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Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01415-1
By:
- Sayah, Anousheh;
- Bencheqroun, Camelia;
- Bhuvaneshwar, Krithika;
- Belouali, Anas;
- Bakas, Spyridon;
- Sako, Chiharu;
- Davatzikos, Christos;
- Alaoui, Adil;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Article
Author Correction: Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features.
Published in:
2022
By:
- Sayah, Anousheh;
- Bencheqroun, Camelia;
- Bhuvaneshwar, Krithika;
- Belouali, Anas;
- Bakas, Spyridon;
- Sako, Chiharu;
- Davatzikos, Christos;
- Alaoui, Adil;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Correction Notice
Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01415-1
By:
- Sayah, Anousheh;
- Bencheqroun, Camelia;
- Bhuvaneshwar, Krithika;
- Belouali, Anas;
- Bakas, Spyridon;
- Sako, Chiharu;
- Davatzikos, Christos;
- Alaoui, Adil;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Article
Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01415-1
By:
- Sayah, Anousheh;
- Bencheqroun, Camelia;
- Bhuvaneshwar, Krithika;
- Belouali, Anas;
- Bakas, Spyridon;
- Sako, Chiharu;
- Davatzikos, Christos;
- Alaoui, Adil;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Article
G-DOC Plus - an integrative bioinformatics platform for precision medicine.
Published in:
BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1010-0
By:
- Bhuvaneshwar, Krithika;
- Belouali, Anas;
- Singh, Varun;
- Johnson, Robert M.;
- Lei Song;
- Alaoui, Adil;
- Harris, Michael A.;
- Clarke, Robert;
- Weiner, Louis M.;
- Gusev, Yuriy;
- Madhavan, Subha
Publication type:
Article
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases.
Published in:
BMC Immunology, 2014, v. 15, n. 1, p. 83, doi. 10.1186/s12865-014-0061-0
By:
- McGarvey, Peter B.;
- Suzek, Baris E.;
- Baraniuk, James N.;
- Rao, Shruti;
- Conkright, Brian;
- Lababidi, Samir;
- Sutherland, Andrea;
- Forshee, Richard;
- Madhavan, Subha
Publication type:
Article
Recurrence of Early Stage Colon Cancer Predicted by Expression Pattern of Circulating microRNAs.
Published in:
PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0084686
By:
- Shivapurkar, Narayan;
- Weiner, Louis M.;
- Marshall, John L.;
- Madhavan, Subha;
- Deslattes Mays, Anne;
- Juhl, Hartmut;
- Wellstein, Anton
Publication type:
Article
miR-21 Expression Determines the Early Vaccine Immunity Induced by LdCen <sup>−/−</sup> Immunization.
Published in:
Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.02273
By:
- Gannavaram, Sreenivas;
- Bhattacharya, Parna;
- Siddiqui, Abid;
- Ismail, Nevien;
- Madhavan, Subha;
- Nakhasi, Hira L.
Publication type:
Article
Correction: Zhang et al. Association between Body Mass Index and Immune-Related Adverse Events (irAEs) among Advanced-Stage Cancer Patients Receiving Immune Checkpoint Inhibitors: A Pan-Cancer Analysis. Cancers 2021, 13 , 6109.
Published in:
2022
By:
- Zhang, Dongyu;
- Shah, Neil J.;
- Cook, Michael;
- Blackburn, Matthew;
- Serzan, Michael T.;
- Advani, Shailesh;
- Potosky, Arnold L.;
- Madhavan, Subha;
- Belouali, Anas;
- Atkins, Michael B.;
- Braithwaite, Dejana
Publication type:
Correction Notice
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.
Published in:
Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay128
By:
- Ren, Jia;
- Li, Gang;
- Ross, Karen;
- Arighi, Cecilia;
- McGarvey, Peter;
- Rao, Shruti;
- Cowart, Julie;
- Madhavan, Subha;
- Vijay-Shanker, K;
- Wu, Cathy H
Publication type:
Article
Recommendations for the safe, effective use of adaptive CDS in the US healthcare system: an AMIA position paper.
