Bibliography

Akashi K., He X., Chen J., Iwasaki H., Niu C., Steenhard B., Zhang J., Haug J., and Li L.

Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis.
Blood, 101 (2): 383-9, 2003.
Abstract.
Full text

Akashi K., Traver D., Miyamoto T., and Weissman I.

A clonogenic common myeloid progenitor that gives rise to all myeloid lineages.
Nature, 404 (6774): 193-7, 2000.
Abstract.
Full text

Amoutzias G., Robertson D., Oliver S., and Bornberg-Bauer E.

Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.
EMBO Rep, 5 (3): 274-279, 2004.
Abstract.
Full text

Andres-Barquin P., Hernandez M., Hayes T., McKay R., and Israel M.

Id genes encoding inhibitors of transcription are expressed during in vitro astrocyte differentiation and in cell lines derived from astrocytic tumors.
Cancer Res, 57 (2): 215-20, 1997.
Abstract.

Barolo S. and Levine M.

hairy mediates dominant repression in the drosophila embryo.
EMBO J, 16 (10): 2883-91, 1997.
Abstract.

Benezra R., Davis R., Lockshon D., Turner D., and Weintraub H.

The protein id: a negative regulator of helix-loop-helix dna binding proteins.
Cell, 61 (1): 49-59, 1990.
Abstract.

Blau H. and Baltimore D.

Differentiation requires continuous regulation.
J Cell Biol, 112 (5): 781-3, 1991.
Abstract.

Blau H. and Blakely B.

Plasticity of cell fate: insights from heterokaryons.
Semin Cell Dev Biol, 10 (3): 267-72, 1999.
Abstract.
Full text

Blau H., Pavlath G., Hardeman E., Chiu C., Silberstein L., Webster S., Miller S., and Webster C.

Plasticity of the differentiated state.
Science, 230 (4727): 758-66, 1985.
Abstract.

Briscoe J., Pierani A., Jessell T., and Ericson J.

A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube.
Cell, 101 (4): 435-45, 2000.
Abstract.

Brown G., Bunce C., Lord J., and McConnell F.

The development of cell lineages: a sequential model.
Differentiation, 39 (2): 83-9, 1988.
Abstract.

Brunet J. and Ghysen A.

Deconstructing cell determination: proneural genes and neuronal identity.
Bioessays, 21 (4): 313-8, 1999.
Abstract.

Chambers R., Leoni P., Kaminski N., Laurent G., and Heller R.

Global expression profiling of fibroblast responses to transforming growth factor-beta1 reveals the induction of inhibitor of differentiation-1 and provides evidence of smooth muscle cell phenotypic switching.
Am J Pathol, 162 (2): 533-46, 2003.
Abstract.

Chen H., Zhang P., Radomska H., Hetherington C., Zhang D., and Tenen D.

Octamer binding factors and their coactivator can activate the murine pu.1 (spi-1) promoter.
J Biol Chem, 271 (26): 15743-52, 1996.
Abstract.

Cherry J. and Adler F.

How to make a biological switch.
J Theor Biol, 203 (2): 117-33, 2000.
Abstract.
Full text

Chiang M. and Melton D.

Single-cell transcript analysis of pancreas development.
Dev Cell, 4 (3): 383-93, 2003.
Abstract.

Chien C., Hsiao C., Jan L., and Jan Y.

Neuronal type information encoded in the basic-helix-loop-helix domain of proneural genes.
Proc Natl Acad Sci U S A, 93 (23): 13239-44, 1996.
Abstract.

Cinquin O. and Demongeot J.

Positive and negative feedback: striking a balance between necessary antagonists.
J Theor Biol, 216 (2): 229-41, 2002.
Abstract.
Full text

Cory S.

Immunology. wavering on commitment.
Nature, 401 (6753): 538-9, 1999.
Abstract.
Full text

Cox D. A., Little J. B., and O'Shea D.

Ideals, Varieties, and Algorithms.
Springer-Verlag, NY, 2nd edition, 1996.
536 pages.

Crittenden S., Bernstein D., Bachorik J., Thompson B., Gallegos M., Petcherski A., Moulder G., Barstead R., Wickens M., and Kimble J.

A conserved rna-binding protein controls germline stem cells in caenorhabditis elegans.
Nature, 417 (6889): 660-3, 2002.
Abstract.
Full text

Cross M. and Enver T.

The lineage commitment of haemopoietic progenitor cells.
Curr Opin Genet Dev, 7 (5): 609-13, 1997.
Abstract.

