Publications

• 1. McCall MN
  2. Chu CY
  3. Wang L
  4. Benoodt L
  5. Thakar J
  6. Corbett A
  7. Holden-Wiltse J
  8. Slaunwhite C
  9. Grier A
  10. Gill SR
  11. Falsey AR
  12. Topham DJ
  13. Caserta MT
  14. Walsh EE
  15. Qiu X
  16. Mariani TJ
  A systems genomics approach uncovers molecular associates of RSV severity.; PLoS computational biology; Vol 17(12). 2021 Dec 28.
• 1. Chavali SS
  2. Mali SM
  3. Bonn R
  4. Saseendran A
  5. Bennett RP
  6. Smith HC
  7. Fasan R
  8. Wedekind JE
  Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells.; The Journal of biological chemistry. 2021 Nov 09.
• 1. Palshikar MG
  2. Hilchey SP
  3. Zand MS
  4. Thakar J
  WikiNetworks: translating manually created biological pathways for topological analysis.; Bioinformatics (Oxford, England). 2021 Oct 12.
• 1. Cognetti JS
  2. Steiner DJ
  3. Abedin M
  4. Bryan MR
  5. Shanahan C
  6. Tokranova N
  7. Young E
  8. Klose AM
  9. Zavriyev A
  10. Judy N
  11. Piorek B
  12. Meinhart C
  13. Jakubowicz R
  14. Warren H
  15. Cady NC
  16. Miller BL
  Disposable photonics for cost-effective clinical bioassays: application to COVID-19 antibody testing.; Lab on a chip. 2021 Jun 23.
• 1. Urban JM
  2. Chiang W
  3. Hammond JW
  4. Cogan NMB
  5. Litzburg A
  6. Burke R
  7. Stern HA
  8. Gelbard HA
  9. Nilsson BL
  10. Krauss TD
  Quantum Dots for Improved Single-Molecule Localization Microscopy.; The journal of physical chemistry. B. 2021 Mar 08.
• 1. Srivastava Y
  2. Bonn-Breach R
  3. Chavali SS
  4. Lippa GM
  5. Jenkins JL
  6. Wedekind JE
  Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.; Crystals; Vol 11(3). 2021 Mar.
• 1. Cornwell A
  2. Palli R
  3. Singh MV
  4. Benoodt L
  5. Tyrell A
  6. Abe JI
  7. Schifitto G
  8. Maggirwar SB
  9. Thakar J
  Molecular characterization of atherosclerosis in HIV positive persons.; Scientific reports; Vol 11(1). 2021 Feb 05.
• 1. Reilly EC
  2. Sportiello M
  3. Emo KL
  4. Amitrano AM
  5. Jha R
  6. Kumar ABR
  7. Laniewski NG
  8. Yang H
  9. Kim M
  10. Topham DJ
  CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection.; Frontiers in immunology; Vol 12. 2021.
• 1. Alon R
  2. Sportiello M
  3. Kozlovski S
  4. Kumar A
  5. Reilly EC
  6. Zarbock A
  7. Garbi N
  8. Topham DJ
  Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19.; Nature reviews. Immunology. 2020 Nov 19.
• 1. Chavali SS
  2. Cavender CE
  3. Mathews DH
  4. Wedekind JE
  Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove.; Journal of the American Chemical Society. 2020 Nov 10.
• 1. Chavali SS
  2. Mali SM
  3. Jenkins JL
  4. Fasan R
  5. Wedekind JE
  Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.; The Journal of biological chemistry. 2020 Oct 13.
• 1. Maji D
  2. Glasser E
  3. Henderson S
  4. Galardi J
  5. Pulvino MJ
  6. Jenkins JL
  7. Kielkopf CL
  Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.; The Journal of biological chemistry. 2020 Oct 05.
• 1. Steiner DJ
  2. Cognetti JS
  3. Luta EP
  4. Klose AM
  5. Bucukovski J
  6. Bryan MR
  7. Schmuke JJ
  8. Nguyen-Contant P
  9. Sangster MY
  10. Topham DJ
  11. Miller BL
  Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients.; Biosensors & bioelectronics; Vol 169. 2020 Sep 21.
• 1. Thakar J
  2. Qian Y
  3. Benoodt L
  4. Roumanes D
  5. Qiu X
  6. Laniewski N
  7. Chu C
  8. Slaunwhite C
  9. Wang L
  10. Mandava A
  11. Chang I
  12. Falsey AR
  13. Caserta MT
  14. Mariani TJ
  15. Scheuermann RH
  16. Walsh EE
  17. Topham DJ
  Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.; Vaccine: X; Vol 5. 2020 Aug 07.
• 1. Hilchey SP
  2. Palshikar MG
  3. Emo JA
  4. Li D
  5. Garigen J
  6. Wang J
  7. Mendelson ES
  8. Cipolla V
  9. Thakar J
  10. Zand MS
  Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch.; BMC immunology; Vol 21(1). 2020 Mar 18.
• 1. Benoodt L
  2. Thakar J
  Network Analysis of Large-Scale Data and Its Application to Immunology.; Methods in molecular biology (Clifton, N.J.); Vol 2131. 2020.
• 1. Maji D
  2. Grossfield AM
  3. Kielkopf CL
  Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.; Biochimica et biophysica acta. Gene regulatory mechanisms. 2019 Nov 07.
• 1. Palli R
  2. Palshikar MG
  3. Thakar J
  Executable pathway analysis using ensemble discrete-state modeling for large-scale data.; PLoS computational biology; Vol 15(9). 2019 Sep.
• 1. Walsh EE
  2. Mariani TJ
  3. Chu C
  4. Grier A
  5. Gill SR
  6. Qiu X
  7. Wang L
  8. Holden-Wiltse J
  9. Corbett A
  10. Thakar J
  11. Benoodt L
  12. McCall MN
  13. Topham DJ
  14. Falsey AR
  15. Caserta MT
  Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.; JMIR research protocols; Vol 8(6). 2019 Jun 06.
• 1. Chavali SS
  2. Bonn-Breach R
  3. Wedekind JE
  Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery.; The Journal of biological chemistry. 2019 May 12.
• 1. Loerch S
  2. Leach JR
  3. Horner SW
  4. Maji D
  5. Jenkins JL
  6. Pulvino M
  7. Kielkopf CL
  The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.; The Journal of biological chemistry. 2018 Dec 19.
• 1. Zhang H
  2. Henry C
  3. Anderson CS
  4. Nogales A
  5. DeDiego ML
  6. Bucukovski J
  7. Martinez-Sobrido L
  8. Wilson PC
  9. Topham DJ
  10. Miller BL
  Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza.; Analytical chemistry. 2018 Jul 09.
• 1. Bucukovski J
  2. Carter JA
  3. Striemer CC
  4. Müllner S
  5. Schulte-Pelkum J
  6. Schulz-Knappe P
  7. Miller BL
  Label-free microarray-based detection of autoantibodies in human serum.; Journal of immunological methods. 2018 May 23.
• 1. Bucukovski J
  2. Latorre-Margalef N
  3. Stallknecht DE
  4. Miller BL
  A Multiplex Label-Free Approach to Avian Influenza Surveillance and Serology.; PloS one; Vol 10(8). 2015.