Published in:
2021
By:
- Petersen, Carolyn;
- Smith, Jeffery;
- Freimuth, Robert R;
- Goodman, Kenneth W;
- Jackson, Gretchen Purcell;
- Kannry, Joseph;
- Liu, Hongfang;
- Madhavan, Subha;
- Sittig, Dean F;
- Wright, Adam
Publication type:
journal article
Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers.
Published in:
2021
By:
- Madhavan, Subha;
- Bastarache, Lisa;
- Brown, Jeffrey S;
- Butte, Atul J;
- Dorr, David A;
- Embi, Peter J;
- Friedman, Charles P;
- Johnson, Kevin B;
- Moore, Jason H;
- Kohane, Isaac S;
- Payne, Philip R O;
- Tenenbaum, Jessica D;
- Weiner, Mark G;
- Wilcox, Adam B;
- Ohno-Machado, Lucila
Publication type:
journal article
An informatics research agenda to support precision medicine: seven key areas.
Published in:
2016
By:
- Tenenbaum, Jessica D.;
- Avillach, Paul;
- Benham-Hutchins, Marge;
- Breitenstein, Matthew K.;
- Crowgey, Erin L.;
- Hoffman, Mark A.;
- Xia Jiang;
- Madhavan, Subha;
- Mattison, John E.;
- Nagarajan, Radhakrishnan;
- Ray, Bisakha;
- Shin, Dmitriy;
- Visweswaran, Shyam;
- Zhongming Zhao;
- Freimuth, Robert R.;
- Jiang, Xia;
- Zhao, Zhongming
Publication type:
journal article
Informatics and data quality at collaborative multicenter Breast and Colon Cancer Family Registries.
Published in:
2012
By:
- McGarvey PB;
- Ladwa S;
- Oberti M;
- Dragomir AD;
- Hedlund EK;
- Tanenbaum DM;
- Suzek BE;
- Madhavan S;
- McGarvey, Peter B;
- Ladwa, Sweta;
- Oberti, Mauricio;
- Dragomir, Anca Dana;
- Hedlund, Erin K;
- Tanenbaum, David Michael;
- Suzek, Baris E;
- Madhavan, Subha
Publication type:
journal article
Informatics and data quality at collaborative multicenter Breast and Colon Cancer Family Registries.
Published in:
Journal of the American Medical Informatics Association, 2012, v. 19, n. e1, p. e125, doi. 10.1136/amiajnl-2011-000546
By:
- McGarvey, Peter B.;
- Ladwa, Sweta;
- Oberti, Mauricio;
- Dragomir, Anca Dana;
- Hedlund, Erin K.;
- Tanenbaum, David Michael;
- Suzek, Baris E.;
- Madhavan, Subha
Publication type:
Article
SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2774-9
By:
- McCoy, Matthew D.;
- Shivakumar, Vikram;
- Nimmagadda, Sridhar;
- Jafri, Mohsin Saleet;
- Madhavan, Subha
Publication type:
Article
Multi-omic molecular comparison of primary versus metastatic pancreatic tumours.
Published in:
2019
By:
- Brar, Gagandeep;
- Blais, Edik M.;
- Joseph Bender, R.;
- Brody, Jonathan R.;
- Sohal, Davendra;
- Madhavan, Subha;
- Picozzi, Vincent J.;
- Hendifar, Andrew E.;
- Chung, Vincent M.;
- Halverson, David;
- Mikhail, Sameh;
- Matrisian, Lynn M.;
- Rahib, Lola;
- Petricoin, Emanuel;
- Pishvaian, Michael J.
Publication type:
journal article
Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients.
Published in:
2019
By:
- Bhuvaneshwar, Krithika;
- Harris, Michael;
- Gusev, Yuriy;
- Madhavan, Subha;
- Iyer, Ramaswamy;
- Vilboux, Thierry;
- Deeken, John;
- Yang, Elizabeth;
- Shankar, Sadhna
Publication type:
journal article
viGEN: An Open Source Pipeline for the Detection and Quanti?cation of Viral RNA in Human Tumors.
