22. CREPE: A Shiny App for Transcription Factor Cataloguing
Rosado-Tristani DA and Rodríguez-Martínez JA.
Bioinformatics Advances doi: 10.1093/bioadv/vbad055
21. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity
Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1866 (1) 194906 doi: 10.1016/j.bbagrm.2023.194906
20. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Ortiz-Ruiz Y, Montgomery SH, Ghezzi A, Rodríguez-Martínez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM.
Genome Research 2022, 32 (10) 1862-1875 doi: 10.1101/gr.276839.122
19. Laser-Activated Membrane Introduction Mass Spectrometry Study of Proton Spillover Promoted Alkane Dehydrogenation
Kim RY, Rivera H, Evarts SE, Rodríguez-Martínez JA, Willis RR, Galloway DB, Falih F, McCall MJ, Smith SJ, Perz K, Smotkin ES.
Analytical Chemistry 2020, 92 (19) 13462–13469 doi: 10.1021/acs.analchem.0c02886
18. De novo design of programmable inducible promoters
Liu X, Gupta STP, Bhimsaria D, Reed JL, Rodríguez-Martínez JA, Ansari AZ, Raman S
Nucleic Acids Research 2019, 47 (19) 10452-10463 doi: 10.1093/nar/gkz772
17. Specificity landscapes unmask submaximal binding site preferences of transcription factors
Bhimsaria D, Rodríguez-Martínez JA, Pan J, Roston D, Korkmaz EN, Cui Q, Ramanathan P, Ansari AZ
Proceedings of the National Academy of Sciences of the United States of America 2018, 115 (45) E10586-E10595 doi.org/10.1073/pnas.1811431115
16. Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif
Yella VR, Bhimsaria D, Ghoshdastidar D, Rodríguez-Martínez JA, Ansari AZ, Bansal M
Nucleic Acids Research, doi.org/10.1093/nar/gky1057
15. Aptamer-Based Impedimetric Assay of Arsenite in Water: Interfacial Properties and Performance
Vega-Figueroa K, Santillán J, Ortiz-Gómez V, Ortiz-Quiles EO, Quiñones-Colón BA, Castilla-Casadiego DA, Almodóvar J, Bayro MJ, Rodríguez-Martínez JA, Nicolau E
ACS Omega 2018, 3 (2), pp 1437–1444 doi: 10.1021/acsomega.7b01710
14. Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ
eLife 2017 doi: 10.7554/eLife.19272
13. Synthetic genome readers target clustered binding sites across diverse chromatin states
Erwin GS, Grieshop MP, Bhimsaria D, Do TJ, Rodríguez-Martínez JA, Mehta C, Khanna K, Swanson SA, Stewart R, Thomson JA, Ramanathan P, Ansari AZ
Proceedings of the National Academy of Sciences of the United States of America 2016, 113 (47) E7418-E7427 doi: 10.1073/pnas.1604847113
12. Genome-wide mapping of drug-DNA interactions in cells with COSMIC (crosslinking of small molecules for isolation of chromatin
Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ
Journal of visualized experiments 2016, 107, e53510. doi: 10.3791/53510
11. Evaluation of a urea bio-electrochemical system for wastewater treatment processes
Nicolau E, Fonseca JJ, Rodríguez-Martínez JA, Richardson TMJ, Flynn M, Griebenow K, Cabrera CR
ACS Sustainable Chemistry and Engineering, 2014, 2 749-754
*Highlighted by ACS Press, ScienceNOW, PBS News Hour, Huffington Post
10. Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity
Campbell, ZT, Bhimsaria, D, Valley, CT, Rodríguez-Martínez JA, Menichelli, E, Williamson, JR, Ansari AZ, Wickens, M
Cell Reports, 2012 1 (5) p570-581
*Highlighted in Cell 2012 149 1413-1415
9. Two-step Nanoprecipitation for the Production of Protein-loaded PLGA Nanospheres
Morales-Cruz M, Flores-Fernandez GM, Morales-Cruz M, Orellano EA, Rodríguez-Martínez JA, Ruiz M, Griebenow K
Results in Pharma Sciences, 2012, 2 79-85
