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Induced pluripotency in the context of stem cell expansion bioprocess development, optimization, and manufacturing: a roadmap to the clinic

Growth Mindset STEM Intervention

Biernaskie J, Colter J, Murari K.
GSID: YF87BxHMDxQJ
J Colter, K Murari, J Biernaskie… - NPJ Regenerative …, 2021 - nature.com

… stem-cell population dynamics in the presence of adequate process control and intervention … b Erosion of phenotype in the presence of inadequate process control and intervention, the …

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Colter, J., Murari, K., Biernaskie, J., & Kallos, M. S. (2021). Induced pluripotency in the context of stem cell expansion bioprocess development, optimization, and manufacturing: a roadmap to the clinic. NPJ Regenerative Medicine, 6(1), 72.
Colter, James, et al. "Induced pluripotency in the context of stem cell expansion bioprocess development, optimization, and manufacturing: a roadmap to the clinic." NPJ Regenerative Medicine 6.1 (2021): 72.
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Monolithic III-V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects.

Scientific reports

Li N, Liu K, Sorger VJ, Sadana DK.
PMID: 26369698
Sci Rep. 2015 Sep 15;5:14067. doi: 10.1038/srep14067.

Monolithic integration of III-V semiconductor lasers with Si circuits can reduce cost and enhance performance for optical interconnects dramatically. We propose and investigate plasmonic III-V nanolasers as monolithically integrated light source on Si chips due to many advantages. First,...

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Li N, Liu K, Sorger VJ, et al. Monolithic III-V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects. Sci Rep. 2015;5:14067doi: 10.1038/srep14067.
Li, N., Liu, K., Sorger, V. J., & Sadana, D. K. (2015). Monolithic III-V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects. Scientific reports, 514067. https://doi.org/10.1038/srep14067
Li, Ning, et al. "Monolithic III-V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects." Scientific reports vol. 5 (2015): 14067. doi: https://doi.org/10.1038/srep14067
Li N, Liu K, Sorger VJ, Sadana DK. Monolithic III-V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects. Sci Rep. 2015 Sep 15;5:14067. doi: 10.1038/srep14067. PMID: 26369698; PMCID: PMC4570205.
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Characterizing rare fluctuations in soft particulate flows.

Nature communications

Rahbari SHE, Saberi AA, Park H, Vollmer J.
PMID: 28396590
Nat Commun. 2017 Apr 10;8(1):11. doi: 10.1038/s41467-017-00022-8.

Soft particulate media include a wide range of systems involving athermal dissipative particles both in non-living and biological materials. Characterization of flows of particulate media is of great practical and theoretical importance. A fascinating feature of these systems is...

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Rahbari SHE, Saberi AA, Park H, et al. Characterizing rare fluctuations in soft particulate flows. Nat Commun. 2017;8(1):11doi: 10.1038/s41467-017-00022-8.
Rahbari, S. H. E., Saberi, A. A., Park, H., & Vollmer, J. (2017). Characterizing rare fluctuations in soft particulate flows. Nature communications, 8(1), 11. https://doi.org/10.1038/s41467-017-00022-8
Rahbari, S H E, et al. "Characterizing rare fluctuations in soft particulate flows." Nature communications vol. 8,1 (2017): 11. doi: https://doi.org/10.1038/s41467-017-00022-8
Rahbari SHE, Saberi AA, Park H, Vollmer J. Characterizing rare fluctuations in soft particulate flows. Nat Commun. 2017 Apr 10;8(1):11. doi: 10.1038/s41467-017-00022-8. PMID: 28396590; PMCID: PMC5431914.
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Single Photon Counting UV Solar-Blind Detectors Using Silicon and III-Nitride Materials.

Sensors (Basel, Switzerland)

Nikzad S, Hoenk M, Jewell AD, Hennessy JJ, Carver AG, Jones TJ, Goodsall TM, Hamden ET, Suvarna P, Bulmer J, Shahedipour-Sandvik F, Charbon E, Padmanabhan P, Hancock B, Bell LD.
PMID: 27338399
Sensors (Basel). 2016 Jun 21;16(6). doi: 10.3390/s16060927.

Ultraviolet (UV) studies in astronomy, cosmology, planetary studies, biological and medical applications often require precision detection of faint objects and in many cases require photon-counting detection. We present an overview of two approaches for achieving photon counting in the...