Delbrück M.

Unités biologiques douées de continuité génétique.
Colloq. Int. C.N.R.S., 8: 33-35, 1949.

Ebrahimi F., Edmondson J., Rothstein R., and Chess A.

Yac transgene-mediated olfactory receptor gene choice.
Dev Dyn, 217 (2): 225-31, 2000.
Abstract.

Eggan K., Baldwin K., Tackett M., Osborne J., Gogos J., Chess A., Axel R., and Jaenisch R.

Mice cloned from olfactory sensory neurons.
Nature, 428 (6978): 44-9, 2004.
Abstract.
Full text

Ellis H., Spann D., and Posakony J.

extramacrochaetae, a negative regulator of sensory organ development in drosophila, defines a new class of helix-loop-helix proteins.
Cell, 61 (1): 27-38, 1990.
Abstract.

Ellis R. and Kimble J.

The fog-3 gene and regulation of cell fate in the germ line of caenorhabditis elegans.
Genetics, 139 (2): 561-77, 1995.
Abstract.

Enver T. and Greaves M.

Loops, lineage, and leukemia.
Cell, 94 (1): 9-12, 1998.
Abstract.

Gardner T., Cantor C., and Collins J.

Construction of a genetic toggle switch in escherichia coli.
Nature, 403 (6767): 339-42, 2000.
Abstract.
Full text

Garrell J. and Modolell J.

The drosophila extramacrochaetae locus, an antagonist of proneural genes that, like these genes, encodes a helix-loop-helix protein.
Cell, 61 (1): 39-48, 1990.
Abstract.

Goolsby J., Marty M., Heletz D., Chiappelli J., Tashko G., Yarnell D., Fishman P., Dhib-Jalbut S., Bever C., Pessac B., and Trisler D.

Hematopoietic progenitors express neural genes.
Proc Natl Acad Sci U S A, 100 (25): 14926-31, 2003.
Abstract.
Full text

Gouzé J.

Positive and negative circuits in dynamical systems.
J. Biol. Syst, 6: 11-15, 1998.

Gowan K., Helms A., Hunsaker T., Collisson T., Ebert P., Odom R., and Johnson J.

Crossinhibitory activities of ngn1 and math1 allow specification of distinct dorsal interneurons.
Neuron, 31 (2): 219-32, 2001.
Abstract.

Grynfeld A., Påhlman S., and Axelson H.

Induced neuroblastoma cell differentiation, associated with transient hes-1 activity and reduced hash-1 expression, is inhibited by notch1.
Int J Cancer, 88 (3): 401-10, 2000.
Abstract.

Gurdon J.

The developmental capacity of nuclei taken from intestinal epithelial cells of feeding tadpoles.
J Embryol Exp Morphol, 10: 622-640, 1962.

Gurdon J., Laskey R., and Reeves O.

The developmental capacity of nuclei transplanted from keratinized cells of adult frogs.
J Embryol Exp Morphol, 34: 93-112, 1975.

Håkelien A., Landsverk H., Robl J., Skålhegg B., and Collas P.

Reprogramming fibroblasts to express t-cell functions using cell extracts.
Nat Biotechnol, 20 (5): 460-6, 2002.
Abstract.
Full text

Hamamori Y., Wu H., Sartorelli V., and Kedes L.

The basic domain of myogenic basic helix-loop-helix (bhlh) proteins is the novel target for direct inhibition by another bhlh protein, twist.
Mol Cell Biol, 17 (11): 6563-73, 1997.
Abstract.

Houldsworth J., Reuter V., Bosl G., and Chaganti R.

Id gene expression varies with lineage during differentiation of pluripotential male germ cell tumor cell lines.
Cell Tissue Res, 303 (3): 371-9, 2001.
Abstract.

Hu M., Krause D., Greaves M., Sharkis S., Dexter M., Heyworth C., and Enver T.

Multilineage gene expression precedes commitment in the hemopoietic system.
Genes Dev, 11 (6): 774-85, 1997.
Abstract.

Ishiguro A., Spirin K., Shiohara M., Tobler A., Gombart A., Israel M., Norton J., and Koeffler H.

Id2 expression increases with differentiation of human myeloid cells.
Blood, 87 (12): 5225-31, 1996.
Abstract.

Iwasaki H., Mizuno S., Wells R., Cantor A., Watanabe S., and Akashi K.

