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Richard I. Sherwood, Ph.D. - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
Development
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34 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
2021 Akinci E, Hamilton MC, Khowpinitchai B, Sherwood RI. Using CRISPR to understand and manipulate gene regulation. Development (Cambridge, England). 148. PMID 33913466 DOI: 10.1242/dev.182667  0.344
2021 Yeo GHT, Juez O, Chen Q, Banerjee B, Chu L, Shen MW, Sabry M, Logister I, Sherwood RI, Gifford DK. Detection of gene cis-regulatory element perturbations in single-cell transcriptomes. Plos Computational Biology. 17: e1008789. PMID 33711017 DOI: 10.1371/journal.pcbi.1008789  0.313
2020 Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Research. PMID 32973041 DOI: 10.1101/gr.263228.120  0.349
2020 Szczesnik T, Chu L, Ho JWK, Sherwood RI. A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding. Cell Systems. PMID 32910904 DOI: 10.1016/J.Cels.2020.08.004  0.319
2020 Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation. Cell Stem Cell. PMID 32459995 DOI: 10.1016/J.Stem.2020.04.020  0.461
2019 Szczesnik T, Ho JWK, Sherwood R. Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding. Epigenetics & Chromatin. 12: 36. PMID 31196130 DOI: 10.1186/S13072-019-0273-X  0.317
2017 Kang D, Sherwood R, Barkal A, Hashimoto T, Engstrom L, Gifford D. DNase-capture reveals differential transcription factor binding modalities. Plos One. 12: e0187046. PMID 29284001 DOI: 10.1371/Journal.Pone.0187046  0.326
2017 Banerjee B, Sherwood RI. A CRISPR view of gene regulation. Current Opinion in Systems Biology. 1: 1-8. PMID 28966990 DOI: 10.1016/J.Coisb.2016.12.016  0.334
2017 Betancur PA, Abraham BJ, Yiu YY, Willingham SB, Khameneh F, Zarnegar M, Kuo AH, McKenna K, Kojima Y, Leeper NJ, Ho P, Gip P, Swigut T, Sherwood RI, Clarke MF, et al. A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nature Communications. 8: 14802. PMID 28378740 DOI: 10.1038/Ncomms14802  0.423
2016 Arbab M, Sherwood RI. Self-Cloning CRISPR. Current Protocols in Stem Cell Biology. 38: 5B.5.1-5B.5.16. PMID 27532819 DOI: 10.1002/Cpsc.14  0.406
2016 Hashimoto TB, Sherwood R, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford D. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Research. PMID 27456004 DOI: 10.1101/Gr.199778.115  0.305
2016 Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proceedings of the National Academy of Sciences of the United States of America. PMID 27078102 DOI: 10.1073/Pnas.1602886113  0.69
2016 Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI. Cas9 Functionally Opens Chromatin. Plos One. 11: e0152683. PMID 27031353 DOI: 10.1371/Journal.Pone.0152683  0.323
2016 Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, Syed T, Emons BJ, Gifford DK, Sherwood RI. High-throughput mapping of regulatory DNA. Nature Biotechnology. PMID 26807528 DOI: 10.1038/nbt.3468  0.323
2015 Arbab M, Srinivasan S, Hashimoto T, Geijsen N, Sherwood RI. Cloning-free CRISPR. Stem Cell Reports. 5: 908-917. PMID 26527385 DOI: 10.1016/J.Stemcr.2015.09.022  0.362
2015 Wamaitha SE, Del Valle I, Cho LT, Wei Y, Fogarty NM, Blakeley P, Sherwood RI, Ji H, Niakan KK. Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells. Genes & Development. 29: 1239-55. PMID 26109048 DOI: 10.1101/Gad.257071.114  0.542
2014 Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK. An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. Plos Computational Biology. 10: e1003501. PMID 24675637 DOI: 10.1371/Journal.Pcbi.1003501  0.307
2014 Nissim S, Sherwood RI, Wucherpfennig J, Saunders D, Harris JM, Esain V, Carroll KJ, Frechette GM, Kim AJ, Hwang KL, Cutting CC, Elledge S, North TE, Goessling W. Prostaglandin E2 regulates liver versus pancreas cell-fate decisions and endodermal outgrowth. Developmental Cell. 28: 423-37. PMID 24530296 DOI: 10.1016/J.Devcel.2014.01.006  0.402