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Nikzad S, Hoenk M, Jewell AD, et al. Single Photon Counting UV Solar-Blind Detectors Using Silicon and III-Nitride Materials. Sensors (Basel). 2016;16(6)doi: 10.3390/s16060927.
Nikzad, S., Hoenk, M., Jewell, A. D., Hennessy, J. J., Carver, A. G., Jones, T. J., Goodsall, T. M., Hamden, E. T., Suvarna, P., Bulmer, J., Shahedipour-Sandvik, F., Charbon, E., Padmanabhan, P., Hancock, B., & Bell, L. D. (2016). Single Photon Counting UV Solar-Blind Detectors Using Silicon and III-Nitride Materials. Sensors (Basel, Switzerland), 16(6), . https://doi.org/10.3390/s16060927
Nikzad, Shouleh, et al. "Single Photon Counting UV Solar-Blind Detectors Using Silicon and III-Nitride Materials." Sensors (Basel, Switzerland) vol. 16,6 (2016). doi: https://doi.org/10.3390/s16060927
Nikzad S, Hoenk M, Jewell AD, Hennessy JJ, Carver AG, Jones TJ, Goodsall TM, Hamden ET, Suvarna P, Bulmer J, Shahedipour-Sandvik F, Charbon E, Padmanabhan P, Hancock B, Bell LD. Single Photon Counting UV Solar-Blind Detectors Using Silicon and III-Nitride Materials. Sensors (Basel). 2016 Jun 21;16(6). doi: 10.3390/s16060927. PMID: 27338399; PMCID: PMC4934352.
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XRN1: A Major 5' to 3' Exoribonuclease in Eukaryotic Cells.

The Enzymes

Geisler S, Coller J.
PMID: 27166442
Enzymes. 2012;31:97-114. doi: 10.1016/B978-0-12-404740-2.00005-7. Epub 2012 Sep 29.

The degradation of RNA is a critical aspect of gene regulation. Correspondingly, ribonucleases exist within the cell to degrade RNA in specific cellular contexts. An important and conserved ribonuclease is called XRN1. This enzyme, an exoribonuclease, degrades RNA in...

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Geisler S, Coller J. XRN1: A Major 5' to 3' Exoribonuclease in Eukaryotic Cells. Enzymes. 2012;31:97-114doi: 10.1016/B978-0-12-404740-2.00005-7.
Geisler, S., & Coller, J. (2012). XRN1: A Major 5' to 3' Exoribonuclease in Eukaryotic Cells. The Enzymes, 3197-114. https://doi.org/10.1016/B978-0-12-404740-2.00005-7
Geisler, Sarah, and Coller, Jeff. "XRN1: A Major 5' to 3' Exoribonuclease in Eukaryotic Cells." The Enzymes vol. 31 (2012): 97-114. doi: https://doi.org/10.1016/B978-0-12-404740-2.00005-7
Geisler S, Coller J. XRN1: A Major 5' to 3' Exoribonuclease in Eukaryotic Cells. Enzymes. 2012;31:97-114. doi: 10.1016/B978-0-12-404740-2.00005-7. Epub 2012 Sep 29. PMID: 27166442.
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Separated response function ratios in exclusive, forward π(±) electroproduction.

Physical review letters

Huber GM, Blok HP, Butuceanu C, Gaskell D, Horn T, Mack DJ, Abbott D, Aniol K, Anklin H, Armstrong C, Arrington J, Assamagan K, Avery S, Baker OK, Barrett B, Beise EJ, Bochna C, Boeglin W, Brash EJ, Breuer H, Chang CC, Chant N, Christy ME, Dunne J, Eden T, Ent R, Fenker H, Gibson EF, Gilman R, Gustafsson K, Hinton W, Holt RJ, Jackson H, Jin S, Jones MK, Keppel CE, Kim PH, Kim W, King PM, Klein A, Koltenuk D, Kovaltchouk V, Liang M, Liu J, Lolos GJ, Lung A, Margaziotis DJ, Markowitz P, Matsumura A, McKee D, Meekins D, Mitchell J, Miyoshi T, Mkrtchyan H, Mueller B, Niculescu G, Niculescu I, Okayasu Y, Pentchev L, Perdrisat C, Pitz D, Potterveld D, Punjabi V, Qin LM, Reimer PE, Reinhold J, Roche J, Roos PG, Sarty A, Shin IK, Smith GR, Stepanyan S, Tang LG, Tadevosyan V, Tvaskis V, van der Meer RL, Vansyoc K, Van Westrum D, Vidakovic S, Volmer J, Vulcan W, Warren G, Wood SA, Xu C, Yan C, Zhao WX, Zheng X, Zihlmann B.
PMID: 24856691
Phys Rev Lett. 2014 May 09;112(18):182501. doi: 10.1103/PhysRevLett.112.182501. Epub 2014 May 05.