Gata-1 converts lymphoid and myelomonocytic progenitors into the megakaryocyte/erythrocyte lineages.
Immunity, 19 (3): 451-62, 2003.
Abstract.

Jagla T., Bidet Y., Ponte J. D., Dastugue B., and Jagla K.

Cross-repressive interactions of identity genes are essential for proper specification of cardiac and muscular fates in drosophila.
Development, 129 (4): 1037-47, 2002.
Abstract.

Jermyn K. and Wiliams J.

Comparison of the dictyostelium rasd and ecma genes reveals two distinct mechanisms whereby an mrna may become enriched in prestalk cells.
Differentiation, 58 (4): 261-7, 1995.
Abstract.

Jögi A., Persson P., Grynfeld A., Påhlman S., and Axelson H.

Modulation of basic helix-loop-helix transcription complex formation by id proteins during neuronal differentiation.
J Biol Chem, 277 (11): 9118-26, 2002.
Abstract.
Full text

Kageyama R., Ohtsuka T., and Tomita K.

The bhlh gene hes1 regulates differentiation of multiple cell types.
Mol Cells, 10 (1): 1-7, 2000.
Abstract.

Kaletta T., Schnabel H., and Schnabel R.

Binary specification of the embryonic lineage in caenorhabditis elegans.
Nature, 390 (6657): 294-8, 1997.
Abstract.
Full text

Kondo M., Scherer D., Miyamoto T., King A., Akashi K., Sugamura K., and Weissman I.

Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines.
Nature, 407 (6802): 383-6, 2000.
Abstract.
Full text

Kulessa H., Frampton J., and Graf T.

Gata-1 reprograms avian myelomonocytic cell lines into eosinophils, thromboblasts, and erythroblasts.
Genes Dev, 9 (10): 1250-62, 1995.
Abstract.

Langlands K., Down G., and Kealey T.

Id proteins are dynamically expressed in normal epidermis and dysregulated in squamous cell carcinoma.
Cancer Res, 60 (21): 5929-33, 2000.
Abstract.

Lin R., Hill R., and Priess J.

Pop-1 and anterior-posterior fate decisions in c. elegans embryos.
Cell, 92 (2): 229-39, 1998.
Abstract.

Lister J., Forrester W., and Baron M.

Inhibition of an erythroid differentiation switch by the helix-loop-helix protein id1.
J Biol Chem, 270 (30): 17939-46, 1995.
Abstract.

Massari M. and Murre C.

Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms.
Mol Cell Biol, 20 (2): 429-40, 2000.
Abstract.

McDevitt M., Shivdasani R., Fujiwara Y., Yang H., and Orkin S.

A "knockdown" mutation created by cis-element gene targeting reveals the dependence of erythroid cell maturation on the level of transcription factor gata-1.
Proc Natl Acad Sci U S A, 94 (13): 6781-5, 1997.
Abstract.

Mével-Ninio M. and Weiss M.

Immunofluorescence analysis of the time-course of extinction, reexpression, and activation of albumin production in rat hepatoma-mouse fibroblast heterokaryons and hybrids.
J Cell Biol, 90 (2): 339-50, 1981.
Abstract.

Miyamoto T., Iwasaki H., Reizis B., Ye M., Graf T., Weissman I., and Akashi K.

Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment.
Dev Cell, 3 (1): 137-47, 2002.
Abstract.

Nagata Y. and Todokoro K.

Activation of helix-loop-helix proteins id1, id2 and id3 during neural differentiation.
Biochem Biophys Res Commun, 199 (3): 1355-62, 1994.
Abstract.

Nerlov C., Querfurth E., Kulessa H., and Graf T.

Gata-1 interacts with the myeloid pu.1 transcription factor and represses pu.1-dependent transcription.
Blood, 95 (8): 2543-51, 2000.
Abstract.

Neves G., Zucker J., Daly M., and Chess A.

Stochastic yet biased expression of multiple dscam splice variants by individual cells.
Nat Genet, 36 (3): 240-6, 2004.
Abstract.
Full text

Norton J.

Id helix-loop-helix proteins in cell growth, differentiation and tumorigenesis.
J Cell Sci, 113 ( Pt 22): 3897-905, 2000.
Abstract.

Norton J., Deed R., Craggs G., and Sablitzky F.

Id helix-loop-helix proteins in cell growth and differentiation.
Trends Cell Biol, 8 (2): 58-65, 1998.
Abstract.