2014 Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nature Biotechnology. 32: 171-8. PMID 24441470 DOI: 10.1038/Nbt.2798  0.361
2013 Chen AE, Borowiak M, Sherwood RI, Kweudjeu A, Melton DA. Functional evaluation of ES cell-derived endodermal populations reveals differences between Nodal and Activin A-guided differentiation. Development (Cambridge, England). 140: 675-86. PMID 23293299 DOI: 10.1242/Dev.085431  0.664
2012 Cho LT, Wamaitha SE, Tsai IJ, Artus J, Sherwood RI, Pedersen RA, Hadjantonakis AK, Niakan KK. Conversion from mouse embryonic to extra-embryonic endoderm stem cells reveals distinct differentiation capacities of pluripotent stem cell states. Development (Cambridge, England). 139: 2866-77. PMID 22791892 DOI: 10.1242/Dev.078519  0.519
2012 Kim BM, Thier MC, Oh S, Sherwood R, Kanellopoulou C, Edenhofer F, Choi MY. MicroRNAs are indispensable for reprogramming mouse embryonic fibroblasts into induced stem cell-like cells. Plos One. 7: e39239. PMID 22737231 DOI: 10.1371/Journal.Pone.0039239  0.459
2012 Hashimoto T, Jaakkola T, Sherwood R, Mazzoni EO, Wichterle H, Gifford D. Lineage-based identification of cellular states and expression programs. Bioinformatics (Oxford, England). 28: i250-7. PMID 22689769 DOI: 10.1093/Bioinformatics/Bts204  0.393
2012 Mou H, Zhao R, Sherwood R, Ahfeldt T, Lapey A, Wain J, Sicilian L, Izvolsky K, Musunuru K, Cowan C, Rajagopal J. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell. 10: 385-97. PMID 22482504 DOI: 10.1016/J.Stem.2012.01.018  0.693
2011 Sherwood RI, Maehr R, Mazzoni EO, Melton DA. Wnt signaling specifies and patterns intestinal endoderm. Mechanisms of Development. 128: 387-400. PMID 21854845 DOI: 10.1016/J.Mod.2011.07.005  0.707
2010 Niakan KK, Ji H, Maehr R, Vokes SA, Rodolfa KT, Sherwood RI, Yamaki M, Dimos JT, Chen AE, Melton DA, McMahon AP, Eggan K. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes & Development. 24: 312-26. PMID 20123909 DOI: 10.1101/Gad.1833510  0.735
2009 Sherwood RI, Chen TY, Melton DA. Transcriptional dynamics of endodermal organ formation. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 238: 29-42. PMID 19097184 DOI: 10.1002/Dvdy.21810  0.582
2008 Cerletti M, Shadrach JL, Jurga S, Sherwood R, Wagers AJ. Regulation and function of skeletal muscle stem cells. Cold Spring Harbor Symposia On Quantitative Biology. 73: 317-22. PMID 19204065 DOI: 10.1101/Sqb.2008.73.054  0.316
2008 Anderson WJ, Zhou Q, Alcalde V, Kaneko OF, Blank LJ, Sherwood RI, Guseh JS, Rajagopal J, Melton DA. Genetic targeting of the endoderm with claudin-6CreER. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 237: 504-12. PMID 18213590 DOI: 10.1002/Dvdy.21437  0.716
2007 Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA. Prospective isolation and global gene expression analysis of definitive and visceral endoderm. Developmental Biology. 304: 541-55. PMID 17328885 DOI: 10.1016/J.Ydbio.2007.01.011  0.647
2006 Sherwood RI, Wagers AJ. Harnessing the potential of myogenic satellite cells. Trends in Molecular Medicine. 12: 189-92. PMID 16595190 DOI: 10.1016/J.Molmed.2006.03.002  0.343
2004 Sherwood RI, Christensen JL, Weissman IL, Wagers AJ. Determinants of skeletal muscle contributions from circulating cells, bone marrow cells, and hematopoietic stem cells. Stem Cells (Dayton, Ohio). 22: 1292-304. PMID 15579647 DOI: 10.1634/Stemcells.2004-0090  0.489
2004 Sherwood RI, Christensen JL, Conboy IM, Conboy MJ, Rando TA, Weissman IL, Wagers AJ. Isolation of adult mouse myogenic progenitors: functional heterogeneity of cells within and engrafting skeletal muscle. Cell. 119: 543-54. PMID 15537543 DOI: 10.1016/J.Cell.2004.10.021  0.504
2002 Wagers AJ, Sherwood RI, Christensen JL, Weissman IL. Little evidence for developmental plasticity of adult hematopoietic stem cells. Science (New York, N.Y.). 297: 2256-9. PMID 12215650 DOI: 10.1126/Science.1074807  0.535
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