The study of exclusive π(±) electroproduction on the nucleon, including separation of the various structure functions, is of interest for a number of reasons. The ratio RL=σL(π-)/σL(π+) is sensitive to isoscalar contamination to the dominant isovector pion exchange amplitude,...

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Huber GM, Blok HP, Butuceanu C, et al. Separated response function ratios in exclusive, forward π(±) electroproduction. Phys Rev Lett. 2014;112(18):182501doi: 10.1103/PhysRevLett.112.182501.
Huber, G. M., Blok, H. P., Butuceanu, C., Gaskell, D., Horn, T., Mack, D. J., Abbott, D., Aniol, K., Anklin, H., Armstrong, C., Arrington, J., Assamagan, K., Avery, S., Baker, O. K., Barrett, B., Beise, E. J., Bochna, C., Boeglin, W., Brash, E. J., Breuer, H., Chang, C. C., Chant, N., Christy, M. E., Dunne, J., Eden, T., Ent, R., Fenker, H., Gibson, E. F., Gilman, R., Gustafsson, K., Hinton, W., Holt, R. J., Jackson, H., Jin, S., Jones, M. K., Keppel, C. E., Kim, P. H., Kim, W., King, P. M., Klein, A., Koltenuk, D., Kovaltchouk, V., Liang, M., Liu, J., Lolos, G. J., Lung, A., Margaziotis, D. J., Markowitz, P., Matsumura, A., McKee, D., Meekins, D., Mitchell, J., Miyoshi, T., Mkrtchyan, H., Mueller, B., Niculescu, G., Niculescu, I., Okayasu, Y., Pentchev, L., Perdrisat, C., Pitz, D., Potterveld, D., Punjabi, V., Qin, L. M., Reimer, P. E., Reinhold, J., Roche, J., Roos, P. G., Sarty, A., Shin, I. K., Smith, G. R., Stepanyan, S., Tang, L. G., Tadevosyan, V., Tvaskis, V., van der Meer, R. L., Vansyoc, K., Van Westrum, D., Vidakovic, S., Volmer, J., Vulcan, W., Warren, G., Wood, S. A., Xu, C., Yan, C., Zhao, W. X., Zheng, X., Zihlmann, B. (2014). Separated response function ratios in exclusive, forward π(±) electroproduction. Physical review letters, 112(18), 182501. https://doi.org/10.1103/PhysRevLett.112.182501
Huber, G M, et al. "Separated response function ratios in exclusive, forward π(±) electroproduction." Physical review letters vol. 112,18 (2014): 182501. doi: https://doi.org/10.1103/PhysRevLett.112.182501
Huber GM, Blok HP, Butuceanu C, Gaskell D, Horn T, Mack DJ, Abbott D, Aniol K, Anklin H, Armstrong C, Arrington J, Assamagan K, Avery S, Baker OK, Barrett B, Beise EJ, Bochna C, Boeglin W, Brash EJ, Breuer H, Chang CC, Chant N, Christy ME, Dunne J, Eden T, Ent R, Fenker H, Gibson EF, Gilman R, Gustafsson K, Hinton W, Holt RJ, Jackson H, Jin S, Jones MK, Keppel CE, Kim PH, Kim W, King PM, Klein A, Koltenuk D, Kovaltchouk V, Liang M, Liu J, Lolos GJ, Lung A, Margaziotis DJ, Markowitz P, Matsumura A, McKee D, Meekins D, Mitchell J, Miyoshi T, Mkrtchyan H, Mueller B, Niculescu G, Niculescu I, Okayasu Y, Pentchev L, Perdrisat C, Pitz D, Potterveld D, Punjabi V, Qin LM, Reimer PE, Reinhold J, Roche J, Roos PG, Sarty A, Shin IK, Smith GR, Stepanyan S, Tang LG, Tadevosyan V, Tvaskis V, van der Meer RL, Vansyoc K, Van Westrum D, Vidakovic S, Volmer J, Vulcan W, Warren G, Wood SA, Xu C, Yan C, Zhao WX, Zheng X, Zihlmann B. Separated response function ratios in exclusive, forward π(±) electroproduction. Phys Rev Lett. 2014 May 09;112(18):182501. doi: 10.1103/PhysRevLett.112.182501. Epub 2014 May 05. PMID: 24856691.
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Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells.