Nutt S., Vambrie S., Steinlein P., Kozmik Z., Rolink A., Weith A., and Busslinger M.

Independent regulation of the two pax5 alleles during b-cell development.
Nat Genet, 21 (4): 390-5, 1999.
Abstract.
Full text

Ogata T., Wozney J., Benezra R., and Noda M.

Bone morphogenetic protein 2 transiently enhances expression of a gene, id (inhibitor of differentiation), encoding a helix-loop-helix molecule in osteoblast-like cells.
Proc Natl Acad Sci U S A, 90 (19): 9219-22, 1993.
Abstract.

Ohtsuka T., Asahi M., Matsuura N., Kikuchi H., Hojo M., Kageyama R., Ohkubo H., and Hoshimaru M.

Regulated expression of neurogenic basic helix-loop-helix transcription factors during differentiation of the immortalized neuronal progenitor cell line hc2s2 into neurons.
Cell Tissue Res, 293 (1): 23-9, 1998.
Abstract.

Okano H., Imai T., and Okabe M.

Musashi: a translational regulator of cell fate.
J Cell Sci, 115 (Pt 7): 1355-9, 2002.
Abstract.

Orkin S.

Diversification of haematopoietic stem cells to specific lineages.
Nat Rev Genet, 1 (1): 57-64, 2000.
Abstract.
Full text

Orkin S.

Priming the hematopoietic pump.
Immunity, 19 (5): 633-634, 2003.
Abstract.

O'Toole P., Inoue T., Emerson L., Morrison I., Mackie A., Cherry R., and Norton J.

Id proteins negatively regulate basic helix-loop-helix transcription factor function by disrupting subnuclear compartmentalization.
J Biol Chem, 278 (46): 45770-6, 2003.
Abstract.
Full text

Ozbudak E., Thattai M., Lim H., Shraiman B., and Oudenaarden A. V.

Multistability in the lactose utilization network of escherichia coli.
Nature, 427 (6976): 737-40, 2004.
Abstract.
Full text

Pierani A., Moran-Rivard L., Sunshine M., Littman D., Goulding M., and Jessell T.

Control of interneuron fate in the developing spinal cord by the progenitor homeodomain protein dbx1.
Neuron, 29 (2): 367-84, 2001.
Abstract.

Plahte E., Mestl T., and Omholt W.

Feedback circuits, stability and multistationarity in dynamical systems.
J. Biol. Syst., 3: 409-413, 1995.

Press W.

Numerical recipes in C : the art of scientific computing.
Cambridge: Cambridge University Press, 1992.

Rallu M., Corbin J., and Fishell G.

Parsing the prosencephalon.
Nat Rev Neurosci, 3 (12): 943-51, 2002.
Abstract.
Full text

Rekhtman N., Radparvar F., Evans T., and Skoultchi A.

Direct interaction of hematopoietic transcription factors pu.1 and gata-1: functional antagonism in erythroid cells.
Genes Dev, 13 (11): 1398-411, 1999.
Abstract.

Rivolta M., Halsall A., Johnson C., Tones M., and Holley M.

Transcript profiling of functionally related groups of genes during conditional differentiation of a mammalian cochlear hair cell line.
Genome Res, 12 (7): 1091-9, 2002.
Abstract.
Full text

Rothenberg E.

Stepwise specification of lymphocyte developmental lineages.
Curr Opin Genet Dev, 10 (4): 370-9, 2000.
Abstract.

Rothenberg E., Telfer J., and Anderson M.

Transcriptional regulation of lymphocyte lineage commitment.
Bioessays, 21 (9): 726-42, 1999.
Abstract.

Sasai Y., Kageyama R., Tagawa Y., Shigemoto R., and Nakanishi S.

Two mammalian helix-loop-helix factors structurally related to drosophila hairy and enhancer of split.
Genes Dev, 6 (12B): 2620-34, 1992.
Abstract.

Serizawa S., Ishii T., Nakatani H., Tsuboi A., Nagawa F., Asano M., Sudo K., Sakagami J., Sakano H., Ijiri T., Matsuda Y., Suzuki M., Yamamori T., Iwakura Y., and Sakano H.

Mutually exclusive expression of odorant receptor transgenes.
Nat Neurosci, 3 (7): 687-93, 2000.
Abstract.
Full text

Sitcheran R., Cogswell P., and Baldwin A.