Published in:
Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.01172
By:
- Bhuvaneshwar, Krithika;
- Lei Song;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Article
Correction: Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study.
Published in:
2016
By:
- Boca, Simina M.;
- Nishida, Maki;
- Harris, Michael;
- Rao, Shruti;
- Cheema, Amrita K.;
- Gill, Kirandeep;
- Wang, Difei;
- An, Lin;
- Gauba, Robinder;
- Seol, Haeri;
- Morgenroth, Lauren P.;
- Henricson, Erik;
- McDonald, Craig;
- Mah, Jean K.;
- Clemens, Paula R.;
- Hoffman, Eric P.;
- Hathout, Yetrib;
- Madhavan, Subha
Publication type:
Correction Notice
Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study.
Published in:
PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0153461
By:
- Boca, Simina M.;
- Nishida, Maki;
- Harris, Michael;
- Rao, Shruti;
- Cheema, Amrita K.;
- Gill, Kirandeep;
- Seol, Haeri;
- Morgenroth, Lauren P.;
- Henricson, Erik;
- McDonald, Craig;
- Mah, Jean K.;
- Clemens, Paula R.;
- Hoffman, Eric P.;
- Hathout, Yetrib;
- Madhavan, Subha
Publication type:
Article
Metabolomic and exome sequence analysis reveal novel molecular signatures associated with colorectal cancer relapse.
Published in:
2012
By:
- Gauba, Robinder;
- Natarajan, Thanemozhi G.;
- Lei Song;
- Bhuvaneshwar, Krithika;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Abstract
CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data.
Published in:
Cancer Informatics, 2017, n. 16, p. 1, doi. 10.1177/1176935117746637
By:
- Song, Lei;
- Bhuvaneshwar, Krithika;
- Wang, Yue;
- Feng, Yuanjian;
- Shih, Ie-Ming;
- Madhavan, Subha;
- Gusev, Yuriy
Publication type:
Article
In Silico Discovery of Mitosis Regulation Networks Associated with Early Distant Metastases in Estrogen Receptor Positive Breast Cancers.
Published in:
Cancer Informatics, 2013, n. 12, p. 31, doi. 10.4137/CIN.S10329
By:
- Gusev, Yuriy;
- Riggins, Rebecca B.;
- Bhuvaneshwar, Krithika;
- Gauba, Robinder;
- Sheahan, Laura;
- Clarke, Robert;
- Madhavan, Subha
Publication type:
Article
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards.
Published in:
Human Mutation, 2018, v. 39, n. 11, p. 1721, doi. 10.1002/humu.23651
By:
- Danos, Arpad M.;
- Ritter, Deborah I.;
- Wagner, Alex H.;
- Krysiak, Kilannin;
- Sonkin, Dmitriy;
- Micheel, Christine;
- McCoy, Matthew;
- Rao, Shruti;
- Raca, Gordana;
- Boca, Simina M.;
- Roy, Angshumoy;
- Barnell, Erica K.;
- McMichael, Joshua F.;
- Kiwala, Susanna;
- Coffman, Adam C.;
- Kujan, Lynzey;
- Kulkarni, Shashikant;
- Griffith, Malachi;
- Madhavan, Subha;
- Griffith, Obi L.
Publication type:
Article
The CAM Software for Nonnegative Blind Source Separation in R-Java.
Published in:
Journal of Machine Learning Research, 2013, v. 14, p. 2899
By:
- Niya Wang;
- Fan Meng;
- Li Chen;
- Madhavan, Subha;
- Clarke, Robert;
- Hoffman, Eric P.;
- Jianhua Xuan;
- Yue Wang
Publication type:
Article
Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02059-3
By:
- Do, Catherine;
- Dumont, Emmanuel L. P.;
- Salas, Martha;
- Castano, Angelica;
- Mujahed, Huthayfa;
- Maldonado, Leonel;
- Singh, Arunjot;
- DaSilva-Arnold, Sonia C.;
- Bhagat, Govind;
- Lehman, Soren;
- Christiano, Angela M.;
- Madhavan, Subha;
- Nagy, Peter L.;
- Green, Peter H. R.;
- Feinman, Rena;
- Trimble, Cornelia;
- Illsley, Nicholas P.;
- Marder, Karen;
- Honig, Lawrence;
- Monk, Catherine
Publication type:
Article
The impact of immunosuppressive agents on immune checkpoint inhibitor efficacy in patients with advanced melanoma: A real‐world, multicenter, retrospective study.