8. Enhanced Stability of a Nanostructured Cytochrome c Biosensor by PEGylation
Santiago-Rodríguez L, Méndez J, Sánchez G, Pagán M, Rodríguez-Martínez JA, Cabrera CR, Griebenow KH
Journal of Electroanalytical Chemistry, 2011, 663 1-7
7. Prevention of benzyl alcohol-induced aggregation of chymotrypsinogen by PEGylation
Rodríguez-Martínez JA, Rivera-Rivera I, Griebenow K
Journal of Pharmacy and Pharmacology, 2011, 63 (6) 800-805
6. Small-molecule regulators that mimic transcription factors
Rodríguez-Martínez JA, Peterson-Kaufman KJ, Ansari AZ
Biochimica et Biophysica Acta – Gene Regulatory Mechanisms, 2010, 1799 (10-12) 768-774
5. Nucleating the assembly of macromolecular complexes
Peterson-Kaufman KJ, Carlson CD, Rodríguez-Martínez JA, Ansari AZ
ChemBioChem, 2010, 11 (14) 1955-1962
4. Enzymatic activity and thermal stability of PEG-α-chymotrypsin conjugates
Rodríguez-Martínez JA, Rivera-Rivera I, Solá RJ, Griebenow K
Biotechnology Letters, 2009 31 (6) 883-887 PMCID: PMC2719889
3. Stabilization of α-chymotrypsin upon PEGylation correlates with reduced structural dynamics
Rodríguez-Martínez JA, Solá RJ, Castillo B, Cintrón HR, Rivera-Rivera I, Barletta G, Griebenow K
Biotechnology and Bioengineering, 2008, 101 (6) 1142-1149
*Highlighted by B& B and by Staying Current: Formulations of Biopharmaceuticals
2. Modulation of protein biophysical properties by chemical glycosylation: biochemical insights and biomedical implications
Solá RJ, Rodríguez-Martínez JA, Griebenow K
Cellular and Molecular Life Sciences, 2007, 64 (16) 2133-2152
1. High-speed laser activated membrane introduction mass spectrometric evaluation of bulk methylcyclohexane dehydrogenation catalysts
Nayar A, Kim YT, Rodríguez J, Willis R, Galloway DB, Falih F, Smotkin ES
Applied Surface Science, 2004, 223 (1-3), 118-123
Rosado-Tristani DA and Rodríguez-Martínez JA.
Bioinformatics Advances doi: 10.1093/bioadv/vbad055
21. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity
Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1866 (1) 194906 doi: 10.1016/j.bbagrm.2023.194906
20. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Ortiz-Ruiz Y, Montgomery SH, Ghezzi A, Rodríguez-Martínez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM.
Genome Research 2022, 32 (10) 1862-1875 doi: 10.1101/gr.276839.122
19. Laser-Activated Membrane Introduction Mass Spectrometry Study of Proton Spillover Promoted Alkane Dehydrogenation
Kim RY, Rivera H, Evarts SE, Rodríguez-Martínez JA, Willis RR, Galloway DB, Falih F, McCall MJ, Smith SJ, Perz K, Smotkin ES.
Analytical Chemistry 2020, 92 (19) 13462–13469 doi: 10.1021/acs.analchem.0c02886
18. De novo design of programmable inducible promoters
Liu X, Gupta STP, Bhimsaria D, Reed JL, Rodríguez-Martínez JA, Ansari AZ, Raman S
Nucleic Acids Research 2019, 47 (19) 10452-10463 doi: 10.1093/nar/gkz772
17. Specificity landscapes unmask submaximal binding site preferences of transcription factors
Bhimsaria D, Rodríguez-Martínez JA, Pan J, Roston D, Korkmaz EN, Cui Q, Ramanathan P, Ansari AZ
Proceedings of the National Academy of Sciences of the United States of America 2018, 115 (45) E10586-E10595 doi.org/10.1073/pnas.1811431115
16. Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif
Yella VR, Bhimsaria D, Ghoshdastidar D, Rodríguez-Martínez JA, Ansari AZ, Bansal M
Nucleic Acids Research, doi.org/10.1093/nar/gky1057
15. Aptamer-Based Impedimetric Assay of Arsenite in Water: Interfacial Properties and Performance
