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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
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 22, p. 1, doi. 10.1093/nar/gku1005
By:
- Xiaojia Tang;
- Baheti, Saurabh;
- Shameer, Khader;
- Thompson, Kevin J.;
- Wills, Quin;
- Nifang Niu;
- Holcomb, Ilona N.;
- Boutet, Stephane C.;
- Ramakrishnan, Ramesh;
- Kachergus, Jennifer M.;
- Kocher, Jean-Pierre A.;
- Weinshilboum, Richard M.;
- Liewei Wang;
- Thompson, E. Aubrey;
- Kalari, Krishna R.
Publication type:
Article
CONVERGENT ANALYSIS OF ENDOPHENOTYPES IN PROGRESSIVE SUPRANUCLEAR PALSY.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2016, v. 12, p. P1032, doi. 10.1016/j.jalz.2016.06.2137
By:
- Allen, Mariet;
- Wang, Xue;
- Younkin, Curtis S.;
- Serie, Daniel;
- Sun, Zhifu;
- Burgess, Jeremy D.;
- Baheti, Saurabh;
- Kouri, Naomi;
- Nguyen, Thuy;
- Lincoln, Sarah;
- Malphrus, Kimberly G.;
- Carrasquillo, Minerva M.;
- Zou, Fanggeng;
- Chai, High-Seng;
- Murray, Melissa E.;
- Schellenberg, Gerard D.;
- Younkin, Steven G.;
- Crook, Julia E.;
- Ordog, Tamas;
- Asmann, Yan W.
Publication type:
Article
Genetic and epigenetic influences on brain gene expression in psp.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2015, v. 11, n. 7, p. P490, doi. 10.1016/j.jalz.2015.06.561
By:
- Allen, Mariet;
- Wang, Xue;
- Younkin, Curtis S.;
- Burgess, Jeremy D.;
- Ballard, Travis;
- Serie, Daniel;
- Wang, Chen;
- Sun, Zhifu;
- Baheti, Saurabh;
- Carrasquillo, Minerva M.;
- Nguyen, Thuy;
- Malphrus, Kimberly G.;
- Lincoln, Sarah;
- Zou, Fanggeng;
- Chai, High-Seng;
- Schellenberg, Gerard D.;
- Younkin, Steven G.;
- Crook, Julia;
- Ordog, Tamas;
- Asmann, Yan W.
Publication type:
Article
Gene expression profiling and dna methylation in Alzheimer's disease brains.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2014, v. 10, p. P216, doi. 10.1016/j.jalz.2014.04.291
By:
- Allen, Mariet;
- Serie, Daniel;
- Sun, Zhifu;
- Baheti, Saurabh;
- Walsh, Mike;
- Zou, Fanggeng;
- Chai, High Seng;
- Younkin, Curtis;
- Siuda, Joanna;
- Burgess, Jeremy;
- Crook, Julia;
- Pancratz, V. Shane;
- Carrasquillo, Minerva M.;
- Nair, Asha;
- Middha, Sumit;
- Maharjan, Sooraj;
- Nguyen, Thuy;
- Ma, Li;
- Malphrus, Kimberly;
- Lincoln, Sarah
Publication type:
Article
Genomewide epigenetic study shows significant DNA hypermethylation in chronic rhinosinusitis versus control ethmoidal tissue.
Published in:
International Forum of Allergy & Rhinology, 2023, v. 13, n. 12, p. 2235, doi. 10.1002/alr.23205
By:
- Brar, Tripti;
- Baheti, Saurabh;
- Bhagwate, Aditya Vijay;
- Kita, Hirohito;
- Marino, Michael J.;
- Lal, Devyani
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
An Integrated Model of the Transcriptome of HER2-Positive Breast Cancer.
Published in:
PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079298
By:
- Kalari, Krishna R.;
- Necela, Brian M.;
- Tang, Xiaojia;
- Thompson, Kevin J.;
- Lau, Melissa;
- Eckel-Passow, Jeanette E.;
- Kachergus, Jennifer M.;
- Anderson, S. Keith;
- Sun, Zhifu;
- Baheti, Saurabh;
- Carr, Jennifer M.;
- Baker, Tiffany R.;
- Barman, Poulami;
- Radisky, Derek C.;
- Joseph, Richard W.;
- McLaughlin, Sarah A.;
- Chai, High-seng;
- Camille, Stephan;
- Rossell, David;
- Asmann, Yan W.