Published in:
Cancer (0008543X), 2023, v. 129, n. 12, p. 1885, doi. 10.1002/cncr.34742
By:
- Lev‐Ari, Shaked;
- Serzan, Michael;
- Wu, Tianmin;
- Ip, Andrew;
- Pascual, Lauren;
- Sinclaire, Brittany;
- Adams, Shari;
- Marafelias, Michael;
- Ayyagari, Lakshmi;
- Gill, Sarvarinder K.;
- Ma, Barbara;
- Zaemes, Jacob P.;
- Della Pia, Alexandra;
- Alaoui, Adil;
- Madhavan, Subha;
- Belouali, Anas;
- Pecora, Andrew;
- Ahn, Jaeil;
- Atkins, Michael B.;
- Shah, Neil J.
Publication type:
Article
AISAIC: a software suite for accurate identification of significant aberrations in cancers.
Published in:
Bioinformatics, 2014, v. 30, n. 3, p. 431, doi. 10.1093/bioinformatics/btt693
By:
- Zhang, Bai;
- Hou, Xuchu;
- Yuan, Xiguo;
- Shih, Ie-Ming;
- Zhang, Zhen;
- Clarke, Robert;
- Wang, Roger R.;
- Fu, Yi;
- Madhavan, Subha;
- Wang, Yue;
- Yu, Guoqiang
Publication type:
Article
DDN: a caBIG® analytical tool for differential network analysis.
Published in:
Bioinformatics, 2011, v. 27, n. 7, p. 1036, doi. 10.1093/bioinformatics/btr052
By:
- Zhang, Bai;
- Tian, Ye;
- Jin, Lu;
- Li, Huai;
- Shih, Ie-Ming;
- Madhavan, Subha;
- Clarke, Robert;
- Hoffman, Eric P.;
- Xuan, Jianhua;
- Hilakivi-Clarke, Leena;
- Wang, Yue
Publication type:
Article
PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification.
Published in:
Bioinformatics, 2011, v. 27, n. 5, p. 736, doi. 10.1093/bioinformatics/btq721
By:
- Yu, Guoqiang;
- Li, Huai;
- Ha, Sook;
- Shih, Ie−Ming;
- Clarke, Robert;
- Hoffman, Eric P.;
- Madhavan, Subha;
- Xuan, Jianhua;
- Wang, Yue
Publication type:
Article
Somatic cancer variant curation and harmonization through consensus minimum variant level data.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0367-z
By:
- Ritter, Deborah I.;
- Roychowdhury, Sameek;
- Roy, Angshumoy;
- Rao, Shruti;
- Landrum, Melissa J.;
- Sonkin, Dmitriy;
- Shekar, Mamatha;
- Davis, Caleb F.;
- Hart, Reece K.;
- Micheel, Christine;
- Weaver, Meredith;
- Van Allen, Eliezer M.;
- Parsons, Donald W.;
- McLeod, Howard L.;
- Watson, Michael S.;
- Plon, Sharon E.;
- Kulkarni, Shashikant;
- Madhavan, Subha
Publication type:
Article
eGARD: Extracting associations between genomic anomalies and drug responses from text.
Published in:
PLoS ONE, 2017, v. 12, n. 12, p. 1, doi. 10.1371/journal.pone.0189663
By:
- Mahmood, A. S. M. Ashique;
- Rao, Shruti;
- McGarvey, Peter;
- Wu, Cathy;
- Madhavan, Subha;
- Vijay-Shanker, K.
Publication type:
Article

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