Posts tagged ‘gene regulatory network’

Just saw this from a friend’s share. It is a great TED talk by Uri Alon on his experience on doing innovative science.


His work has inspired many including myself. Here are a few seminal papers by his groups.

  1. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002 Oct 25;298(5594):824-7. PubMed PMID: 12399590.
  2. Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 2002 May;31(1):64-8. Epub 2002 Apr 22. PubMed PMID: 11967538.
  3. Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet. 2007 Jun;8(6):450-61. Review. PubMed PMID: 17510665.


Stem cells/ regenerative medicine

  1. Zhong X, Gutierrez C, Xue T, Hampton C, Vergara MN, Cao LH, Peters A, Park TS, Zambidis ET, Meyer JS, Gamm DM, Yau KW, Canto-Soler MV. Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs. Nat Commun. 2014 Jun 10;5:4047. doi: 10.1038/ncomms5047. PubMed PMID: 24915161.
  2. Reichman S, Terray A, Slembrouck A, Nanteau C, Orieux G, Habeler W, Nandrot EF, Sahel JA, Monville C, Goureau O. From confluent human iPS cells to self-forming neural retina and retinal pigmented epithelium. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8518-23. doi: 10.1073/pnas.1324212111. Epub 2014 May 27. PubMed PMID: 24912154.
  3. Chong JJ, Yang X, Don CW, Minami E, Liu YW, Weyers JJ, Mahoney WM, Van Biber B, Cook SM, Palpant NJ, Gantz JA, Fugate JA, Muskheli V, Gough GM, Vogel KW, Astley CA, Hotchkiss CE, Baldessari A, Pabon L, Reinecke H, Gill EA, Nelson V, Kiem HP, Laflamme MA, Murry CE. Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts. Nature. 2014 Jun 12;510(7504):273-7. doi: 10.1038/nature13233. Epub 2014 Apr 30. PubMed PMID: 24776797.
  4. Normile D, Vogel G. Cell biology. STAP cells succumb to pressure. Science. 2014 Jun 13;344(6189):1215-6. doi: 10.1126/science.344.6189.1215. PubMed PMID: 24925996.

Eye diseases

  1. Agbaga MP, Tam BM, Wong JS, Yang LL, Anderson RE, Moritz OL. Mutant ELOVL4 That Causes Autosomal Dominant Stargardt-3 Macular Dystrophy Is Misrouted to Rod Outer Segment Disks. Invest Ophthalmol Vis Sci. 2014 May 15;55(6):3669-3680. doi: 10.1167/iovs.13-13099. PubMed PMID: 24833735.

Oxidative stress

  1. Moussavi Nik SH, Croft K, Mori TA, Lardelli M. The comparison of methods for measuring oxidative stress in zebrafish brains. Zebrafish. 2014 Jun;11(3):248-54. doi: 10.1089/zeb.2013.0958. Epub 2014 May 5. PubMed PMID: 24798242.

Molecular Biology

  1. Roberts JW. Molecular biology. Molecular basis of transcription pausing. Science. 2014 Jun 13;344(6189):1226-7. doi: 10.1126/science.1255712. PubMed PMID: 24926002.

Systems Biology

  1. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014 Jun 11. doi: 10.1038/nature13437. [Epub ahead of print] PubMed PMID: 24919153.

Synthetic Biology/Gene regulatory Network

  1. Attwater J, Holliger P. A synthetic approach to abiogenesis. Nat Methods. 2014 May;11(5):495-8. doi: 10.1038/nmeth.2893. PubMed PMID: 24781322.
  2. Brophy JA, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014 May;11(5):508-20. doi: 10.1038/nmeth.2926. Review. PubMed PMID: 24781324.


  1. Zhou Y, Cattley RT, Cario CL, Bai Q, Burton EA. Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications. Nat Protoc. 2014 Jul;9(7):1533-48. doi: 10.1038/nprot.2014.094. Epub 2014 Jun 5. PubMed PMID: 24901738.


