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Kenneth D. Birnbaum, Ph.D. - Publications

Affiliations: 
2000 New York University, New York, NY, United States 
Area:
Genetics, Environmental Sciences, Botany Biology
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70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Camo-Escobar D, Alcalá-Gutiérrez C, Palafox-Figueroa E, Guillotin B, Hernández-Coronado M, Coyac-Rodríguez JL, Cerbantez-Bueno VE, Vélez-Ramírez A, de Folter S, Birnbaum KD, Ortiz-Ramírez C. A common regulatory switch controls a suite of C4 traits in multiple cell types. Biorxiv : the Preprint Server For Biology. PMID 38260543 DOI: 10.1101/2023.12.21.572850  0.631
2023 Lee LR, Guillotin B, Hutchison C, Desvoyes B, Gutierrez C, Birnbaum KD. Nuclear GSH import precedes coordinated cell cycle changes during regeneration. Biorxiv : the Preprint Server For Biology. PMID 38168452 DOI: 10.1101/2023.11.28.569014  0.621
2023 Coruzzi GM, Birnbaum KD. Philip N. Benfey (1953-2023). Science (New York, N.Y.). 382: 1127. PMID 38060662 DOI: 10.1126/science.adl4710  0.701
2023 Huang T, Guillotin B, Rahni R, Birnbaum KD, Wagner D. A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol. Plant Methods. 19: 131. PMID 37993896 DOI: 10.1186/s13007-023-01108-9  0.628
2023 Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature. PMID 37165193 DOI: 10.1038/s41586-023-06053-0  0.652
2022 Rice SL, Lazarus E, Anderton C, Birnbaum K, Brophy J, Cole B, Dickel D, Ehrhardt D, Fahlgren N, Frank M, Haswell E, Huang SC, Leiboff S, Libault M, Otegui MS, et al. First Plant Cell Atlas symposium report. Plant Direct. 6: e406. PMID 35774620 DOI: 10.1002/pld3.406  0.559
2022 Hernández-Coronado M, Dias Araujo PC, Ip PL, Nunes CO, Rahni R, Wudick MM, Lizzio MA, Feijó JA, Birnbaum KD. Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense. Developmental Cell. PMID 35148835 DOI: 10.1016/j.devcel.2022.01.013  0.614
2021 Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, ... ... Birnbaum KD, et al. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science (New York, N.Y.). 374: eaba5531. PMID 34941412 DOI: 10.1126/science.aba5531  0.79
2021 Birnbaum KD, Otegui MS, Bailey-Serres J, Rhee SY. The Plant Cell Atlas: Focusing New Technologies on the Kingdom that Nourishes the Planet. Plant Physiology. PMID 34935969 DOI: 10.1093/plphys/kiab584  0.615
2021 Ortiz-Ramírez C, Guillotin B, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D, Gallagher KL, Birnbaum KD. Ground tissue circuitry regulates organ complexity in maize and . Science (New York, N.Y.). 374: 1247-1252. PMID 34855479 DOI: 10.1126/science.abj2327  0.523
2021 Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, ... ... Birnbaum KD, et al. Vision, challenges and opportunities for a Plant Cell Atlas. Elife. 10. PMID 34491200 DOI: 10.7554/eLife.66877  0.652
2021 Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A, Gude I, Cabrera J, Ip PL, Birnbaum KD, Moreno-Risueno MA. RECONSTRUCTION OF LATERAL ROOT FORMATION THROUGH SINGLE-CELL RNA-SEQ REVEALS ORDER OF TISSUE INITIATION. Molecular Plant. PMID 34062316 DOI: 10.1016/j.molp.2021.05.028  0.796
2021 Seyfferth C, Renema J, Wendrich JR, Eekhout T, Seurinck R, Vandamme N, Blob B, Saeys Y, Helariutta Y, Birnbaum KD, De Rybel B. Advances and Opportunities of Single-Cell Transcriptomics for Plant Research. Annual Review of Plant Biology. PMID 33730513 DOI: 10.1146/annurev-arplant-081720-010120  0.756
2020 Rice S, Fryer E, Ghosh Jha S, Malkovskiy A, Meyer H, Thomas J, Weizbauer R, Zhao K, Birnbaum K, Ehrhardt D, Wang Z, Rhee SY. First plant cell atlas workshop report. Plant Direct. 4: e00271. PMID 33083684 DOI: 10.1002/pld3.271  0.66