Frontiers in cellular neuroscience

Alural B, Ozerdem A, Allmer J, Genc K, Genc S.
PMID: 26074776
Front Cell Neurosci. 2015 May 28;9:209. doi: 10.3389/fncel.2015.00209. eCollection 2015.

Lithium is a mood stabilizing agent commonly used for the treatment of bipolar disorder. Here, we investigated the potential neuroprotective effect of lithium against paraquat toxicity and its underlying mechanisms in vitro. SH-SY5Y human neuroblastoma cells were treated with...

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Alural B, Ozerdem A, Allmer J, et al. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015;9:209doi: 10.3389/fncel.2015.00209.
Alural, B., Ozerdem, A., Allmer, J., Genc, K., & Genc, S. (2015). Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Frontiers in cellular neuroscience, 9209. https://doi.org/10.3389/fncel.2015.00209
Alural, Begum, et al. "Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells." Frontiers in cellular neuroscience vol. 9 (2015): 209. doi: https://doi.org/10.3389/fncel.2015.00209
Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28;9:209. doi: 10.3389/fncel.2015.00209. eCollection 2015. PMID: 26074776; PMCID: PMC4446540.
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A subset of human plasmacytoid dendritic cells expresses CD8α upon exposure to herpes simplex virus type 1.

Frontiers in microbiology

Schuster P, Thomann S, Werner M, Vollmer J, Schmidt B.
PMID: 26082771
Front Microbiol. 2015 Jun 02;6:557. doi: 10.3389/fmicb.2015.00557. eCollection 2015.

Classical and plasmacytoid dendritic cells (DC) play important roles in the defense against murine and human infections with herpes simplex virus (HSV). So far, CD8α expression has only been reported for murine DC. CD8α(+) DC have prominent cross-presenting activities,...

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Schuster P, Thomann S, Werner M, et al. A subset of human plasmacytoid dendritic cells expresses CD8α upon exposure to herpes simplex virus type 1. Front Microbiol. 2015;6:557doi: 10.3389/fmicb.2015.00557.
Schuster, P., Thomann, S., Werner, M., Vollmer, J., & Schmidt, B. (2015). A subset of human plasmacytoid dendritic cells expresses CD8α upon exposure to herpes simplex virus type 1. Frontiers in microbiology, 6557. https://doi.org/10.3389/fmicb.2015.00557
Schuster, Philipp, et al. "A subset of human plasmacytoid dendritic cells expresses CD8α upon exposure to herpes simplex virus type 1." Frontiers in microbiology vol. 6 (2015): 557. doi: https://doi.org/10.3389/fmicb.2015.00557
Schuster P, Thomann S, Werner M, Vollmer J, Schmidt B. A subset of human plasmacytoid dendritic cells expresses CD8α upon exposure to herpes simplex virus type 1. Front Microbiol. 2015 Jun 02;6:557. doi: 10.3389/fmicb.2015.00557. eCollection 2015. PMID: 26082771; PMCID: PMC4451679.
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Delineating the impact of machine learning elements in pre-microRNA detection.

PeerJ

Saçar Demirci MD, Allmer J.
PMID: 28367373
PeerJ. 2017 Mar 29;5:e3131. doi: 10.7717/peerj.3131. eCollection 2017.

Gene regulation modulates RNA expression via transcription factors. Post-transcriptional gene regulation in turn influences the amount of protein product through, for example, microRNAs (miRNAs). Experimental establishment of miRNAs and their effects is complicated and even futile when aiming to...

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Saçar Demirci MD, Allmer J. Delineating the impact of machine learning elements in pre-microRNA detection. PeerJ. 2017;5:e3131doi: 10.7717/peerj.3131.
Saçar Demirci, M. D., & Allmer, J. (2017). Delineating the impact of machine learning elements in pre-microRNA detection. PeerJ, 5e3131. https://doi.org/10.7717/peerj.3131
Saçar Demirci, Müşerref Duygu, and Allmer, Jens. "Delineating the impact of machine learning elements in pre-microRNA detection." PeerJ vol. 5 (2017): e3131. doi: https://doi.org/10.7717/peerj.3131
Saçar Demirci MD, Allmer J. Delineating the impact of machine learning elements in pre-microRNA detection. PeerJ. 2017 Mar 29;5:e3131. doi: 10.7717/peerj.3131. eCollection 2017. PMID: 28367373; PMCID: PMC5374968.
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Impact of microphysics on the growth of one-dimensional breath figures.