  1. Wieman CE. Large-scale comparison of science teaching methods sends clear message. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8319-20. doi: 10.1073/pnas.1407304111. Epub 2014 May 22. PubMed PMID: 24853505.
  2. Zhou M, Lee J. Assessing what is cultural about Asian Americans’ academic advantage. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8321-2. doi: 10.1073/pnas.1407309111. Epub 2014 May 29. PubMed PMID: 24876277.
  3. Freeman S, Eddy SL, McDonough M, Smith MK, Okoroafor N, Jordt H, Wenderoth MP. Active learning increases student performance in science, engineering, and mathematics. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8410-5. doi: 10.1073/pnas.1319030111. Epub 2014 May 12. PubMed PMID: 24821756.
  4. Hsin A, Xie Y. Explaining Asian Americans’ academic advantage over whites. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8416-21. doi: 10.1073/pnas.1406402111. Epub 2014 May 5. PubMed PMID: 24799702.

Scientific Career

  1. van Dijk D, Manor O, Carey LB. Publication metrics and success on the academic job market. Curr Biol. 2014 Jun 2;24(11):R516-7. doi: 10.1016/j.cub.2014.04.039. PubMed PMID: 24892909.

Genome Editing

  1. Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs. PLoS One. 2014 May 29;9(5):e98186. doi: 10.1371/journal.pone.0098186. eCollection 2014. PubMed PMID: 24873830.
  2. Hsu PD, Lander ES, Zhang F. Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell. 2014 Jun 5;157(6):1262-1278. doi: 10.1016/j.cell.2014.05.010. Review. PubMed PMID: 24906146.
  3. Torres R, Martin MC, Garcia A, Cigudosa JC, Ramirez JC, Rodriguez-Perales S. Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nat Commun. 2014 Jun 3;5:3964. doi: 10.1038/ncomms4964. PubMed PMID: 24888982.
  4. Yu C, Zhang Y, Yao S, Wei Y. A PCR Based Protocol for Detecting Indel Mutations Induced by TALENs and CRISPR/Cas9 in Zebrafish. PLoS One. 2014 Jun 5;9(6):e98282. doi: 10.1371/journal.pone.0098282. eCollection 2014. PubMed PMID: 24901507.


  1. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. N Engl J Med. 2014 Jun 4. [Epub ahead of print] PubMed PMID: 4896819.
  2. Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA. Genome sequencing identifies major causes of severe intellectual disability. Nature. 2014 Jun 4. doi: 10.1038/nature13394. [Epub ahead of print] PubMed PMID: 24896178.

Stem cells

  1. Dunn SJ, Martello G, Yordanov B, Emmott S, Smith AG. Defining an essential transcription factor program for naïve pluripotency. Science. 2014 Jun 6;344(6188):1156-60. doi: 10.1126/science.1248882. PubMed PMID: 24904165.

Gene regulatory network

  1. Barsi JC, Tu Q, Davidson E. General approach for in vivo recovery of cell type specific effector gene sets. Genome Res. 2014 Mar 6. [Epub ahead of print] PubMed PMID: 24604781.


  1. Project to Improve Poor Children’s Intellect Led to Better Health, Data Show
  2. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a. PubMed PMID: 22460880.


  1. Portugues R, Feierstein CE, Engert F, Orger MB. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron. 2014 Mar 19;81(6):1328-43. doi: 10.1016/j.neuron.2014.01.019. PubMed PMID: 24656252.
  2. Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA. Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9. doi: 10.1038/nature12517. Epub 2013 Aug 28. PubMed PMID: 23995685; PubMed Central
    PMCID: PMC3817409.

    • Brüstle O. Developmental neuroscience: Miniature human brains. Nature. 2013
      Sep 19;501(7467):319-20. doi: 10.1038/nature12552. Epub 2013 Aug 28. PubMed PMID: 23995687.

Genome editing

  1. Auer TO, Del Bene F. CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. Methods. 2014 Apr 1. pii: S1046-2023(14)00129-7. doi: 10.1016/j.ymeth.2014.03.027. [Epub ahead of print] PubMed PMID: 24704174.
  2. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W. High-throughput screening
    of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014 Apr
    9. doi: 10.1038/nature13166. [Epub ahead of print] PubMed PMID: 24717434.
  3. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp
    PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014 Mar 30. doi: 10.1038/nbt.2884. [Epub ahead of print] PubMed PMID: 24681508.

Stem cells

  1. Becker S, Jayaram H, Limb GA. Recent Advances towards the Clinical Application of Stem Cells for Retinal Regeneration. Cells. 2012 Oct 18;1(4):851-73. doi: 10.3390/cells1040851. PubMed PMID: 24710533.
  2. Assawachananont J et al., Transplantation of Embryonic and Induced Pluripotent Stem Cell-Derived 3D Retinal Sheets into Retinal Degenerative Mice. Stem Cell Reports. 2014; 2: 662-674.

