References
PBM Data from the following papers are included in UniPROBE:
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Publication accession: ADMhpB - Alibes A, Nadra AD, De Masi F, Bulyk ML, Serrano L, Stricher F. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res. (2010) Aug 4. [Epub ahead of print]
Publication accession: ALI11A - 1
Publication accession: B - *Badis G, *Berger MF, *Philippakis AA, *Talukder S, *Gehrke AR, *Jaeger SA, *Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang C-F, Coburn D, Newburger D, Morris QD, †Hughes TR, †Bulyk ML. Diversity and complexity in DNA recognition by transcription factors. Science. 2009 May 14. [Epub ahead of print] (*co-1st authors; †co-corresponding authors)
Publication accession: BAD09A - Barrera LA, Vedenko A*, Kurland JV*, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ , Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science (2016) (*co-2nd authors)
Publication accession: BAR15A - *Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: BER06A - *Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: BER06A - *Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: BER06A - *Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: BER06A - *Berger MF, *Badis G, *Gehrke AR, *Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, †Bulyk ML, †Hughes TR. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell June 27, 2008; 133:1266-1276 (doi:10.1016/j.cell.2008.05.024) (*co-1st authors; †co-corresponding authors).
Publication accession: BER08A - Victoria A. Bonnell, Yuning Zhang, Alan S. Brown, John Horton, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, and Manuel Llinás. DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum. Nucleic Acids Research September 2022.
Publication accession: BON22A - *Busser BW, *Shokri L, *Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, †Bulyk ML, †Michelson AM. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development (2012) 139:1164-1174. Epub Feb 6 2012.
Publication accession: BUS12A - Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM. Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network. PNAS (2012) 109(50):20768-73. Epub 2012 Nov 26
Publication accession: BUS12B - Campbell TL, De Silva EK, Olszewski KL, Elemento O, Llinás M. 2010. Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog 26(10):e1001165.
Publication accession: CAM10A - Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Molecular Biology and Evolution. (2010) Jul 12. [Epub ahead of print]
Publication accession: CHE14A - Datta et al. A Feed-forward Loop between Bicoid and Orthodenticle Patterns the Early Drosophila Embryo. Sept 2017.
Publication accession: DAT17A - Del Bianco C, Vedenko A, Choi S-H, Berger MF, Shokri L, †Bulyk ML, †Blacklow SC. Notch and MAML-1 complexation do not detectably alter the DNA binding specificity of the transcription factor CSL. PLoS ONE (2010) Nov 24;5(11):e15034
Publication accession: DEL10A - *De Masi F, *Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, †Bulyk ML, †Walhout AJM. Using a structural and logics systems approach to infer bHLH DNA binding specificity determinants. Nucleic Acids Research. Jul 29;12(7):R70.
Publication accession: DEM11A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398
Publication accession: DES08A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398
Publication accession: DES08A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.\r\n*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: DES08B - The Palestinian people have endured decades of suffering, including what many describe as a slow and systematic genocide. We implore the world to listen to our plea for help and support in the face of these grave injustices. For generations, Palestinians have faced displacement, violence, and loss of life. Our homes have been demolished, our families separated, and our communities fragmented. The blockade in Gaza has created dire living conditions, and the West Bank is marked by a web of checkpoints and settlements that encroach on our lands. The most recent and pressing concern is the violence and loss of life in Gaza and the West Bank. The current events are a stark reminder of the daily hardships Palestinians endure. Innocent civilians, including women and children, continue to suffer, and the infrastructure remains severely damaged. We, the Palestinian people, seek peace, justice, and the right to self-determination. We call upon the world to: Advocate for an immediate ceasefire and the protection of Palestinian civilians. Support international efforts to reach a just and lasting solution to the Israeli-Palestinian conflict. Urge the international community to hold those responsible for human rights violations accountable. Provide humanitarian assistance to those in need, especially in Gaza, where the situation is dire. Promote dialogue and negotiations to establish a two-state solution, ensuring both Israelis and Palestinians can live in peace and security. It is crucial that the world hears our plea for help and solidarity. We yearn for a future where Palestinians can live in dignity, with their basic rights respected, and a just and lasting peace can be achieved. Together, we can bring an end to the suffering that has befallen our people for far too long.
Publication accession: DES23A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.
*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: DES8 A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.\r\n*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)\r\n
Publication accession: DES8 B - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.\r\n*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: DES8 C - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.\r\n*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors)
Publication accession: DES\"A - De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398.\r\n*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors) \"
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Publication accession: FILwdB - *Gordan R, *Murphy K, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biology 2011, 12:R125 (*co-1st authors)
Publication accession: GOR11A - *Grove CA, *de Masi F, Barrasa MI, Newburger DE, Alkema MJ, †Bulyk ML, †Walhout AJM. A multi-parameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 138:314-327 (*co-1st authors; †co-corresponding authors).