Publication type:
Article
Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2494-8
By:
- Baheti, Saurabh;
- Kanwar, Rahul;
- Goelzenleuchter, Meike;
- Kocher, Jean-Pierre A.;
- Beutler, Andreas S.;
- Zhifu Sun
Publication type:
Article
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Published in:
BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-224
By:
- Kalari, Krishna R.;
- Nair, Asha A.;
- Bhavsar, Jaysheel D.;
- O'Brien, Daniel R.;
- Davila, Jaime I.;
- Bockol, Matthew A.;
- Jinfu Nie;
- Xiaojia Tang;
- Baheti, Saurabh;
- Doughty, Jay B.;
- Middha, Sumit;
- Sicotte, Hugues;
- Thompson, Aubrey E.;
- Asmann, Yan W.;
- Kocher, Jean-Pierre A.
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
Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data.
Published in:
Briefings in Bioinformatics, 2018, v. 19, n. 3, p. 374, doi. 10.1093/bib/bbw133
By:
- Yun Zhang;
- Baheti, Saurabh;
- Zhifu Sun
Publication type:
Article
Next-Generation Sequencing of CYP2C19 in Stent Thrombosis: Implications for Clopidogrel Pharmacogenomics.
Published in:
Cardiovascular Drugs & Therapy, 2021, v. 35, n. 3, p. 549, doi. 10.1007/s10557-020-06988-w
By:
- Morales-Rosado, Joel A.;
- Goel, Kashish;
- Zhang, Lingxin;
- Åkerblom, Axel;
- Baheti, Saurabh;
- Black, John L.;
- Eriksson, Niclas;
- Wallentin, Lars;
- James, Stefan;
- Storey, Robert F.;
- Goodman, Shaun G.;
- Jenkins, Gregory D.;
- Eckloff, Bruce W.;
- Bielinski, Suzette J.;
- Sicotte, Hugues;
- Johnson, Stephen;
- Roger, Veronique L.;
- Wang, Liewei;
- Weinshilboum, Richard;
- Klee, Eric W.
Publication type:
Article
Germline miRNA DNA variants and the risk of colorectal cancer by subtype.
Published in:
Genes, Chromosomes & Cancer, 2017, v. 56, n. 3, p. 177, doi. 10.1002/gcc.22420
By:
- Lindor, Noralane M.;
- Larson, Melissa C.;
- DeRycke, Melissa S.;
- McDonnell, Shannon K.;
- Baheti, Saurabh;
- Fogarty, Zachary C.;
- Win, Aung Ko;
- Potter, John D.;
- Buchanan, Daniel D.;
- Clendenning, Mark;
- Newcomb, Polly A.;
- Casey, Graham;
- Gallinger, Steven;
- Le Marchand, Loïc;
- Hopper, John L.;
- Jenkins, Mark A.;
- Goode, Ellen L.;
- Thibodeau, Stephen N.
Publication type:
Article
Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci.
Published in:
Acta Neuropathologica, 2016, v. 132, n. 2, p. 197, doi. 10.1007/s00401-016-1576-7
By:
- Allen, Mariet;
- Burgess, Jeremy;
- Ballard, Travis;
- Serie, Daniel;
- Wang, Xue;
- Younkin, Curtis;
- Sun, Zhifu;
- Kouri, Naomi;
- Baheti, Saurabh;
- Wang, Chen;
- Carrasquillo, Minerva;
- Nguyen, Thuy;
- Lincoln, Sarah;
- Malphrus, Kimberly;
- Murray, Melissa;
- Golde, Todd;
- Price, Nathan;
- Younkin, Steven;
- Schellenberg, Gerard;
- Asmann, Yan
Publication type:
Article
Association of intraneural perineurioma with neurofibromatosis type 2.
Published in:
Acta Neurochirurgica, 2020, v. 162, n. 8, p. 1891, doi. 10.1007/s00701-020-04439-x
By:
- Pendleton, Courtney;
- Spinner, Robert J.;
- Dyck, P. James B.;
- Mauermann, Michelle L.;
- Ladak, Adil;
- Restrepo, Carlos E.;
- Baheti, Saurabh;
- Klein, Christopher J.