Retinal degeneration

  1. Wasfy MM, Matsui JI, Miller J, Dowling JE, Perkins BD. myosin 7aa(-/-) mutant zebrafish show mild photoreceptor degeneration and reduced electroretinographic responses. Exp Eye Res. 2014 Apr 1. pii: S0014-4835(14)00083-9. doi: 10.1016/j.exer.2014.03.007. [Epub ahead of print] PubMed PMID: 24698764.

Retinal development

  1. Weber IP, Ramos AP, Strzyz PJ, Leung LC, Young S, Norden C. Mitotic Position and Morphology of Committed Precursor Cells in the Zebrafish Retina Adapt to Architectural Changes upon Tissue Maturation. Cell Rep. 2014 Apr 2. pii: S2211-1247(14)00192-2. doi: 10.1016/j.celrep.2014.03.014. [Epub ahead of print] PubMed PMID: 24703843.
  2. Almeida AD, Boije H, Chow RW, He J, Tham J, Suzuki SC, Harris WA. Spectrum of Fates: a new approach to the study of the developing zebrafish retina. Development. 2014 Apr 9. [Epub ahead of print] PubMed PMID: 24718991.
  3. Yoshimatsu T, Williams PR, D’Orazi FD, Suzuki SC, Fadool JM, Allison WT, Raymond PA, Wong RO. Transmission from the dominant input shapes the stereotypic ratio of photoreceptor inputs onto horizontal cells. Nat Commun. 2014 May 15;5:3699. doi: 10.1038/ncomms4699. PubMed PMID: 24832361.


  1. Bianchi E, Doe B, Goulding D, Wright GJ. Juno is the egg Izumo receptor and is essential for mammalian fertilization. Nature. 2014 Apr 24;508(7497):483-7. doi: 10.1038/nature13203. Epub 2014 Apr 16. PubMed PMID: 24739963; PubMed Central PMCID: PMC3998876.

Genetics/Synthetic biology

  1. Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR Jr, Romesberg FE. A semi-synthetic organism with an expanded genetic alphabet. Nature. 2014 May 15;509(7500):385-8. doi: 10.1038/nature13314. Epub 2014 May 7. PubMed PMID: 24805238.
    • Commentary: Thyer R, Ellefson J. Synthetic biology: New letters for life’s alphabet. Nature. 2014 May 15;509(7500):291-2. doi: 10.1038/nature13335. Epub 2014 May 7. PubMed PMID: 24805244.


  1. Widmann A, Schröger E. Filter effects and filter artifacts in the analysis of  electrophysiological data. Front Psychol. 2012 Jul 9;3:233. doi: 10.3389/fpsyg.2012.00233. eCollection 2012. PubMed PMID: 22787453; PubMed Central PMCID: PMC3391960.
  2. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013 Dec 19;155(7):1451-63. doi: 10.1016/j.cell.2013.11.024. Epub 2013 Dec 5. PubMed PMID: 24315484.
  3. Stern P. The heavily connected brain. Connection, connection, connection… Introduction. Science. 2013 Nov 1;342(6158):577. doi: 10.1126/science.342.6158.577. PubMed PMID: 24179217.
  4. Zatorre RJ. Predispositions and plasticity in music and speech learning: neural correlates and implications. Science. 2013 Nov 1;342(6158):585-9. doi: 10.1126/science.1238414. Review. PubMed PMID: 24179219.
  5. Turk-Browne NB. Functional interactions as big data in the human brain.Science. 2013 Nov 1;342(6158):580-4. doi: 10.1126/science.1238409. Review. PubMed PMID: 24179218.
  6. DeCaen PG, Delling M, Vien TN, Clapham DE. Direct recording and molecular identification of the calcium channel of primary cilia. Nature. 2013 Dec 12;504(7479):315-8. doi: 10.1038/nature12832. PubMed PMID: 24336289.
  7. Delling M, DeCaen PG, Doerner JF, Febvay S, Clapham DE. Primary cilia are specialized calcium signalling organelles. Nature. 2013 Dec 12;504(7479):311-4. doi: 10.1038/nature12833. PubMed PMID: 24336288.