2020 Wang L, Lu Z, delaBastide M, Van Buren P, Wang X, Ghiban C, Regulski M, Drenkow J, Xu X, Ortiz-Ramirez C, Marco CF, Goodwin S, Dobin A, Birnbaum KD, Jackson DP, et al. Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science. 11: 289. PMID 32296450 DOI: 10.3389/Fpls.2020.00289  0.567
2020 Guillotin B, Birnbaum KD. Just passing through: The auxin gradient of the root meristem. Current Topics in Developmental Biology. 137: 433-454. PMID 32143752 DOI: 10.1016/Bs.Ctdb.2019.12.001  0.682
2019 Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, et al. Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct. 3: e00133. PMID 31245771 DOI: 10.1002/pld3.133  0.716
2019 Rahni R, Birnbaum KD. Week-long imaging of cell divisions in the Arabidopsis root meristem. Plant Methods. 15: 30. PMID 30988691 DOI: 10.1186/S13007-019-0417-9  0.639
2019 Rhee SY, Birnbaum KD, Ehrhardt DW. Towards Building a Plant Cell Atlas. Trends in Plant Science. PMID 30777643 DOI: 10.1016/J.Tplants.2019.01.006  0.674
2018 Mello A, Efroni I, Rahni R, Birnbaum KD. The New Phytologist. PMID 30614003 DOI: 10.1111/Nph.15630  0.66
2018 Birnbaum KD. Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues. Annual Review of Genetics. PMID 30192636 DOI: 10.1146/Annurev-Genet-120417-031247  0.617
2018 Ortiz-Ramírez C, Arevalo ED, Xu X, Jackson DP, Birnbaum KD. An Efficient Cell Sorting Protocol for Maize Protoplasts. Current Protocols in Plant Biology. e20072. PMID 30138552 DOI: 10.1002/cppb.20072  0.654
2017 Birnbaum KD, Roudier F. Epigenetic memory and cell fate reprogramming in plants. Regeneration (Oxford, England). 4: 15-20. PMID 28316791 DOI: 10.1002/reg2.73  0.661
2016 Ristova D, Carré C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G. Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. Science Signaling. 9: rs13. PMID 27811143 DOI: 10.1126/Scisignal.Aaf2768  0.797
2016 Birnbaum KD. How many ways are there to make a root? Current Opinion in Plant Biology. 34: 61-67. PMID 27780106 DOI: 10.1016/J.Pbi.2016.10.001  0.656
2016 Rahni R, Efroni I, Birnbaum KD. A Case for Distributed Control of Local Stem Cell Behavior in Plants. Developmental Cell. 38: 635-42. PMID 27676436 DOI: 10.1016/J.Devcel.2016.08.015  0.657
2016 Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD. Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell. PMID 27212234 DOI: 10.1016/J.Cell.2016.04.046  0.773
2016 Efroni I, Birnbaum KD. The potential of single-cell profiling in plants. Genome Biology. 17: 65. PMID 27048384 DOI: 10.1186/S13059-016-0931-2  0.704
2016 Rahni R, Birnbaum KD. Plant Cell Shape: Trafficking Gets Edgy. Developmental Cell. 36: 353-4. PMID 26906728 DOI: 10.1016/J.Devcel.2016.02.005  0.64
2015 Birnbaum KD. Development: Acting your cellular age. Nature Plants. 1: 15100. PMID 27250264 DOI: 10.1038/Nplants.2015.100  0.672
2015 Li B, Byrt CS, Qiu J, Baumann U, Hrmova M, Evrard A, Johnson AA, Birnbaum KD, Mayo GM, Jha D, Henderson SW, Tester M, Gilliham M, Roy SJ. Identification of a stelar-localised transport protein that facilitates root-to-shoot transfer of chloride in Arabidopsis. Plant Physiology. PMID 26662602 DOI: 10.1104/Pp.15.01163  0.638
2015 Adrian J, Chang J, Ballenger CE, Bargmann BO, Alassimone J, Davies KA, Lau OS, Matos JL, Hachez C, Lanctot A, Vatén A, Birnbaum KD, Bergmann DC. Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population. Developmental Cell. 33: 107-18. PMID 25850675 DOI: 10.1016/J.Devcel.2015.01.025  0.681
2015 Ip PL, Birnbaum KD. Tissue-specific gene expression profiling by cell sorting. Methods in Molecular Biology (Clifton, N.J.). 1284: 175-83. PMID 25757772 DOI: 10.1007/978-1-4939-2444-8_8  0.62