Publication type:
Article
HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.
Published in:
BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2260-9
By:
- Baheti, Saurabh;
- Tang, Xiaojia;
- O'Brien, Daniel R.;
- Chia, Nicholas;
- Roberts, Lewis R.;
- Nelson, Heidi;
- Boughey, Judy C.;
- Wang, Liewei;
- Goetz, Matthew P.;
- Kocher, Jean-Pierre A.;
- Kalari, Krishna R.
Publication type:
Article
An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set.
Published in:
PLoS ONE, 2019, v. 14, n. 4, p. 1, doi. 10.1371/journal.pone.0214588
By:
- DeRycke, Melissa S.;
- Larson, Melissa C.;
- Nair, Asha A.;
- McDonnell, Shannon K.;
- French, Amy J.;
- Tillmans, Lori S.;
- Riska, Shaun M.;
- Baheti, Saurabh;
- Fogarty, Zachary C.;
- Larson, Nicholas B.;
- O’Brien, Daniel R.;
- Cheville, John C.;
- Wang, Liang;
- Schaid, Daniel J.;
- Thibodeau, Stephen N.
Publication type:
Article
Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4<sup>+</sup> Lymphocytes in Crohn's Disease.
Published in:
Journal of Crohn's & Colitis, 2023, v. 17, n. 11, p. 1847, doi. 10.1093/ecco-jcc/jjad093
By:
- Sun, Zhifu;
- Braga-Neto, Manuel B;
- Xiong, Yuning;
- Bhagwate, Adytia V;
- Gibbons, Hunter R;
- Sagstetter, Mary R;
- Hamdan, Feda H;
- Baheti, Saurabh;
- Friton, Jessica;
- Nair, Asha;
- Ye, Zhenqing;
- Faubion, William A
Publication type:
Article
RVboost: RNA-seq variants prioritization using a boosting method.
Published in:
Bioinformatics, 2014, v. 30, n. 23, p. 3414, doi. 10.1093/bioinformatics/btu577
By:
- Wang, Chen;
- Davila, Jaime I.;
- Baheti, Saurabh;
- Bhagwate, Aditya V.;
- Wang, Xue;
- Kocher, Jean-Pierre A.;
- Slager, Susan L.;
- Feldman, Andrew L.;
- Novak, Anne J.;
- Cerhan, James R.;
- Thompson, E. Aubrey;
- Asmann, Yan W.
Publication type:
Article
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Published in:
Bioinformatics, 2012, v. 28, n. 16, p. 2180, doi. 10.1093/bioinformatics/bts337
By:
- Sun, Zhifu;
- Baheti, Saurabh;
- Middha, Sumit;
- Kanwar, Rahul;
- Zhang, Yuji;
- Li, Xing;
- Beutler, Andreas S.;
- Klee, Eric;
- Asmann, Yan W.;
- Thompson, E. Aubrey;
- Kocher, Jean-Pierre A.
Publication type:
Article
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Published in:
Bioinformatics, 2012, v. 28, n. 2, p. 277, doi. 10.1093/bioinformatics/btr612
By:
- Asmann, Yan W.;
- Middha, Sumit;
- Hossain, Asif;
- Baheti, Saurabh;
- Li, Ying;
- Chai, High-Seng;
- Sun, Zhifu;
- Duffy, Patrick H.;
- Hadad, Ahmed A.;
- Nair, Asha;
- Liu, Xiaoyu;
- Zhang, Yuji;
- Klee, Eric W.;
- Kalari, Krishna R.;
- Kocher, Jean-Pierre A.
Publication type:
Article
Genome-wide Epigenetic Study of Chronic Rhinosinusitis Tissues Reveals Dysregulated Inflammatory, Immunologic and Remodeling Pathways.
Published in:
American Journal of Rhinology & Allergy, 2023, v. 37, n. 6, p. 692, doi. 10.1177/19458924231193526
By:
- Brar, Tripti;
- Baheti, Saurabh;
- Marino, Michael J.;
- Kita, Hirohito;
- Lal, Devyani
Publication type:
Article

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