  1. Korf I. Genomics: the state of the art in RNA-seq analysis. Nat Methods. 2013 Nov 26;10(12):1165-6. doi: 10.1038/nmeth.2735. PubMed PMID: 24296473.
  2. Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Engström PG, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Kokocinski F, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, Niermann P, Rätsch G, Reymond A, Ribeca P, Richard H, Rougemont J, Rozowsky J, Sammeth M, Sboner A, Schulz MH, Searle SM, Solorzano ND, Solovyev V, Stanke M, Steijger T, Stevenson BJ, Stockinger H, Valsesia A, Weese D, White S, Wold BJ, Wu J, Wu TD, Zeller G, Zerbino D, Zhang MQ, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3. PubMed PMID: 24185837; PubMed Central PMCID: PMC3851240.
  3. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R, Campagna D, Davis CA, Dobin A, Engström PG, Gingeras TR, Goldman N, Grant GR, Guigó R, Harrow J, Hubbard TJ, Jean G, Kahles A, Kosarev P, Li S, Liu J, Mason CE, Molodtsov V, Ning Z, Ponstingl H, Prins JF, Rätsch G, Ribeca P, Seledtsov I, Sipos B, Solovyev V, Steijger T, Valle G, Vitulo N, Wang K, Wu TD, Zeller G, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data.  Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. PubMed PMID: 24185836.
  4. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10. PubMed PMID: 24119843; PubMed Central PMCID: PMC3841062.
  5. Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. N Engl J Med. 2013 Dec 19;369(25):2369-71. doi: 10.1056/NEJMp1314561. Epub 2013 Nov 19. PubMed PMID: 24251383.


  1. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System. Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001. PubMed PMID: 24360272.
  2. Ma H, Reyes-Gutierrez P, Pederson T. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. Proc Natl Acad Sci U S A. 2013 Dec 9. [Epub ahead of print] PubMed PMID: 24324157.
  3. Elia N, Ott C, Lippincott-Schwartz J. Incisive imaging and computation for cellular mysteries: lessons from abscission. Cell. 2013 Dec 5;155(6):1220-31. doi: 10.1016/j.cell.2013.11.011. PubMed PMID: 24315094.
  4. Marx V. Is super-resolution microscopy right for you? Nat Methods. 2013 Nov 26;10(12):1157-63. doi: 10.1038/nmeth.2756. PubMed PMID: 24296472.

Genome editing

  1. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F. Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res. 2013 Dec 2. [Epub ahead of print] PubMed PMID: 24179142.
  2. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013 Nov;8(11):2281-308. doi: 10.1038/nprot.2013.143. Epub 2013 Oct 24. PubMed PMID: 24157548.
  3. Cradick TJ, Fine EJ, Antico CJ, Bao G. CRISPR/Cas9 systems targeting ß-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 2013 Nov 1;41(20):9584-92. doi: 10.1093/nar/gkt714. Epub 2013 Aug 11. PubMed PMID: 23939622; PubMed Central PMCID: PMC3814385.
  4. Zu Y, Tong X, Wang Z, Liu D, Pan R, Li Z, Hu Y, Luo Z, Huang P, Wu Q, Zhu Z, Zhang B, Lin S. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods. 2013 Apr;10(4):329-31. doi: 10.1038/nmeth.2374. Epub 2013 Feb 24. PubMed PMID: 23435258.

Gene regulatory network

  1. Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nat Methods. 2013 Nov 26;10(12):1169-76. doi: 10.1038/nmeth.2728. PubMed PMID:24296474.

Genomics/Systems biology

  1. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25. PubMed PMID: 24277855.
  2. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12;504(7479):306-10. doi: 10.1038/nature12716. Epub 2013 Nov 10. PubMed PMID: 24213634.
  3. Markson JS, Piechura JR, Puszynska AM, O’Shea EK. Circadian Control of Global Gene Expression by the Cyanobacterial Master Regulator RpaA. Cell. 2013 Dec 5;155(6):1396-408. doi: 10.1016/j.cell.2013.11.005. PubMed PMID: 24315105.