2015 Efroni I, Ip PL, Nawy T, Mello A, Birnbaum KD. Quantification of cell identity from single-cell gene expression profiles. Genome Biology. 16: 9. PMID 25608970 DOI: 10.1186/S13059-015-0580-X  0.754
2015 Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM. Correction: Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture (Proceedings of the National Academy of Sciences of the United States of America (2015) 110 (15133-15138) DOI: 0.1073/pnas.1305883110) Proceedings of the National Academy of Sciences of the United States of America. 112: E2555. DOI: 10.1073/Pnas.1507065112  0.765
2014 Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 111: 10371-6. PMID 24958886 DOI: 10.1073/Pnas.1404657111  0.707
2014 Bargmann BO, Birnbaum KD, Brenner ED. An undergraduate study of two transcription factors that promote lateral root formation. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. 42: 237-45. PMID 24615800 DOI: 10.1002/Bmb.20780  0.639
2013 Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD. Plasticity regulators modulate specific root traits in discrete nitrogen environments. Plos Genetics. 9: e1003760. PMID 24039603 DOI: 10.1371/Journal.Pgen.1003760  0.801
2013 Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD. A map of cell type-specific auxin responses. Molecular Systems Biology. 9: 688. PMID 24022006 DOI: 10.1038/Msb.2013.40  0.765
2013 Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proceedings of the National Academy of Sciences of the United States of America. 110: 15133-8. PMID 23980140 DOI: 10.1073/Pnas.1305883110  0.8
2013 Efroni I, Han SK, Kim HJ, Wu MF, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Developmental Cell. 24: 438-45. PMID 23449474 DOI: 10.1016/J.Devcel.2013.01.019  0.631
2013 Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G. TARGET: a transient transformation system for genome-wide transcription factor target discovery. Molecular Plant. 6: 978-80. PMID 23335732 DOI: 10.1093/Mp/Sst010  0.669
2013 Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiology. 161: 1086-96. PMID 23335624 DOI: 10.1104/Pp.112.210872  0.742
2012 Evrard A, Bargmann BO, Birnbaum KD, Tester M, Baumann U, Johnson AA. Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice. Methods in Molecular Biology (Clifton, N.J.). 913: 265-76. PMID 22895766 DOI: 10.1007/978-1-61779-986-0_18  0.659
2012 Fernandez AG, Bargmann BO, Mis EK, Edgley ML, Birnbaum KD, Piano F. High-throughput fluorescence-based isolation of live C. elegans larvae. Nature Protocols. 7: 1502-10. PMID 22814389 DOI: 10.1038/Nprot.2012.084  0.585
2012 Birnbaum KD. Low-cost sequencing opens new insights into diverse plant genomes. Genome Biology. 13: 311. PMID 22289505 DOI: 10.1186/Gb-2012-13-1-311  0.635
2011 Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM. Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proceedings of the National Academy of Sciences of the United States of America. 108: 18524-9. PMID 22025711 DOI: 10.1073/Pnas.1108684108  0.75
2011 Birnbaum KD, Kussell E. Measuring cell identity in noisy biological systems. Nucleic Acids Research. 39: 9093-107. PMID 21803789 DOI: 10.1093/Nar/Gkr591  0.656
2011 Sena G, Frentz Z, Birnbaum KD, Leibler S. Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. Plos One. 6: e21303. PMID 21731697 DOI: 10.1371/Journal.Pone.0021303  0.799
2010 Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD. Predicting genome-wide redundancy using machine learning. Bmc Evolutionary Biology. 10: 357. PMID 21087504 DOI: 10.1186/1471-2148-10-357  0.58
2010 Nawy T, Bayer M, Mravec J, Friml J, Birnbaum KD, Lukowitz W. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. Developmental Cell. 19: 103-13. PMID 20643354 DOI: 10.1016/J.Devcel.2010.06.004  0.743