Nf-kappab mediates inhibition of mesenchymal cell differentiation through a posttranscriptional gene silencing mechanism.
Genes Dev, 17 (19): 2368-73, 2003.
Abstract.
Full text

Snoussi E.

Necessary conditions for multistationarity and stable periodicity.
J. Biol. Syst, 6: 3-9, 1998.

Soulé C.

Graphic requirements for multistationarity.
Complexus, 1: 123-33, 2003.

Spicer D., Rhee J., Cheung W., and Lassar A.

Inhibition of myogenic bhlh and mef2 transcription factors by the bhlh protein twist.
Science, 272 (5267): 1476-80, 1996.
Abstract.

Sternberg P. and Horvitz H.

The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in c. elegans.
Cell, 58 (4): 679-93, 1989.
Abstract.

Stewart H., Zoidl G., Rossner M., Brennan A., Zoidl C., Nave K., Mirsky R., and Jessen K.

Helix-loop-helix proteins in schwann cells: a study of regulation and subcellular localization of ids, reb, and e12/47 during embryonic and postnatal development.
J Neurosci Res, 50 (5): 684-701, 1997.
Abstract.

Tchkonia T., Giorgadze N., Pirtskhalava T., Tchoukalova Y., Karagiannides I., Forse R., DePonte M., Stevenson M., Guo W., Han J., Waloga G., Lash T., Jensen M., and Kirkland J.

Fat depot origin affects adipogenesis in primary cultured and cloned human preadipocytes.
Am J Physiol Regul Integr Comp Physiol, 282 (5): R1286-96, 2002.
Abstract.
Full text

Theise N. and Krause D.

Toward a new paradigm of cell plasticity.
Leukemia, 16 (4): 542-8, 2002.
Abstract.
Full text

Thomas R.

On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations.
Springer Ser. Synergetics, 9: 180-193, 1981.

Visvader J., Elefanty A., Strasser A., and Adams J.

Gata-1 but not scl induces megakaryocytic differentiation in an early myeloid line.
EMBO J, 11 (12): 4557-64, 1992.
Abstract.

Wardle F. and Smith J.

Refinement of gene expression patterns in the early xenopus embryo.
Development, 131 (19): 4687-96, 2004.
Abstract.
Full text

Weimann J., Johansson C., Trejo A., and Blau H.

Stable reprogrammed heterokaryons form spontaneously in purkinje neurons after bone marrow transplant.
Nat Cell Biol, 5 (11): 959-66, 2003.
Abstract.
Full text

Weintraub H.

The myod family and myogenesis: redundancy, networks, and thresholds.
Cell, 75 (7): 1241-4, 1993.
Abstract.

Wickens M., Bernstein D., Kimble J., and Parker R.

A puf family portrait: 3'utr regulation as a way of life.
Trends Genet, 18 (3): 150-7, 2002.
Abstract.

Wickens M., Goodwin E., Kimble J., Strickland S., and Hentze M.

Translational control in developmental decisions.
In Sonenberg N., editor, Translational control of gene expression, pages 295-370. New York: Cold Spring Harbor Press, 2000.

Ye M., Iwasaki H., Laiosa C., Stadtfeld M., Xie H., Heck S., Clausen B., Akashi K., and Graf T.

Hematopoietic stem cells expressing the myeloid lysozyme gene retain long-term, multilineage repopulation potential.
Immunity, 19 (5): 689-699, 2003.
Abstract.

Zhang D., Hohaus S., Voso M., Chen H., Smith L., Hetherington C., and Tenen D.

Function of pu.1 (spi-1), c/ebp, and aml1 in early myelopoiesis: regulation of multiple myeloid csf receptor promoters.
Curr Top Microbiol Immunol, 211: 137-47, 1996.
Abstract.

Zhang P., Behre G., Pan J., Iwama A., Wara-Aswapati N., Radomska H., Auron P., Tenen D., and Sun Z.

Negative cross-talk between hematopoietic regulators: Gata proteins repress pu.1.
Proc Natl Acad Sci U S A, 96 (15): 8705-10, 1999.
Abstract.

Zhu J. and Emerson S.

Hematopoietic cytokines, transcription factors and lineage commitment.
Oncogene, 21 (21): 3295-313, 2002.
Abstract.
Full text

Zhuang Y., Cheng P., and Weintraub H.

B-lymphocyte development is regulated by the combined dosage of three basic helix-loop-helix genes, e2a, e2-2, and heb.
Mol Cell Biol, 16 (6): 2898-905, 1996.
Abstract.