  1. Xu C, Tabebordbar M, Iovino S, Ciarlo C, Liu J, Castiglioni A, Price E, Liu M, Barton ER, Kahn CR, Wagers AJ, Zon LI. A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species. Cell. 2013 Nov 7;155(4):909-21. doi: 10.1016/j.cell.2013.10.023. PubMed PMID: 24209627.
  2. Wilkinson RN, Elworthy S, Ingham PW, van Eeden FJ. A method for high-throughput PCR-based genotyping of larval zebrafish tail biopsies. Biotechniques. 2013 Dec;55(6):314-6. doi: 10.2144/000114116. PubMed PMID: 24344681.
  3. Maaswinkel H, Zhu L, Weng W. Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish. J Vis Exp. 2013 Dec 5;(82). doi: 10.3791/50681. PubMed PMID: 24336189.


  1. Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013 Dec 12;504(7479):231-6. doi: 10.1038/nature12779. PubMed PMID: 24336283.


  1. Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. PubMed PMID: 24346702.
  2. Koyanagi-Aoi M, Ohnuki M, Takahashi K, Okita K, Noma H, Sawamura Y, Teramoto I, Narita M, Sato Y, Ichisaka T, Amano N, Watanabe A, Morizane A, Yamada Y, Sato T, Takahashi J, Yamanaka S. Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc Natl Acad Sci U S A. 2013 Nov 20. [Epub ahead of print] PubMed PMID: 24259714.
  3. Plouhinec JL, Zakin L, Moriyama Y, De Robertis EM. Chordin forms a self-organizing morphogen gradient in the extracellular space between ectoderm and mesoderm in the Xenopus embryo. Proc Natl Acad Sci U S A. 2013 Nov 27. [Epub ahead of print] PubMed PMID: 24284174.
  4. Tan L, Zong C, Xie XS. Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. Proc Natl Acad Sci U S A. 2013 Dec 16. [Epub ahead of print] PubMed PMID: 24344257.


  1. Weber A, Hochmann S, Cimalla P, Gärtner M, Kuscha V, Hans S, Geffarth M, Kaslin J, Koch E, Brand M. Characterization of light lesion paradigms and optical coherence tomography as tools to study adult retina regeneration in zebrafish. PLoS One. 2013 Nov 26;8(11):e80483. doi: 10.1371/journal.pone.0080483. PubMed PMID: 24303018; PubMed Central PMCID: PMC3841302.


  1. Mervis J, Malakoff D. Science funding. U.S. budget deal offers researchers some sequester relief. Science. 2013 Dec 20;342(6165):1426-7. doi: 10.1126/science.342.6165.1426. PubMed PMID: 24357280.


  1. Johnson SC, Yanos ME, Kayser EB, Quintana A, Sangesland M, Castanza A, Uhde L, Hui J, Wall VZ, Gagnidze A, Oh K, Wasko BM, Ramos FJ, Palmiter RD, Rabinovitch PS, Morgan PG, Sedensky MM, Kaeberlein M. mTOR inhibition alleviates mitochondrial disease in a mouse model of Leigh syndrome. Science. 2013 Dec 20;342(6165):1524-8. doi: 10.1126/science.1244360. Epub 2013 Nov 14. PubMed PMID: 24231806.
    • Vafai SB, Mootha VK. Medicine. A common pathway for a rare disease? Science. 2013 Dec 20;342(6165):1453-4. doi: 10.1126/science.1248449. PubMed PMID: 24357304.


  1. Xie XS. Biochemistry. Enzyme kinetics, past and present. Science. 2013 Dec 20;342(6165):1457-9. doi: 10.1126/science.1248859. PubMed PMID: 24357307.


  1. Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V. Gene regulatory logic for reading the sonic hedgehog signaling gradient in the vertebrate neural tube. Cell. 2012 Jan 20;148(1-2):273-84. PubMed PMID: 22265416; PubMed Central PMCID: PMC3267043.
  2. Lassar A. Finding MyoD with a little help from my friends. Nat Cell Biol. 2012 Feb 2;14(2):116. doi: 10.1038/ncb2421. PubMed PMID: 22298038.
    • An interesting personal account of the discovery of MyoD.

Retinal Regeneration

  1. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Nov;93(5):726-34. Epub 2011 Sep 17. PubMed PMID: 21945172; PubMed Central PMCID: PMC3243491.
  2. Hochmann S, Kaslin J, Hans S, Weber A, Machate A, Geffarth M, Funk RH, Brand M. Fgf Signaling is Required for Photoreceptor Maintenance in the Adult Zebrafish Retina. PLoS One. 2012;7(1):e30365. Epub 2012 Jan 26. PubMed PMID: 22291943; PubMed Central PMCID: PMC3266925.