2010 Sena G, Birnbaum KD. Built to rebuild: in search of organizing principles in plant regeneration. Current Opinion in Genetics & Development. 20: 460-5. PMID 20537526 DOI: 10.1016/J.Gde.2010.04.011  0.81
2010 Fernandez AG, Mis EK, Bargmann BO, Birnbaum KD, Piano F. Automated sorting of live C. elegans using laFACS. Nature Methods. 7: 417-8. PMID 20436474 DOI: 10.1038/Nmeth.F.304  0.617
2010 Bargmann BO, Birnbaum KD. Fluorescence activated cell sorting of plant protoplasts. Journal of Visualized Experiments : Jove. PMID 20168296 DOI: 10.3791/1673  0.69
2009 Benfey PN, Birnbaum KD. Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 238: 2449-58. PMID 19653311 DOI: 10.1002/dvdy.22042  0.708
2009 Sena G, Wang X, Liu HY, Hofhuis H, Birnbaum KD. Organ regeneration does not require a functional stem cell niche in plants. Nature. 457: 1150-3. PMID 19182776 DOI: 10.1038/Nature07597  0.815
2009 Bargmann BO, Birnbaum KD. Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts. Plant Physiology. 149: 1231-9. PMID 19168642 DOI: 10.1104/Pp.108.133975  0.677
2008 Birnbaum KD, Sánchez Alvarado A. Slicing across kingdoms: regeneration in plants and animals. Cell. 132: 697-710. PMID 18295584 DOI: 10.1016/J.Cell.2008.01.040  0.682
2008 Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD. Cell-specific nitrogen responses mediate developmental plasticity. Proceedings of the National Academy of Sciences of the United States of America. 105: 803-8. PMID 18180456 DOI: 10.1073/Pnas.0709559105  0.807
2008 Krouk G, Gutiérrez R, Gifford M, Birnbaum K, Shasha G, Coruzzi G. A systems approach to nitrogen regulatory networks and the Virtual Plant Comparative Biochemistry and Physiology Part a: Molecular & Integrative Physiology. 150: S46. DOI: 10.1016/J.Cbpa.2008.04.024  0.723
2006 Galbraith DW, Birnbaum K. Global studies of cell type-specific gene expression in plants. Annual Review of Plant Biology. 57: 451-75. PMID 16669770 DOI: 10.1146/Annurev.Arplant.57.032905.105302  0.701
2006 Gifford ML, Gutierrez RA, Birnbaum KD, Coruzzi GM. A systems approach to understanding N_control of gene networks in the Arabidopsis root Developmental Biology. 295: 334. DOI: 10.1016/J.Ydbio.2006.04.041  0.774
2005 Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nature Methods. 2: 615-9. PMID 16170893 DOI: 10.1038/Nmeth0805-615  0.741
2005 Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN. Transcriptional profile of the Arabidopsis root quiescent center. The Plant Cell. 17: 1908-25. PMID 15937229 DOI: 10.1105/Tpc.105.031724  0.791
2004 Birnbaum K, Benfey PN. Network building: transcriptional circuits in the root. Current Opinion in Plant Biology. 7: 582-8. PMID 15337102 DOI: 10.1016/J.Pbi.2004.07.010  0.738
2003 Birnbaum K, Desalle R, Peters CM, Benfey PN. Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae). American Journal of Botany. 90: 1619-27. PMID 21653337 DOI: 10.3732/Ajb.90.11.1619  0.7
2003 Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN. A gene expression map of the Arabidopsis root. Science (New York, N.Y.). 302: 1956-60. PMID 14671301 DOI: 10.1126/Science.1090022  0.717
2002 Colinas J, Birnbaum K, Benfey PN. Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiology. 129: 451-4. PMID 12068091 DOI: 10.1104/Pp.002501  0.748
2002 Birnbaum K, Benfey PN, Peters CM, Desalle R. MANAGEDPOP: A computer simulation to project allelic diversity in managed populations with overlapping generations Molecular Ecology Notes. 2: 615-617. DOI: 10.1046/J.1471-8286.2002.00284.X  0.64
2001 Birnbaum K, Benfey PN, Shasha DE. cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Research. 11: 1567-73. PMID 11544201 DOI: 10.1101/Gr.158301  0.68
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