Physical review. E, Statistical, nonlinear, and soft matter physics

Stricker L, Vollmer J.
PMID: 26565256
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Oct;92(4):042406. doi: 10.1103/PhysRevE.92.042406. Epub 2015 Oct 21.

Droplet patterns condensing on solid substrates (breath figures) tend to evolve into a self-similar regime, characterized by a bimodal droplet size distribution. The distributions comprise a bell-shaped peak of monodisperse large droplets and a broad range of smaller droplets....

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Stricker L, Vollmer J. Impact of microphysics on the growth of one-dimensional breath figures. Phys Rev E Stat Nonlin Soft Matter Phys. 2015;92(4):042406doi: 10.1103/PhysRevE.92.042406.
Stricker, L., & Vollmer, J. (2015). Impact of microphysics on the growth of one-dimensional breath figures. Physical review. E, Statistical, nonlinear, and soft matter physics, 92(4), 042406. https://doi.org/10.1103/PhysRevE.92.042406
Stricker, L, and Vollmer, J. "Impact of microphysics on the growth of one-dimensional breath figures." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 92,4 (2015): 042406. doi: https://doi.org/10.1103/PhysRevE.92.042406
Stricker L, Vollmer J. Impact of microphysics on the growth of one-dimensional breath figures. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Oct;92(4):042406. doi: 10.1103/PhysRevE.92.042406. Epub 2015 Oct 21. PMID: 26565256.
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Computational and bioinformatics methods for microRNA gene prediction.

Methods in molecular biology (Clifton, N.J.)

Allmer J.
PMID: 24272436
Methods Mol Biol. 2014;1107:157-75. doi: 10.1007/978-1-62703-748-8_9.

MicroRNAs (miRNAs) have attracted ever-increasing interest in recent years. Since experimental approaches for determining miRNAs are nontrivial in their application, computational methods for the prediction of miRNAs have gained popularity. Such methods can be grouped into two broad categories...

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Allmer J. Computational and bioinformatics methods for microRNA gene prediction. Methods Mol Biol. 2014;1107:157-75doi: 10.1007/978-1-62703-748-8_9.
Allmer, J. (2014). Computational and bioinformatics methods for microRNA gene prediction. Methods in molecular biology (Clifton, N.J.), 1107157-75. https://doi.org/10.1007/978-1-62703-748-8_9
Allmer, Jens. "Computational and bioinformatics methods for microRNA gene prediction." Methods in molecular biology (Clifton, N.J.) vol. 1107 (2014): 157-75. doi: https://doi.org/10.1007/978-1-62703-748-8_9
Allmer J. Computational and bioinformatics methods for microRNA gene prediction. Methods Mol Biol. 2014;1107:157-75. doi: 10.1007/978-1-62703-748-8_9. PMID: 24272436.
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[Investigation about development of alternative efficacy verifications of swine erysipelas vaccines].

ALTEX

Gyra H, Volmer R, Hausleithner D.
PMID: 11178407
ALTEX. 1994;11(5):46-54.

Vaccination is the most effective prophylaxis against swine erysipelas. Vaccines are usually tested for efficacy by a challenge of vaccinated and untreated pigs. Up to now the efforts to replace the infection test by a serological method have been...

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Gyra H, Volmer R, Hausleithner D. Untersuchungen zur Entwicklung alternativer Wirksamkeitsprüfungen von Rotlaufimpfstoffen. [Investigation about development of alternative efficacy verifications of swine erysipelas vaccines]. ALTEX. 1994;11(5):46-54
Gyra, H., Volmer, R., & Hausleithner, D. (1994). Untersuchungen zur Entwicklung alternativer Wirksamkeitsprüfungen von Rotlaufimpfstoffen. [Investigation about development of alternative efficacy verifications of swine erysipelas vaccines]. ALTEX, 11(5), 46-54.
Gyra, Heike, et al. "Untersuchungen zur Entwicklung alternativer Wirksamkeitsprüfungen von Rotlaufimpfstoffen." [Investigation about development of alternative efficacy verifications of swine erysipelas vaccines]. ALTEX vol. 11,5 (1994): 46-54.
Gyra H, Volmer R, Hausleithner D. Untersuchungen zur Entwicklung alternativer Wirksamkeitsprüfungen von Rotlaufimpfstoffen. [Investigation about development of alternative efficacy verifications of swine erysipelas vaccines]. ALTEX. 1994;11(5):46-54. PMID: 11178407.
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Showing 1 to 12 of 252 entries