  1. Visscher PM, Brown MA, McCarthy MI, Yang J. Five Years of GWAS Discovery. Am J Hum Genet. 2012 Jan 13;90(1):7-24. PubMed PMID: 22243964.


  1. Baker M. Structural variation: the genome’s hidden architecture. Nat Methods. 2012 Jan 30;9(2):133-7. doi: 10.1038/nmeth.1858. PubMed PMID: 22290183.
  2. Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res. 2012 Feb;22(2):386-97. Epub 2011 Sep 22. PubMed PMID: 21940837.


  1. Cox S, Rosten E, Monypenny J, Jovanovic-Talisman T, Burnette DT, Lippincott-Schwartz J, Jones GE, Heintzmann R. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods. 2011 Dec 4;9(2):195-200. doi: 10.1038/nmeth.1812. PubMed PMID: 22138825.
    • Commentary: Lidke KA. Super resolution for common probes and common microscopes. Nat Methods. 2012 Jan 30;9(2):139-41. doi: 10.1038/nmeth.1863. PubMed PMID: 22290184.
    • This looks like an interesting article that talks about how to use common fluorescent setup for super-resolution imaging.
  2. Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012 Jan 8;9(2):185-8. doi: 10.1038/nmeth.1841. PubMed PMID: 22231642.

Gene Regulatory Network

  1. Damle SS, Davidson EH. Synthetic in vivo validation of gene network circuitry. Proc Natl Acad Sci U S A. 2012 Jan 11. [Epub ahead of print] PubMed PMID: 22238426.
  2. Weaver J. New signaling chemicals spur worms to seek company. PLoS Biol. 2012 Jan;10(1):e1001240. Epub 2012 Jan 10. PubMed PMID: 22253575; PubMed Central PMCID: PMC3254651.
  3. Gross L. Built-in Timer Delays Differentiation. PLoS Biol. 2012 Jan;10(1):e1001254. Epub 2012 Jan 31. PubMed PMID: 22303284.
  4. van Dijk AD, van Mourik S, van Ham RC. Mutational robustness of gene regulatory networks. PLoS One. 2012;7(1):e30591. Epub 2012 Jan 25. PubMed PMID: 22295094; PubMed Central PMCID: PMC3266278.


  1. Heidinger BJ, Blount JD, Boner W, Griffiths K, Metcalfe NB, Monaghan P. Telomere length in early life predicts lifespan. Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print] PubMed PMID: 22232671.


  1. Curtis CD, Griffin CT. The chromatin-remodeling enzymes BRG1 and CHD4 antagonistically regulate vascular Wnt signaling. Mol Cell Biol. 2012 Jan 30. [Epub ahead of print] PubMed PMID: 22290435.


  1. Macilwain C. Funding in 2012: “great recession” starts to bite. Cell. 2012 Jan 20;148(1-2):14-6. PubMed PMID: 22265395.

There are so many different kinds of neurons in the brain and they control all sorts of mechanisms. In C.elegans, several dopamine(a neurotransmitter) -secreting neurons are differentiated from different lineage, but they are all producing dopamine. This has raised an interesting question: are the genes controlling the dopamine synthesis regulated differently or the same way in different dopamine-secreting neurons?

A recent study by Nuria Flames & Oliver Hobert from Columbia University has revealed the latter is true. They made extensive promoter constructs of all the genes involved in dopamine production (which is a good example for those of us who are going to do similar promoter analyses). Their results showed all five genes were regulated by the same regulatory element, presumably by the same transcription factor(s). Therefore, these dopamine synthesis genes are regulated the same way in different dopaminergic neurons. More importantly, they have also found that this regulatory mechanism is conserved in mice!


This is the terminal differentiation we have just discussed. The study has demonstrated that this differentiation circuit is modular and has been incorporated in different types of dopaminergic neurons to carry out the same final function. In other words, the final output function of the gene network is the same while the upstream specification architecture can be quite different.


Flames N, Hobert O. Gene regulatory logic of dopamine neuron differentiation. Nature. 2009 Apr 16;458(7240):885-9. [PubMed][Nature][Commentary in Nature]