gnanaolivu, Rohan D;
- McWilliams, Robert R;
- Oberg, Ann L;
- Couch, Fergus J;
- Petersen, Gloria M
Publication type:
journal article
Triple-Negative Breast Cancer Risk Genes Identified by Multigene Hereditary Cancer Panel Testing.
Published in:
2018
By:
- Shimelis, Hermela;
- LaDuca, Holly;
- Hu, Chunling;
- Hart, Steven N;
- Na, Jie;
- Thomas, Abigail;
- Akinhanmi, Margaret;
- Moore, Raymond M;
- Brauch, Hiltrud;
- Cox, Angela;
- Eccles, Diana M;
- Ewart-Toland, Amanda;
- Fasching, Peter A;
- Fostira, Florentia;
- Garber, Judy;
- Godwin, Andrew K;
- Konstantopoulou, Irene;
- Nevanlinna, Heli;
- Sharma, Priyanka;
- Yannoukakos, Drakoulis
Publication type:
journal article
Organizational preparedness for the use of large language models in pathology informatics.
Published in:
Journal of Pathology Informatics, 2023, v. 14, p. 1, doi. 10.1016/j.jpi.2023.100338
By:
- Hart, Steven N.;
- Hoffman, Noah G.;
- Gershkovich, Peter;
- Christenson, Chancey;
- McClintock, David S.;
- Miller, Lauren J.;
- Jackups, Ronald;
- Azimi, Vahid;
- Spies, Nicholas;
- Brodsky, Victor
Publication type:
Article
Dicom_wsi: A Python Implementation for Converting Whole-Slide Images to Digital Imaging and Communications in Medicine Compliant Files.
Published in:
Journal of Pathology Informatics, 2021, v. 12, p. 1, doi. 10.4103/jpi.jpi_88_20
By:
- Qiangqiang Gu;
- Prodduturi, Naresh;
- Jun Jiang;
- Flotte, Thomas J.;
- Hart, Steven N.
Publication type:
Article
Classification of Melanocytic Lesions in Selected and Whole-Slide Images via Convolutional Neural Networks.
Published in:
Journal of Pathology Informatics, 2019, p. 1, doi. 10.4103/jpi.jpi_32_18
By:
- Hart, Steven N.;
- Flotte, William;
- Norgan, Andrew P.;
- Shah, Kabeer K.;
- Buchan, Zachary R.;
- Mounajjed, Taofic;
- Flotte, Thomas J.
Publication type:
Article
Will Digital Pathology be as Disruptive as Genomics?
Published in:
Journal of Pathology Informatics, 2018, p. 1, doi. 10.4103/jpi.jpi_25_18
By:
- Hart, Steven N.
Publication type:
Article

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