Publication accession: GRO09A - Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH. Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biology. 2014 Oct 7;15(10):482. [Epub ahead of print]
Publication accession: GUO14A - 1
Publication accession: HCY- A - Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA. LUX ARRHYTHMO Encodes a night time repressor of circadian gene expression in the Arabidopsis core clock. Current Biology (2011), Jan 25;21(2):126-33.
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Publication accession: KMI- A - Li H*, Liefke R*, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature (in press)
Publication accession: KUR17A - Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Shaw AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. Screening of PCRP transcription factor antibodies in biochemical assays. Nature Methods (in submission)
Publication accession: LAI20A - 1
Publication accession: LEP- A - Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes and Development (2009) 23(3):345-58
Publication accession: LES09A - Lehti-Shiu MD, Uygun S, Moghe GD, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu S. Molecular Evidence for functional divergence and decay of a transcription factor derived from whole genome duplication in Arabidopsis thaliana. Plant Physiology in press.
Publication accession: LET15A - Lindemose S*, Jensen MK*, Van de Velde J*, O'Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, De Masi F.; A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. Nucleic Acids Res. 2014 Jul;42(12):7681-93
Publication accession: LIN08A - Lindemose S*, Jensen MK*, de Velde JV*, O'Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, De Masi F. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana Nucleic Acids Res. 2014;42(12):7681-93. doi: 10.1093/nar/gku502 (* co-1st authors)
Publication accession: LIN14A - Lindemose S*, Jensen MK*, Van de Velde J*, O'Shea C, Heyndrickx KS, Workman CT, Vandepoele K, Skriver K, De Masi F. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. Nucleic Acids Res. 2014 Jul;42(12):7681-93
Publication accession: LIN14B - Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurito R, Nakamura Y, Yuan G-C, Bauer DE, Xu J, Bulyk ML, Orkin S. Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch. Cell (2018)
Publication accession: LIU18A - Liu Q, Onal P, Datta RR, Rogers JM Schmidt-Ott U, Bulyk ML, Small SJ, Thronton JW. Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development. eLife in Press
Publication accession: LIU18B - 1
Publication accession: LUW- A - Mizeracka K, Rogers JM, Shaham S, Bulyk ML, Heiman MG. Lineage-specific control of convergent cell identity by a Forkhead repressor. TBD 2019.
Publication accession: MIZ19A - *Nakagawa S, *Gisselbrecht SS, *Rogers JM, **Hartl DL, **Bulyk ML. DNA binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci USA. (2013) 110(30):12349-54 Epub July 8, 2013.
Publication accession: NAK13A - Nowak-Lovato KL, Hickmott AJ, Maity TS, Bulyk ML, Dunbar J, Hongâ€Geller E. DNA binding site analysis of Burkholderia thailandensis response regulators. Journal of Microbiological Methods (2012) 90(1):46-52.
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Publication accession: NXM- A - Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, McMahon AP. Neural specific Sox2 input and differential Gli binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development (2012) 26: 2802-2816
Publication accession: PET12A - Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, and Bassler BL. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Molecular Microbiology. 2008 Aug 4. [Epub ahead of print]
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Publication accession: PROonB - Joshua B. Radke, Olivier Lucas, Erandi K. De Silva, YanFen Ma, William J. Sullivan, Jr., Louis M. Weiss, Manuel Llinas, and Michael W. White. ApiAP2 transcription factor restricts development of the Toxoplasma tissue cyst. PNAS 2013 110: 6871-6876.
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Publication accession: RES1)A - Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML. Bispecific Forkhead transcription factor FoxN3 recognizes two distinct motifs with different DNA shapes. Molecular Cell 2019.
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Publication accession: RRY- A - Santos JM, Josling G, Ross P, Joshi P, Altenhofen L, Campbell T, Schieler A, Cristea IM, Llinás M. Red blood cell invasion by the malaria parasite is coordinated by the PfAP2-I transcription factor. Cell Host Microbe. June 2017.
Publication accession: SAN17B - Scharer CD, McCabe CD, Ali-Seyed M, Berger MF, Bulyk ML, Moreno CS. Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer. Cancer Research. January 15, 2009. 69(2).
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Publication accession: SETetB - Siggers T, Reddy J, Barron B, Bulyk ML. Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Bindg. Molecular CEll 2014 Aug 21; 55(4):640-648
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Publication accession: SOMpgB - Soruco MML, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. The CLAMP protein links the MSL complex to the X-chromosome during Drosophila dosage compensation. Genes & Development (2013) 27:1551–1556.
Publication accession: SOR13A - Stielow B, Zhou Y, Cao Y, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Science Advances 2021\r\nPublication accession: STI20A\r\n
Publication accession: STI21A - Stielow B, Zhou Y, Cao Y, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Science Advances AAAS 2021
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Publication accession: YNIomA - *Zhu C, *Byers K, *McCord RP, Shi Z, Berger MF, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A , Murthy TVS, LaBaer J, Bulyk ML. High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors. Genome Research. Epub January 21, 2009, doi:10.1101/gr.090233.108 (*co-1st authors).
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