Vega-Figueroa K, Santillán J, Ortiz-Gómez V, Ortiz-Quiles EO, Quiñones-Colón BA, Castilla-Casadiego DA, Almodóvar J, Bayro MJ, Rodríguez-Martínez JA, Nicolau E
ACS Omega 2018, 3 (2), pp 1437–1444 doi: 10.1021/acsomega.7b01710
14. Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ
eLife 2017 doi: 10.7554/eLife.19272
13. Synthetic genome readers target clustered binding sites across diverse chromatin states
Erwin GS, Grieshop MP, Bhimsaria D, Do TJ, Rodríguez-Martínez JA, Mehta C, Khanna K, Swanson SA, Stewart R, Thomson JA, Ramanathan P, Ansari AZ
Proceedings of the National Academy of Sciences of the United States of America 2016, 113 (47) E7418-E7427 doi: 10.1073/pnas.1604847113
12. Genome-wide mapping of drug-DNA interactions in cells with COSMIC (crosslinking of small molecules for isolation of chromatin
Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ
Journal of visualized experiments 2016, 107, e53510. doi: 10.3791/53510
11. Evaluation of a urea bio-electrochemical system for wastewater treatment processes
Nicolau E, Fonseca JJ, Rodríguez-Martínez JA, Richardson TMJ, Flynn M, Griebenow K, Cabrera CR
ACS Sustainable Chemistry and Engineering, 2014, 2 749-754
*Highlighted by ACS Press, ScienceNOW, PBS News Hour, Huffington Post
10. Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity
Campbell, ZT, Bhimsaria, D, Valley, CT, Rodríguez-Martínez JA, Menichelli, E, Williamson, JR, Ansari AZ, Wickens, M
Cell Reports, 2012 1 (5) p570-581
*Highlighted in Cell 2012 149 1413-1415
9. Two-step Nanoprecipitation for the Production of Protein-loaded PLGA Nanospheres
Morales-Cruz M, Flores-Fernandez GM, Morales-Cruz M, Orellano EA, Rodríguez-Martínez JA, Ruiz M, Griebenow K
Results in Pharma Sciences, 2012, 2 79-85
8. Enhanced Stability of a Nanostructured Cytochrome c Biosensor by PEGylation
Santiago-Rodríguez L, Méndez J, Sánchez G, Pagán M, Rodríguez-Martínez JA, Cabrera CR, Griebenow KH
Journal of Electroanalytical Chemistry, 2011, 663 1-7
7. Prevention of benzyl alcohol-induced aggregation of chymotrypsinogen by PEGylation
Rodríguez-Martínez JA, Rivera-Rivera I, Griebenow K
Journal of Pharmacy and Pharmacology, 2011, 63 (6) 800-805
6. Small-molecule regulators that mimic transcription factors
Rodríguez-Martínez JA, Peterson-Kaufman KJ, Ansari AZ
Biochimica et Biophysica Acta – Gene Regulatory Mechanisms, 2010, 1799 (10-12) 768-774
5. Nucleating the assembly of macromolecular complexes
Peterson-Kaufman KJ, Carlson CD, Rodríguez-Martínez JA, Ansari AZ
ChemBioChem, 2010, 11 (14) 1955-1962
4. Enzymatic activity and thermal stability of PEG-α-chymotrypsin conjugates
Rodríguez-Martínez JA, Rivera-Rivera I, Solá RJ, Griebenow K
Biotechnology Letters, 2009 31 (6) 883-887 PMCID: PMC2719889
3. Stabilization of α-chymotrypsin upon PEGylation correlates with reduced structural dynamics
Rodríguez-Martínez JA, Solá RJ, Castillo B, Cintrón HR, Rivera-Rivera I, Barletta G, Griebenow K
Biotechnology and Bioengineering, 2008, 101 (6) 1142-1149
*Highlighted by B& B and by Staying Current: Formulations of Biopharmaceuticals
2. Modulation of protein biophysical properties by chemical glycosylation: biochemical insights and biomedical implications
Solá RJ, Rodríguez-Martínez JA, Griebenow K
Cellular and Molecular Life Sciences, 2007, 64 (16) 2133-2152
1. High-speed laser activated membrane introduction mass spectrometric evaluation of bulk methylcyclohexane dehydrogenation catalysts
Nayar A, Kim YT, Rodríguez J, Willis R, Galloway DB, Falih F, Smotkin ES
Applied Surface Science, 2004, 223 (1-3), 118-123